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[galaxyproject/usegalaxy-playbook] 46a31d: PostgreSQL backups on radegast.
by GitHub 27 Apr '15

27 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 46a31dcb0479351687157613b68576d288968aad https://github.com/galaxyproject/usegalaxy-playbook/commit/46a31dcb04793516… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M common/inventory M common_infrastructure.yml M toolshed_infrastructure.yml Log Message: ----------- PostgreSQL backups on radegast.

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[galaxyproject/usegalaxy-playbook] d66672: Decrease retry limits on Main Pulsar
by GitHub 27 Apr '15

27 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d666720c00fe31f08255015f032840d3519eb6bb https://github.com/galaxyproject/usegalaxy-playbook/commit/d666720c00fe31f0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M production/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Decrease retry limits on Main Pulsar Commit: 1da8ba669239f7c107f1aaad318979abae35eb92 https://github.com/galaxyproject/usegalaxy-playbook/commit/1da8ba669239f7c1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Do not attempt to contact Rodeo slurm controller. Also decrease concurrency limits to hopefully make a workshop tomorrow more responsive. Commit: e7e1bb705716d5f9fce238413a3186cade07ed70 https://github.com/galaxyproject/usegalaxy-playbook/commit/e7e1bb705716d5f9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-27 (Mon, 27 Apr 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated mutable configs from Test. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/49ce0d190edb...…

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[galaxyproject/usegalaxy-playbook] 49ce0d: A couple minor additions for the tool shed.
by GitHub 23 Apr '15

23 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49ce0d190edb1f899adaec76b7df42a7d4a80fa5 https://github.com/galaxyproject/usegalaxy-playbook/commit/49ce0d190edb1f89… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M production/group_vars/toolshedservers.yml Log Message: ----------- A couple minor additions for the tool shed.

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[galaxyproject/usegalaxy-playbook] bdcd1c: Infrastructure and hopefully proper Tool Shed conf...
by GitHub 22 Apr '15

22 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: bdcd1cbfbdbf73bbe8ffd78bfbbbb17891c6441c https://github.com/galaxyproject/usegalaxy-playbook/commit/bdcd1cbfbdbf73bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: A common/group_vars/webservers.yml M common/host_vars/radegast.galaxyproject.org.yml M common/inventory A common/secret_vars/ssl.yml M common_infrastructure.yml A files/toolshed/toolshed.g2.bx.psu.edu/error A production/group_vars/toolsheddbservers.yml A production/group_vars/toolshedservers.yml A production/host_vars/radegast.galaxyproject.org.yml M production/inventory A production/secret_vars/toolshedservers.yml M stage/group_vars/toolshedservers.yml M stage/host_vars/radegast.galaxyproject.org.yml R stage/secret_vars/ssl.yml M templates/nginx/testtoolshed.j2 A templates/nginx/toolshed.j2 A templates/supervisor/testtoolshed.conf.j2 M toolshed_infrastructure.yml Log Message: ----------- Infrastructure and hopefully proper Tool Shed config for the Main Tool Shed on Radegast. Just waiting for the DB dump/restore to finish.

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[galaxyproject/usegalaxy-playbook] cfde67: Update Test Tool Shed
by GitHub 22 Apr '15

22 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: cfde673acc26555e9a07be808cdb7ab2eec061e5 https://github.com/galaxyproject/usegalaxy-playbook/commit/cfde673acc26555e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- Update Test Tool Shed

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commit/galaxy-central: natefoo: Merge stable to default
by commits-noreply＠bitbucket.org 22 Apr '15

22 Apr '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0aa4dd8af7cf/ Changeset: 0aa4dd8af7cf User: natefoo Date: 2015-04-22 19:35:19+00:00 Summary: Merge stable to default Affected #: 61 files diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca .hgtags --- a/.hgtags +++ b/.hgtags @@ -25,4 +25,5 @@ 5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 -9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 latest_15.03 +bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 +bfd4635011e39aa210b2b1498dd65831dd2a365e latest_15.03 diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/history/history-model.js --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -257,7 +257,7 @@ setAsCurrent : function(){ var history = this, - xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id ); xhr.done( function(){ history.trigger( 'set-as-current', history ); @@ -361,7 +361,7 @@ var HistoryCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - + /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -116,7 +116,7 @@ }, downloadDataset: function(){ - var url = '/api/libraries/datasets/download/uncompressed'; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/uncompressed'; var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, @@ -232,7 +232,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch dataset permissions.'); @@ -273,7 +273,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#access_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -320,7 +320,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#modify_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -367,7 +367,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#manage_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -413,7 +413,7 @@ self.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options var template = self.templateAccessSelect(); - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); self.accessSelectObject = $('#access_select').select2(); }).fail(function() { @@ -436,7 +436,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -447,7 +447,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -478,7 +478,7 @@ modify_ids.push(modify_roles[i].id); }; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/library/library-folder-view.js --- a/client/galaxy/scripts/mvc/library/library-folder-view.js +++ b/client/galaxy/scripts/mvc/library/library-folder-view.js @@ -81,7 +81,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch folder permissions.'); @@ -125,7 +125,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/folders/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -195,7 +195,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -294,7 +294,7 @@ dataset_ids.push( this.parentElement.parentElement.id ); } } ); - var url = '/api/libraries/datasets/download/' + format; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format; var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, @@ -386,7 +386,7 @@ fetchExtAndGenomes: function(){ var that = this; mod_utils.get({ - url : galaxy_config.root + "api/datatypes?extension_only=False", + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/datatypes?extension_only=False", success : function( datatypes ) { for (key in datatypes) { that.list_extensions.push({ @@ -403,7 +403,7 @@ } }); mod_utils.get({ - url: galaxy_config.root + "api/genomes", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/genomes", success: function( genomes ) { for ( key in genomes ) { that.list_genomes.push({ @@ -689,7 +689,7 @@ for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) { history_dataset_id = history_dataset_ids[i]; var folder_item = new mod_library_model.Item(); - folder_item.url = '/api/folders/' + this.options.id + '/contents'; + folder_item.url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/' + this.options.id + '/contents'; folder_item.set( { 'from_hda_id':history_dataset_id } ); hdas_to_add.push( folder_item ); } @@ -749,7 +749,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + @@ -788,7 +788,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&preserve_dirs=' + options.preserve_dirs + diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/library/library-library-view.js --- a/client/galaxy/scripts/mvc/library/library-library-view.js +++ b/client/galaxy/scripts/mvc/library/library-library-view.js @@ -87,7 +87,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch library permissions.'); @@ -134,7 +134,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -193,7 +193,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -204,7 +204,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -230,7 +230,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca 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 @@ -4,7 +4,7 @@ // LIBRARY RELATED MODELS var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries/', + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/', /** based on show_deleted would this lib show in the list of lib's? * @param {Boolean} show_deleted are we including deleted libraries? @@ -19,7 +19,7 @@ }); var Libraries = Backbone.Collection.extend({ - url: '/api/libraries', + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries', model: Library, @@ -84,15 +84,15 @@ // FOLDER RELATED MODELS var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var Ldda = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders' }); var Folder = Backbone.Collection.extend({ @@ -152,7 +152,7 @@ var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), - urlRoot : "/api/folders/", + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/', id : "unknown" }, parse : function(obj) { @@ -169,11 +169,11 @@ // TODO UNITE var HistoryItem = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var HistoryContents = Backbone.Collection.extend({ - urlRoot : '/api/histories/', + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/', initialize: function(options){ this.id = options.id; }, @@ -184,11 +184,11 @@ }); var GalaxyHistory = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var GalaxyHistories = Backbone.Collection.extend({ - url : '/api/histories', + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories', model : GalaxyHistory }); @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/remote_files' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/remote_files' }); return { diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/mvc/tools/tools-parameters.js --- a/client/galaxy/scripts/mvc/tools/tools-parameters.js +++ b/client/galaxy/scripts/mvc/tools/tools-parameters.js @@ -145,6 +145,7 @@ data : options, error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, + optional : input_def.optional, searchable : input_def.searchable, onchange : function() { self.app.trigger('refresh'); diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca client/galaxy/scripts/viz/circster.js --- a/client/galaxy/scripts/viz/circster.js +++ b/client/galaxy/scripts/viz/circster.js @@ -1,16 +1,20 @@ // load required libraries -require( -[ +require([ 'utils/utils', - 'mvc/ui/icon-button', - 'libs/farbtastic', -], function(mod_utils, mod_icon_btn) +], function(mod_utils) { // load css mod_utils.cssLoadFile("static/style/circster.css"); }); -define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) { +define([ + "libs/underscore", + "libs/d3", + "viz/visualization", + "utils/config", + 'mvc/ui/icon-button', + 'libs/farbtastic' +], function(_, d3, visualization, config, mod_icon_btn) { /** * Utility class for working with SVG. @@ -71,7 +75,7 @@ else { tick_coords = [1, 0, 4, 0]; text_coords = [0, 4, ".35em", ""]; - + } ticks.append("line") @@ -80,7 +84,7 @@ .attr("x2", tick_coords[2]) .attr("y1", tick_coords[3]) .style("stroke", "#000"); - + return ticks.append("text") .attr("x", text_coords[0]) .attr("y", text_coords[1]) @@ -98,11 +102,11 @@ // Use default of 2 sig. digits. if (sigDigits === undefined) sigDigits = 2; - + // Verify input number if (num === null) return null; - + // Calculate return value var rval = null; if (Math.abs(num) < 1) { @@ -141,7 +145,7 @@ */ var CircsterView = Backbone.View.extend({ className: 'circster', - + initialize: function(options) { this.genome = options.genome; this.label_arc_height = 50; @@ -188,7 +192,7 @@ track_gap = this.model.get('config').get_value('track_gap'), // Subtract 20 to make sure chrom labels are on screen. min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20, - // Compute radius start based on model, will be centered + // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - circular_tracks.length * (dataset_arc_height + track_gap) + @@ -198,14 +202,14 @@ // Compute range of track starting radii. tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap); - + // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { return [radius, radius + dataset_arc_height]; }); }, - + /** * Renders circular tracks, chord tracks, and label tracks. */ @@ -254,7 +258,7 @@ })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g').attr('class', 'tracks'); - + // -- Render circular tracks. -- // Create a view for each track in the visualization and render. @@ -266,12 +270,12 @@ genome: self.genome, total_gap: total_gap }); - + view.render(); - + return view; }); - + // -- Render chords tracks. -- this.chords_views = chords_tracks.map(function(track) { @@ -289,10 +293,10 @@ }); // -- Render label track. -- - + // Track bounds are: // (a) outer radius of last circular track; - // (b) + // (b) var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1], track_bounds = [ outermost_radius, @@ -305,7 +309,7 @@ genome: self.genome, total_gap: total_gap }); - + this.label_track_view.render(); }, @@ -356,7 +360,7 @@ // Update label track. /* - FIXME: should never have to update label track because vis always expands to fit area + FIXME: should never have to update label track because vis always expands to fit area within label track. var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; track_bounds[1] = track_bounds[0]; @@ -373,7 +377,7 @@ var track_view = this.circular_views[options.index]; this.circular_views.splice(options.index, 1); track_view.$el.remove(); - + // Recompute and update track bounds. var new_track_bounds = this.get_tracks_bounds(); _.each(this.circular_views, function(track_view, i) { @@ -392,7 +396,7 @@ _.each(this.chords_views, function(track_view) { track_view.update_radius_bounds(new_track_bounds[0]); }); - + } }); @@ -455,7 +459,7 @@ // Append titles to paths. chroms_paths.append("title").text(function(d) { return d.data.chrom; }); - + // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. -- var self = this, @@ -490,7 +494,7 @@ var new_d = d3.svg.arc() .innerRadius(this.radius_bounds[0]) .outerRadius(this.radius_bounds[1]); - + this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d); this._transition_chrom_data(); @@ -511,7 +515,7 @@ } // -- Scale increased, so render visible data with more detail. -- - + var self = this, utils = new SVGUtils(); @@ -539,7 +543,7 @@ $.when(data_deferred).then(function(data) { // Remove current data path. path_elt.remove(); - + // Update data bounds with new data. self._update_data_bounds(); @@ -598,12 +602,12 @@ _transition_labels: function() {}, /** - * Update data bounds. If there are new_bounds, use them; otherwise use + * Update data bounds. If there are new_bounds, use them; otherwise use * default data bounds. */ _update_data_bounds: function(new_bounds) { var old_bounds = this.data_bounds; - this.data_bounds = new_bounds || + this.data_bounds = new_bounds || this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome)); this._transition_chrom_data(); }, @@ -624,7 +628,7 @@ // Set min, max value in config so that they can be adjusted. Make this silent // because these attributes are watched for changes and the viz is updated - // accordingly (set up in initialize). Because we are setting up, we don't want + // accordingly (set up in initialize). Because we are setting up, we don't want // the watch to trigger events here. track.get('config').set_value('min_value', self.data_bounds[0], {silent: true}); track.get('config').set_value('max_value', self.data_bounds[1], {silent: true}); @@ -660,7 +664,7 @@ _get_path_function: function(chrom_arc, chrom_data) {}, /** - * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle + * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle * separated by gaps. */ _chroms_layout: function() { @@ -700,14 +704,14 @@ * Render labels. */ _render_data: function(svg) { - // -- Add chromosome label where it will fit; an alternative labeling mechanism + // -- Add chromosome label where it will fit; an alternative labeling mechanism // would be nice for small chromosomes. -- var self = this, chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') .attr('id', function(d) { return 'label-' + d.data.chrom; }); - + chrom_arcs.append("svg:text") .filter(function(d) { return d.endAngle - d.startAngle > self.min_arc_len; @@ -857,12 +861,12 @@ return "rotate(90)"; }; - // FIXME: + // FIXME: // (1) using min_max class below is needed for _update_min_max, which could be improved. // (2) showing config on tick click should be replaced by proper track config icon. // Draw min, max on first chrom only. - var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], + var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true) .classed('min_max', true); @@ -872,7 +876,7 @@ var view = new config.ConfigSettingCollectionView({ collection: self.track.get('config') }); - view.render_in_modal('Configure Track'); + view.render_in_modal('Configure Track'); }); }); @@ -951,7 +955,7 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ get_data_bounds: function(data) { - // Set max across dataset by extracting all values, flattening them into a + // Set max across dataset by extracting all values, flattening them into a // single array, and getting third quartile. var values = _.flatten( _.map(data, function(d) { if (d) { @@ -965,8 +969,8 @@ return 0; } }) ); - - // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 + + // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 // for sparsely populated data, so use max in that case. return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ]; } @@ -1068,13 +1072,13 @@ genome : genome, model : vis }); - + // Render vizualization viz_view.render(); - + // setup title $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey); - + // setup menu var menu = mod_icon_btn.create_icon_buttons_menu([ { @@ -1100,7 +1104,7 @@ { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - + // send to server $.ajax({ url: galaxy_config.root + "visualization/save", @@ -1132,11 +1136,11 @@ window.location = galaxy_config.root + "visualization/list"; } }], { tooltip_config: { placement: 'bottom' } }); - + // add menu menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); - + // manual tooltip config because default gravity is S and cannot be changed $(".menu-button").tooltip( { placement: 'bottom' } ); } diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -580,6 +580,13 @@ # requests. #nginx_upload_path = False +# Galaxy can also use nginx_upload_module to receive files staged out upon job +# completion by remote job runners (i.e. Pulsar) that initiate staging +# operations on the remote end. See the Galaxy nginx documentation for the +# corresponding nginx configuration. +#nginx_upload_job_files_store = False +#nginx_upload_job_files_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 # default though you do need to install node+npm and do an npm install from @@ -960,6 +967,17 @@ # always, onsuccess, never #cleanup_job = always +# For sites where all users in Galaxy match users on the system on which Galaxy +# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the +# actual user instead of as the user running the Galaxy server process. For +# details on these options, see the documentation at: +# +# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster +# +#drmaa_external_runjob_script = scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = scripts/drmaa_external_killer.py +#external_chown_script = scripts/external_chown_script.py + # File to source to set up the environment when running jobs. By default, the # environment in which the Galaxy server starts is used when running jobs # locally, and the environment set up per the DRM's submission method and diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -252,10 +252,7 @@ --></destination><destination id="real_user_cluster" runner="drmaa"> -  - <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> - <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> - <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination><destination id="dynamic" runner="dynamic"> diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -293,6 +293,8 @@ self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False ) self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False ) self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False ) + self.nginx_upload_job_files_store = kwargs.get( 'nginx_upload_job_files_store', False ) + self.nginx_upload_job_files_path = kwargs.get( 'nginx_upload_job_files_path', False ) if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) self.object_store = kwargs.get( 'object_store', 'disk' ) @@ -466,7 +468,7 @@ datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ], - job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml','config/job_metrics_conf.xml.sample' ], dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -962,12 +962,11 @@ job.set_state( job.states.PAUSED ) self.sa_session.add( job ) - def mark_as_resubmitted( self ): + def mark_as_resubmitted( self, info=None ): job = self.get_job() self.sa_session.refresh( job ) - for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]: - dataset._state = model.Dataset.states.RESUBMITTED - self.sa_session.add( dataset ) + if info is not None: + job.info = info job.set_state( model.Job.states.RESUBMITTED ) self.sa_session.add( job ) self.sa_session.flush() @@ -1251,6 +1250,16 @@ if job.user: job.user.total_disk_usage += bytes + # Emperically, we need to update job.user and + # job.workflow_invocation_step.workflow_invocation in separate + # transactions. Best guess as to why is that the workflow_invocation + # may or may not exist when the job is first loaded by the handler - + # and depending on whether it is or not sqlalchemy orders the updates + # differently and deadlocks can occur (one thread updates user and + # waits on invocation and the other updates invocation and waits on + # user). + self.sa_session.flush() + # fix permissions for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -341,8 +341,8 @@ except: log.exception('Caught exception in runner state handler:') - def mark_as_resubmitted( self, job_state ): - job_state.job_wrapper.mark_as_resubmitted() + def mark_as_resubmitted( self, job_state, info=None ): + job_state.job_wrapper.mark_as_resubmitted( info=info ) if not self.app.config.track_jobs_in_database: job_state.job_wrapper.change_state( model.Job.states.QUEUED ) self.app.job_manager.job_handler.dispatcher.put( job_state.job_wrapper ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -342,7 +342,12 @@ encoded_job_id = self.app.security.encode_id(job_id) job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) - files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % ( + endpoint_base = "%s/api/jobs/%s?job_key=%s" + if self.app.config.nginx_upload_job_files_path: + endpoint_base = "%s" + \ + self.app.config.nginx_upload_job_files_path + \ + "?job_id=%s&job_key=%s" + files_endpoint = endpoint_base % ( self.galaxy_url, encoded_job_id, job_key diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/jobs/runners/state_handlers/resubmit.py --- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py +++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py @@ -1,4 +1,5 @@ import logging + from galaxy import model @@ -13,31 +14,45 @@ def failure(app, job_runner, job_state): - if getattr( job_state, 'runner_state', None ) and job_state.runner_state in ( job_state.runner_states.WALLTIME_REACHED, job_state.runner_states.MEMORY_LIMIT_REACHED ): - # Intercept jobs that hit the walltime and have a walltime or nonspecific resubmit destination configured + if (getattr(job_state, 'runner_state', None) + and job_state.runner_state in + (job_state.runner_states.WALLTIME_REACHED, + job_state.runner_states.MEMORY_LIMIT_REACHED)): + # Intercept jobs that hit the walltime and have a walltime or + # nonspecific resubmit destination configured for resubmit in job_state.job_destination.get('resubmit'): - if resubmit.get('condition', None) and resubmit['condition'] != job_state.runner_state: - continue # There is a resubmit defined for the destination but its condition is not for walltime_reached - log.info("(%s/%s) Job will be resubmitted to '%s' because %s at the '%s' destination", - job_state.job_wrapper.job_id, - job_state.job_id, - resubmit['destination'], - MESSAGES[job_state.runner_state], - job_state.job_wrapper.job_destination.id ) + if (resubmit.get('condition', None) and resubmit['condition'] != + job_state.runner_state): + # There is a resubmit defined for the destination but + # its condition is not for walltime_reached + continue + log.info("(%s/%s) Job will be resubmitted to '%s' because %s at " + "the '%s' destination", + job_state.job_wrapper.job_id, + job_state.job_id, + resubmit['destination'], + MESSAGES[job_state.runner_state], + job_state.job_wrapper.job_destination.id ) # fetch JobDestination for the id or tag - new_destination = app.job_config.get_destination(resubmit['destination']) + new_destination = app.job_config.get_destination( + resubmit['destination']) # Resolve dynamic if necessary - new_destination = job_state.job_wrapper.job_runner_mapper.cache_job_destination( new_destination ) + new_destination = (job_state.job_wrapper.job_runner_mapper + .cache_job_destination(new_destination)) # Reset job state job = job_state.job_wrapper.get_job() if resubmit.get('handler', None): - log.debug('(%s/%s) Job reassigned to handler %s', job_state.job_wrapper.job_id, job_state.job_id, resubmit['handler']) + log.debug('(%s/%s) Job reassigned to handler %s', + job_state.job_wrapper.job_id, job_state.job_id, + resubmit['handler']) job.set_handler(resubmit['handler']) job_runner.sa_session.add( job ) # Is this safe to do here? job_runner.sa_session.flush() - # Cache the destination to prevent rerunning dynamic after resubmit - job_state.job_wrapper.job_runner_mapper.cached_job_destination = new_destination + # Cache the destination to prevent rerunning dynamic after + # resubmit + job_state.job_wrapper.job_runner_mapper \ + .cached_job_destination = new_destination job_state.job_wrapper.set_job_destination(new_destination) # Clear external ID (state change below flushes the change) job.job_runner_external_id = None @@ -45,5 +60,7 @@ if job.params is None: job.params = {} job_state.runner_state_handled = True - job_runner.mark_as_resubmitted( job_state ) + info = "This job was resubmitted to the queue because %s on its " \ + "compute resource." % MESSAGES[job_state.runner_state] + job_runner.mark_as_resubmitted(job_state, info=info) return diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -700,8 +700,8 @@ setattr( item, key, val ) return val - def deserialize_basestring( self, trans, item, key, val ): - val = self.validate.basestring( key, val ) + def deserialize_basestring( self, trans, item, key, val, convert_none_to_empty=False ): + val = '' if ( convert_none_to_empty and val is None ) else self.validate.basestring( key, val ) return self.default_deserializer( trans, item, key, val ) def deserialize_bool( self, trans, item, key, val ): diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/managers/hdas.py --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -154,8 +154,9 @@ # error here if disallowed - before jobs are stopped #TODO: poss. move to DatasetAssociationManager self.dataset_manager.error_unless_dataset_purge_allowed( trans, hda ) + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) super( HDAManager, self ).purge( trans, hda, flush=flush ) - if hda.creating_job_associations: job = hda.creating_job_associations[0].job if not job.finished: @@ -195,6 +196,32 @@ break return job + def _job_state_history_query( self, hda ): + """ + Return a query of the job's state history for the job that created this hda. + """ + session = self.app.model.context + JobToOutputDatasetAssociation = model.JobToOutputDatasetAssociation + JobStateHistory = model.JobStateHistory + + # TODO: this does not play well with copied hdas + # NOTE: don't eagerload (JODA will load the hda were using!) + hda_id = hda.id + query = ( session.query( JobToOutputDatasetAssociation, JobStateHistory ) + .filter( JobToOutputDatasetAssociation.dataset_id == hda_id ) + .filter( JobStateHistory.job_id == JobToOutputDatasetAssociation.job_id ) + .enable_eagerloads( False ) ) + return query + + def has_been_resubmitted( self, hda ): + """ + Return True if the hda's job was resubmitted at any point. + """ + job_states = model.Job.states + query = ( self._job_state_history_query( hda ) + .filter( model.JobStateHistory.state == job_states.RESUBMITTED ) ) + return self.app.model.context.query( query.exists() ).scalar() + # .... serialization def get_display_apps( self, trans, hda ): """ @@ -324,7 +351,7 @@ 'history_content_type', 'dataset_id', 'state', 'extension', - 'deleted', 'purged', 'visible', 'resubmitted', + 'deleted', 'purged', 'visible', 'type', 'url' ]) self.add_view( 'detailed', [ @@ -340,7 +367,8 @@ 'file_ext', 'file_size', 'create_time', 'update_time', - 'metadata', 'meta_files', 'data_type', + 'resubmitted', + 'metadata', 'meta_files', 'data_type', 'peek', #TODO: why is this named uuid!? The hda doesn't have a uuid - it's the underlying dataset's uuid! @@ -388,7 +416,7 @@ 'hda_ldda' : lambda *a: 'hda', # remapped - 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info, + 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else '', 'misc_info' : lambda t, i, k: self.serializers[ 'info' ]( t, i, k ), 'misc_blurb' : lambda t, i, k: i.blurb, 'genome_build' : lambda t, i, k: i.dbkey, @@ -400,7 +428,7 @@ 'copied_from_history_dataset_association_id' : self.serialize_id, 'copied_from_library_dataset_dataset_association_id': self.serialize_id, - 'resubmitted' : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED, + 'resubmitted' : lambda t, i, k: self.hda_manager.has_been_resubmitted( i ), 'meta_files' : self.serialize_meta_files, 'file_path' : self.serialize_file_path, @@ -583,7 +611,8 @@ # remapped 'genome_build' : lambda t, i, k, v: self.deserialize_genome_build( t, i, 'dbkey', v ), - 'misc_info' : lambda t, i, k, v: self.deserialize_basestring( t, i, 'info', v ), + 'misc_info' : lambda t, i, k, v: ( + self.deserialize_basestring( t, i, 'info', v, convert_none_to_empty=True ) ), #TODO: mixin: deletable 'deleted' : self.deserialize_bool, diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -569,7 +569,7 @@ for step_index in step_indices: step_dict = supplied_steps[ step_index ] uuid = step_dict.get("uuid", None) - if uuid: + if uuid and uuid != "None": if uuid in discovered_uuids: raise exceptions.DuplicatedIdentifierException("Duplicate step UUID in request.") discovered_uuids.add(uuid) @@ -586,10 +586,9 @@ type-specific functionality from the incoming dicitionary. """ step = model.WorkflowStep() - # TODO: Consider handling position inside module. step.position = step_dict['position'] - if "uuid" in step_dict: + if "uuid" in step_dict and step_dict['uuid'] != "None": step.uuid = step_dict["uuid"] if "label" in step_dict: step.label = step_dict["label"] diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1335,9 +1335,8 @@ DISCARDED = 'discarded', PAUSED = 'paused', SETTING_METADATA = 'setting_metadata', - FAILED_METADATA = 'failed_metadata', - RESUBMITTED = 'resubmitted' ) - # failed_metadata and resubmitted are only valid as DatasetInstance states currently + FAILED_METADATA = 'failed_metadata') + # failed_metadata is only valid as DatasetInstance state currently non_ready_states = ( states.UPLOAD, diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/model/orm/logging_connection_proxy.py --- a/lib/galaxy/model/orm/logging_connection_proxy.py +++ b/lib/galaxy/model/orm/logging_connection_proxy.py @@ -2,7 +2,7 @@ import inspect import os -from galaxy.model.orm import * +from galaxy.model.orm import ConnectionProxy import logging diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -417,13 +417,14 @@ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) default_template = 'tool_form.mako' - def __init__( self, config_file, tool_source, app, guid=None, repository_id=None ): + def __init__( self, config_file, tool_source, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -704,14 +705,15 @@ # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # User interface hints uihints_elem = root.find( "uihints" ) @@ -2433,7 +2435,7 @@ continue # state for subsection/group - group_state = state_inputs[input.name] + group_state = state_inputs.get(input.name, {}) # iterate and update values if input.type == 'repeat': @@ -2444,10 +2446,12 @@ elif input.type == 'conditional': if 'test_param' in tool_dict: test_param = tool_dict['test_param'] - test_param['value'] = jsonify(group_state[test_param['name']]) - if '__current_case__' in group_state: - i = group_state['__current_case__'] - iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, group_state, other_values) + test_param['value'] = jsonify(group_state.get(test_param['name'], None)) + for i in range (len ( tool_dict['cases'] ) ): + current_state = {} + if i == group_state.get('__current_case__', None): + current_state = group_state + iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values) else: # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options try: @@ -2459,11 +2463,15 @@ input_name = tool_dict.get('name') if input_name: # backup default value - tool_dict['default_value'] = input.get_initial_value(trans, other_values) + try: + tool_dict['default_value'] = input.get_initial_value(trans, other_values) + except Exception: + # get initial value failed due to improper late validation + tool_dict['default_value'] = None + pass # update input value from tool state - if input_name in state_inputs: - tool_dict['value'] = state_inputs[input_name] + tool_dict['value'] = state_inputs.get(input_name, None) # sanitize values sanitize(tool_dict, 'value') @@ -2584,28 +2592,44 @@ # dataset used; parameter should be the analygous dataset in the # current history. history = trans.get_history() - hda_source_dict = {} # Mapping from HDA in history to source HDAs. + + # Create index for hdas. + hda_source_dict = {} for hda in history.datasets: - source_hda = hda.copied_from_history_dataset_association - while source_hda: - if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid: - hda_source_dict[ source_hda.dataset.id ] = hda - source_hda = source_hda.copied_from_history_dataset_association + key = '%s_%s' % (hda.hid, hda.dataset.id) + hda_source_dict[ hda.dataset.id ] = hda_source_dict[ key ] = hda # Ditto for dataset collections. hdca_source_dict = {} for hdca in history.dataset_collections: - source_hdca = hdca.copied_from_history_dataset_collection_association - while source_hdca: - if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid: - hdca_source_dict[ source_hdca.collection.id ] = hdca - source_hdca = source_hdca.copied_from_history_dataset_collection_association + key = '%s_%s' % (hdca.hid, hdca.collection.id) + hdca_source_dict[ hdca.collection.id ] = hdca_source_dict[ key ] = hdca + + # Map dataset or collection to current history + def map_to_history(value): + id = None + source = None + if isinstance(value, trans.app.model.HistoryDatasetAssociation): + id = value.dataset.id + source = hda_source_dict + elif isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation): + id = value.collection.id + source = hdca_source_dict + else: + return None + key = '%s_%s' % (value.hid, id) + if key in source: + return source[ key ] + elif id in source: + return source[ id ] + else: + return None # Unpack unvalidated values to strings, they'll be validated when the # form is submitted (this happens when re-running a job that was # initially run by a workflow) #This needs to be done recursively through grouping parameters - def rerun_callback( input, value, prefixed_name, prefixed_label ): + def mapping_callback( input, value, prefixed_name, prefixed_label ): if isinstance( value, UnvalidatedValue ): try: return input.to_html_value( value.value, trans.app ) @@ -2617,22 +2641,17 @@ if isinstance(value,list): values = [] for val in value: - if isinstance(val, trans.app.model.HistoryDatasetAssociation): - if val.dataset.id in hda_source_dict: - values.append( hda_source_dict[ val.dataset.id ] ) - else: - values.append( val ) + new_val = map_to_history( val ) + if new_val: + values.append( new_val ) + else: + values.append( val ) return values - if isinstance(value, trans.app.model.HistoryDatasetAssociation): - if value.dataset.id in hda_source_dict: - return hda_source_dict[ value.dataset.id ] - if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation): - if value.collection.id in hdca_source_dict: - return hdca_source_dict[ value.collection.id ] + else: + return map_to_history( value ) elif isinstance( input, DataCollectionToolParameter ): - if value.collection.id in hdca_source_dict: - return hdca_source_dict[ value.collection.id ] - visit_input_values( tool_inputs, params, rerun_callback ) + return map_to_history( value ) + visit_input_values( tool_inputs, params, mapping_callback ) def _compare_tool_version( self, trans, job ): """ diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -15,6 +15,7 @@ from galaxy.util import string_as_bool, sanitize_param, unicodify from galaxy.util import listify from galaxy.util.odict import odict +from galaxy.util.expressions import ExpressionContext from sanitize import ToolParameterSanitizer import validation import dynamic_options @@ -802,8 +803,9 @@ self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) def _get_dynamic_options_call_other_values( self, trans, other_values ): - call_other_values = { "__trans__": trans } + call_other_values = ExpressionContext({ "__trans__": trans }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) return call_other_values @@ -1505,8 +1507,9 @@ def _get_options_from_code( self, trans=None, value=None, other_values=None ): assert self.dynamic_options, Exception( "dynamic_options was not specifed" ) - call_other_values = { '__trans__': trans, '__value__': value } + call_other_values = ExpressionContext({ '__trans__': trans, '__value__': value }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) try: return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -978,7 +978,9 @@ if tool_key in val.elems: self._tool_panel[ key ].elems[ tool_key ] = new_tool break - self._tools_by_id[ tool_id ] = new_tool + # (Re-)Register the reloaded tool, this will handle + # _tools_by_id and _tool_versions_by_id + self.register_tool( new_tool ) message = "Reloaded the tool:<br/>" message += "<b>name:</b> %s<br/>" % old_tool.name message += "<b>id:</b> %s<br/>" % old_tool.id diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -38,7 +38,7 @@ for dataset in datasets: rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) user = trans.user - if user and 'dbkeys' in user.preferences: + if user and hasattr( user, 'preferences' ) and 'dbkeys' in user.preferences: user_keys = loads( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/version.py --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "15.03" -VERSION_MINOR = "1" +VERSION_MINOR = "2" VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '') diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -668,7 +668,8 @@ """ history = None if self.galaxy_session: - history = self.galaxy_session.current_history + if hasattr( self.galaxy_session, 'current_history' ): + history = self.galaxy_session.current_history if not history and util.string_as_bool( create ): history = self.new_history() return history diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -83,9 +83,21 @@ self.__check_job_can_write_to_path( trans, job, path ) # Is this writing an unneeded file? Should this just copy in Python? - input_file = payload.get( "file", payload.get( "__file", None ) ).file + if '__file_path' in payload: + file_path = payload.get( '__file_path' ) + upload_store = trans.app.config.nginx_upload_job_files_store + assert upload_store, ( "Request appears to have been processed by" + " nginx_upload_module but Galaxy is not" + " configured to recognize it" ) + assert file_path.startswith( upload_store ), \ + ( "Filename provided by nginx (%s) is not in correct" + " directory (%s)" % ( file_path, upload_store ) ) + input_file = open( file_path ) + else: + input_file = payload.get( "file", + payload.get( "__file", None ) ).file try: - shutil.copyfile( input_file.name, path ) + shutil.move( input_file.name, path ) finally: input_file.close() return {"message": "ok"} diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -145,7 +145,6 @@ if success: trans.response.set_content_type( 'application/x-gzip' ) download_file = open( tool_tarball ) - os.unlink( tool_tarball ) tarball_path, filename = os.path.split( tool_tarball ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.tgz"' % ( id ) return download_file @@ -332,7 +331,7 @@ # job's previous parameters and incoming parameters. Incoming parameters # have priority. # - original_job = self.hda_manager.creating_job( original_dataset ) + original_job = self.hda_manager.creating_job( trans, original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -106,13 +106,13 @@ pack_scripts() # Close any pooled database connections before forking try: - galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled galaxy model database connections.") try: - galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.tool_shed_install.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled toolshed install model database connections.") if not app.config.is_uwsgi: postfork_setup() diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -852,22 +852,24 @@ status = 'done' try: id = trans.app.security.decode_id( dataset_id ) - history = trans.get_history() user = trans.get_user() hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) # Invalid HDA assert hda, 'Invalid history dataset ID' + # Walk up parent datasets to find the containing history + history = trans.get_history() topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent - assert topmost_parent in history.datasets, "Data does not belong to current history" # If the user is anonymous, make sure the HDA is owned by the current session. if not user: - assert trans.galaxy_session.current_history_id == trans.history.id, 'Invalid history dataset ID' + current_history_id = trans.galaxy_session.current_history_id + assert topmost_parent.history.id == current_history_id, 'Data does not belong to current user' # If the user is known, make sure the HDA is owned by the current user. else: - assert topmost_parent.history.user == trans.user, 'Invalid history dataset ID' + assert topmost_parent.history.user == user, 'Data does not belong to current user' + # Ensure HDA is deleted hda.deleted = True # HDA is purgeable @@ -890,8 +892,8 @@ except: log.exception( 'Unable to purge dataset (%s) on purge of HDA (%s):' % ( hda.dataset.id, hda.id ) ) trans.sa_session.flush() - except Exception: - msg = 'HDA purge failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) + except Exception, exc: + msg = 'HDA purge failed (encoded: %s, decoded: %s): %s' % ( dataset_id, id, exc ) log.exception( msg ) trans.log_event( msg ) message = 'Dataset removal from disk failed' diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -605,9 +605,13 @@ except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) - history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. ' - + 'Please contact a Galaxy administrator if the problem persists.' ) + log.exception( 'Error bootstrapping history for user %s: %s', user_id, exc ) + if isinstance( exc, exceptions.ItemAccessibilityException ): + error_msg = 'You do not have permission to view this history.' + else: + error_msg = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) + return trans.show_error_message( error_msg, use_panels=use_panels ) return trans.fill_template_mako( "history/view.mako", history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner, diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -1136,7 +1136,7 @@ def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): link_data_only = params.get( 'link_data_only', 'copy_files' ) uuid_str = params.get( 'uuid', None ) - file_type = params.get( 'file_type' ) + file_type = params.get( 'file_type', None ) library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() new_name = name @@ -1152,8 +1152,8 @@ uploaded_dataset.type = type uploaded_dataset.ext = None uploaded_dataset.file_type = file_type - uploaded_dataset.dbkey = params.get( 'dbkey' ) - uploaded_dataset.space_to_tab = params.get( 'space_to_tab' ) + uploaded_dataset.dbkey = params.get( 'dbkey', None ) + uploaded_dataset.space_to_tab = params.get( 'space_to_tab', None ) if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/controllers/tag.py --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -42,7 +42,7 @@ # Apply tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tag.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tag.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=new_tag ) @@ -57,7 +57,7 @@ # Remove tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).remove_item_tag( trans, user, item, tag_name.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).remove_item_tag( user, item, tag_name.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=tag_name ) @@ -73,8 +73,8 @@ # Apply tags. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).delete_item_tags( trans, user, item ) - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tags.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).delete_item_tags( user, item ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tags.encode( 'utf-8' ) ) trans.sa_session.flush() @web.expose diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -985,7 +985,7 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - job = self.hda_manager.creating_job( dataset ) + job = self.hda_manager.creating_job( trans, dataset ) viz_config = { 'dataset_id': dataset_id, 'tool_id': job.tool_id, @@ -1017,7 +1017,7 @@ if dataset_id: decoded_id = self.decode_id( dataset_id ) hda = self.hda_manager.get_accessible( trans, decoded_id, trans.user ) - hda = self.hda_manager.error_if_uploading( hda ) + hda = self.hda_manager.error_if_uploading( trans, hda ) else: return trans.show_message( "Phyloviz couldn't find a dataset_id" ) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -70,12 +70,13 @@ webapp = wrap_in_static( webapp, global_conf, **kwargs ) # Close any pooled database connections before forking try: - galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled galaxy model database connections.") # Return return webapp + def wrap_in_middleware( app, global_conf, **local_conf ): """Based on the configuration wrap `app` in a set of common and useful middleware.""" # Merge the global and local configurations diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -134,13 +134,28 @@ # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, **kwargs ) + # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + is_uwsgi = False + try: + # The uwsgi module is automatically injected by the parent uwsgi + # process and only exists that way. If anything works, this is a + # uwsgi-managed process. + import uwsgi + is_uwsgi = uwsgi.numproc + is_uwsgi = True + except ImportError: + # This is not a uwsgi process, or something went horribly wrong. + pass + if asbool( kwargs.get( 'static_enabled', True) ): + if is_uwsgi: + log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") + else: + webapp = wrap_in_static( webapp, global_conf, **kwargs ) # Close any pooled database connections before forking try: - galaxy.webapps.tool_shed.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled tool_shed model database connections.") # Return return webapp diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -456,8 +456,8 @@ try: exported_workflow_dict = json.loads( workflow_text ) except Exception, e: - log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" \ - % str( relative_path ), str( e ) ) + log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" + % ( str( relative_path ), str( e ) ) ) valid_exported_galaxy_workflow = False if valid_exported_galaxy_workflow and \ 'a_galaxy_workflow' in exported_workflow_dict and \ diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -237,12 +237,19 @@ if invalid: # We're attempting to display a tool in the tool shed that has been determined to have errors, so is invalid. return state + try: + # Attempt to generate the tool state using the standard Galaxy-side code + return tool.new_state( trans ) + except Exception, e: + # Fall back to building tool state as below + log.debug( 'Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e ) inputs = tool.inputs_by_page[ 0 ] context = ExpressionContext( state.inputs, parent=None ) for input in inputs.itervalues(): try: state.inputs[ input.name ] = input.get_initial_value( trans, context ) except: + # FIXME: not all values should be an empty list state.inputs[ input.name ] = [] return state diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -257,7 +257,7 @@ setAsCurrent : function(){ var history = this, - xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id ); xhr.done( function(){ history.trigger( 'set-as-current', history ); @@ -361,7 +361,7 @@ var HistoryCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - + /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -116,7 +116,7 @@ }, downloadDataset: function(){ - var url = '/api/libraries/datasets/download/uncompressed'; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/uncompressed'; var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, @@ -232,7 +232,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch dataset permissions.'); @@ -273,7 +273,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#access_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -320,7 +320,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#modify_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -367,7 +367,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#manage_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -413,7 +413,7 @@ self.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options var template = self.templateAccessSelect(); - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); self.accessSelectObject = $('#access_select').select2(); }).fail(function() { @@ -436,7 +436,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -447,7 +447,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -478,7 +478,7 @@ modify_ids.push(modify_roles[i].id); }; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/library/library-folder-view.js --- a/static/scripts/mvc/library/library-folder-view.js +++ b/static/scripts/mvc/library/library-folder-view.js @@ -81,7 +81,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch folder permissions.'); @@ -125,7 +125,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/folders/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -195,7 +195,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -294,7 +294,7 @@ dataset_ids.push( this.parentElement.parentElement.id ); } } ); - var url = '/api/libraries/datasets/download/' + format; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format; var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, @@ -386,7 +386,7 @@ fetchExtAndGenomes: function(){ var that = this; mod_utils.get({ - url : galaxy_config.root + "api/datatypes?extension_only=False", + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/datatypes?extension_only=False", success : function( datatypes ) { for (key in datatypes) { that.list_extensions.push({ @@ -403,7 +403,7 @@ } }); mod_utils.get({ - url: galaxy_config.root + "api/genomes", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/genomes", success: function( genomes ) { for ( key in genomes ) { that.list_genomes.push({ @@ -689,7 +689,7 @@ for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) { history_dataset_id = history_dataset_ids[i]; var folder_item = new mod_library_model.Item(); - folder_item.url = '/api/folders/' + this.options.id + '/contents'; + folder_item.url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/' + this.options.id + '/contents'; folder_item.set( { 'from_hda_id':history_dataset_id } ); hdas_to_add.push( folder_item ); } @@ -749,7 +749,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + @@ -788,7 +788,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&preserve_dirs=' + options.preserve_dirs + diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/library/library-library-view.js --- a/static/scripts/mvc/library/library-library-view.js +++ b/static/scripts/mvc/library/library-library-view.js @@ -87,7 +87,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch library permissions.'); @@ -134,7 +134,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -193,7 +193,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -204,7 +204,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -230,7 +230,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -4,7 +4,7 @@ // LIBRARY RELATED MODELS var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries/', + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/', /** based on show_deleted would this lib show in the list of lib's? * @param {Boolean} show_deleted are we including deleted libraries? @@ -19,7 +19,7 @@ }); var Libraries = Backbone.Collection.extend({ - url: '/api/libraries', + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries', model: Library, @@ -84,15 +84,15 @@ // FOLDER RELATED MODELS var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var Ldda = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders' }); var Folder = Backbone.Collection.extend({ @@ -152,7 +152,7 @@ var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), - urlRoot : "/api/folders/", + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/', id : "unknown" }, parse : function(obj) { @@ -169,11 +169,11 @@ // TODO UNITE var HistoryItem = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var HistoryContents = Backbone.Collection.extend({ - urlRoot : '/api/histories/', + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/', initialize: function(options){ this.id = options.id; }, @@ -184,11 +184,11 @@ }); var GalaxyHistory = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var GalaxyHistories = Backbone.Collection.extend({ - url : '/api/histories', + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories', model : GalaxyHistory }); @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/remote_files' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/remote_files' }); return { diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/mvc/tools/tools-parameters.js --- a/static/scripts/mvc/tools/tools-parameters.js +++ b/static/scripts/mvc/tools/tools-parameters.js @@ -145,6 +145,7 @@ data : options, error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, + optional : input_def.optional, searchable : input_def.searchable, onchange : function() { self.app.trigger('refresh'); diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 6395e70351435911f7ab75863c1b48b54e20a919 -r 0aa4dd8af7cf8303ef9dd9af95c2e2676854ecca static/scripts/packed/mvc/library/library-folder-view.js --- a/static/scripts/packed/mvc/library/library-folder-view.js +++ b/static/scripts/packed/mvc/library/library-folder-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch folder permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:"/api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set folder permissions.")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get((window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch folder permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post((window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set folder permissions.")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. 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: 2 new changesets
by commits-noreply＠bitbucket.org 22 Apr '15

22 Apr '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bfd4635011e3/ Changeset: bfd4635011e3 Branch: stable User: natefoo Date: 2015-04-22 19:29:22+00:00 Summary: Merge release_15.03 for v15.03.2 Affected #: 60 files diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/history/history-model.js --- a/client/galaxy/scripts/mvc/history/history-model.js +++ b/client/galaxy/scripts/mvc/history/history-model.js @@ -257,7 +257,7 @@ setAsCurrent : function(){ var history = this, - xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id ); xhr.done( function(){ history.trigger( 'set-as-current', history ); @@ -361,7 +361,7 @@ var HistoryCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - + /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -116,7 +116,7 @@ }, downloadDataset: function(){ - var url = '/api/libraries/datasets/download/uncompressed'; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/uncompressed'; var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, @@ -232,7 +232,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch dataset permissions.'); @@ -273,7 +273,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#access_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -320,7 +320,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#modify_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -367,7 +367,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#manage_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -413,7 +413,7 @@ self.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options var template = self.templateAccessSelect(); - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); self.accessSelectObject = $('#access_select').select2(); }).fail(function() { @@ -436,7 +436,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -447,7 +447,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -478,7 +478,7 @@ modify_ids.push(modify_roles[i].id); }; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/library/library-folder-view.js --- a/client/galaxy/scripts/mvc/library/library-folder-view.js +++ b/client/galaxy/scripts/mvc/library/library-folder-view.js @@ -81,7 +81,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch folder permissions.'); @@ -125,7 +125,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/folders/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -195,7 +195,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -294,7 +294,7 @@ dataset_ids.push( this.parentElement.parentElement.id ); } } ); - var url = '/api/libraries/datasets/download/' + format; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format; var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, @@ -386,7 +386,7 @@ fetchExtAndGenomes: function(){ var that = this; mod_utils.get({ - url : galaxy_config.root + "api/datatypes?extension_only=False", + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/datatypes?extension_only=False", success : function( datatypes ) { for (key in datatypes) { that.list_extensions.push({ @@ -403,7 +403,7 @@ } }); mod_utils.get({ - url: galaxy_config.root + "api/genomes", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/genomes", success: function( genomes ) { for ( key in genomes ) { that.list_genomes.push({ @@ -689,7 +689,7 @@ for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) { history_dataset_id = history_dataset_ids[i]; var folder_item = new mod_library_model.Item(); - folder_item.url = '/api/folders/' + this.options.id + '/contents'; + folder_item.url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/' + this.options.id + '/contents'; folder_item.set( { 'from_hda_id':history_dataset_id } ); hdas_to_add.push( folder_item ); } @@ -749,7 +749,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + @@ -788,7 +788,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&preserve_dirs=' + options.preserve_dirs + diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/library/library-library-view.js --- a/client/galaxy/scripts/mvc/library/library-library-view.js +++ b/client/galaxy/scripts/mvc/library/library-library-view.js @@ -87,7 +87,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch library permissions.'); @@ -134,7 +134,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -193,7 +193,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -204,7 +204,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -230,7 +230,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e 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 @@ -4,7 +4,7 @@ // LIBRARY RELATED MODELS var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries/', + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/', /** based on show_deleted would this lib show in the list of lib's? * @param {Boolean} show_deleted are we including deleted libraries? @@ -19,7 +19,7 @@ }); var Libraries = Backbone.Collection.extend({ - url: '/api/libraries', + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries', model: Library, @@ -84,15 +84,15 @@ // FOLDER RELATED MODELS var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var Ldda = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders' }); var Folder = Backbone.Collection.extend({ @@ -152,7 +152,7 @@ var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), - urlRoot : "/api/folders/", + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/', id : "unknown" }, parse : function(obj) { @@ -169,11 +169,11 @@ // TODO UNITE var HistoryItem = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var HistoryContents = Backbone.Collection.extend({ - urlRoot : '/api/histories/', + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/', initialize: function(options){ this.id = options.id; }, @@ -184,11 +184,11 @@ }); var GalaxyHistory = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var GalaxyHistories = Backbone.Collection.extend({ - url : '/api/histories', + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories', model : GalaxyHistory }); @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/remote_files' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/remote_files' }); return { diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/mvc/tools/tools-parameters.js --- a/client/galaxy/scripts/mvc/tools/tools-parameters.js +++ b/client/galaxy/scripts/mvc/tools/tools-parameters.js @@ -145,6 +145,7 @@ data : options, error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, + optional : input_def.optional, searchable : input_def.searchable, onchange : function() { self.app.trigger('refresh'); diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e client/galaxy/scripts/viz/circster.js --- a/client/galaxy/scripts/viz/circster.js +++ b/client/galaxy/scripts/viz/circster.js @@ -1,16 +1,20 @@ // load required libraries -require( -[ +require([ 'utils/utils', - 'mvc/ui/icon-button', - 'libs/farbtastic', -], function(mod_utils, mod_icon_btn) +], function(mod_utils) { // load css mod_utils.cssLoadFile("static/style/circster.css"); }); -define(["libs/underscore", "libs/d3", "viz/visualization", "utils/config"], function(_, d3, visualization, config) { +define([ + "libs/underscore", + "libs/d3", + "viz/visualization", + "utils/config", + 'mvc/ui/icon-button', + 'libs/farbtastic' +], function(_, d3, visualization, config, mod_icon_btn) { /** * Utility class for working with SVG. @@ -71,7 +75,7 @@ else { tick_coords = [1, 0, 4, 0]; text_coords = [0, 4, ".35em", ""]; - + } ticks.append("line") @@ -80,7 +84,7 @@ .attr("x2", tick_coords[2]) .attr("y1", tick_coords[3]) .style("stroke", "#000"); - + return ticks.append("text") .attr("x", text_coords[0]) .attr("y", text_coords[1]) @@ -98,11 +102,11 @@ // Use default of 2 sig. digits. if (sigDigits === undefined) sigDigits = 2; - + // Verify input number if (num === null) return null; - + // Calculate return value var rval = null; if (Math.abs(num) < 1) { @@ -141,7 +145,7 @@ */ var CircsterView = Backbone.View.extend({ className: 'circster', - + initialize: function(options) { this.genome = options.genome; this.label_arc_height = 50; @@ -188,7 +192,7 @@ track_gap = this.model.get('config').get_value('track_gap'), // Subtract 20 to make sure chrom labels are on screen. min_dimension = Math.min(this.$el.width(), this.$el.height()) - 20, - // Compute radius start based on model, will be centered + // Compute radius start based on model, will be centered // and fit entirely inside element by default. radius_start = min_dimension / 2 - circular_tracks.length * (dataset_arc_height + track_gap) + @@ -198,14 +202,14 @@ // Compute range of track starting radii. tracks_start_radii = d3.range(radius_start, min_dimension / 2, dataset_arc_height + track_gap); - + // Map from track start to bounds. var self = this; return _.map(tracks_start_radii, function(radius) { return [radius, radius + dataset_arc_height]; }); }, - + /** * Renders circular tracks, chord tracks, and label tracks. */ @@ -254,7 +258,7 @@ })) .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")") .append('svg:g').attr('class', 'tracks'); - + // -- Render circular tracks. -- // Create a view for each track in the visualization and render. @@ -266,12 +270,12 @@ genome: self.genome, total_gap: total_gap }); - + view.render(); - + return view; }); - + // -- Render chords tracks. -- this.chords_views = chords_tracks.map(function(track) { @@ -289,10 +293,10 @@ }); // -- Render label track. -- - + // Track bounds are: // (a) outer radius of last circular track; - // (b) + // (b) var outermost_radius = this.circular_views[this.circular_views.length-1].radius_bounds[1], track_bounds = [ outermost_radius, @@ -305,7 +309,7 @@ genome: self.genome, total_gap: total_gap }); - + this.label_track_view.render(); }, @@ -356,7 +360,7 @@ // Update label track. /* - FIXME: should never have to update label track because vis always expands to fit area + FIXME: should never have to update label track because vis always expands to fit area within label track. var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; track_bounds[1] = track_bounds[0]; @@ -373,7 +377,7 @@ var track_view = this.circular_views[options.index]; this.circular_views.splice(options.index, 1); track_view.$el.remove(); - + // Recompute and update track bounds. var new_track_bounds = this.get_tracks_bounds(); _.each(this.circular_views, function(track_view, i) { @@ -392,7 +396,7 @@ _.each(this.chords_views, function(track_view) { track_view.update_radius_bounds(new_track_bounds[0]); }); - + } }); @@ -455,7 +459,7 @@ // Append titles to paths. chroms_paths.append("title").text(function(d) { return d.data.chrom; }); - + // -- Render track data and, when track data is rendered, apply preferences and update chrom_elts fill. -- var self = this, @@ -490,7 +494,7 @@ var new_d = d3.svg.arc() .innerRadius(this.radius_bounds[0]) .outerRadius(this.radius_bounds[1]); - + this.parent_elt.selectAll('g>path.chrom-background').transition().duration(1000).attr('d', new_d); this._transition_chrom_data(); @@ -511,7 +515,7 @@ } // -- Scale increased, so render visible data with more detail. -- - + var self = this, utils = new SVGUtils(); @@ -539,7 +543,7 @@ $.when(data_deferred).then(function(data) { // Remove current data path. path_elt.remove(); - + // Update data bounds with new data. self._update_data_bounds(); @@ -598,12 +602,12 @@ _transition_labels: function() {}, /** - * Update data bounds. If there are new_bounds, use them; otherwise use + * Update data bounds. If there are new_bounds, use them; otherwise use * default data bounds. */ _update_data_bounds: function(new_bounds) { var old_bounds = this.data_bounds; - this.data_bounds = new_bounds || + this.data_bounds = new_bounds || this.get_data_bounds(this.track.get('data_manager').get_genome_wide_data(this.genome)); this._transition_chrom_data(); }, @@ -624,7 +628,7 @@ // Set min, max value in config so that they can be adjusted. Make this silent // because these attributes are watched for changes and the viz is updated - // accordingly (set up in initialize). Because we are setting up, we don't want + // accordingly (set up in initialize). Because we are setting up, we don't want // the watch to trigger events here. track.get('config').set_value('min_value', self.data_bounds[0], {silent: true}); track.get('config').set_value('max_value', self.data_bounds[1], {silent: true}); @@ -660,7 +664,7 @@ _get_path_function: function(chrom_arc, chrom_data) {}, /** - * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle + * Returns arc layouts for genome's chromosomes/contigs. Arcs are arranged in a circle * separated by gaps. */ _chroms_layout: function() { @@ -700,14 +704,14 @@ * Render labels. */ _render_data: function(svg) { - // -- Add chromosome label where it will fit; an alternative labeling mechanism + // -- Add chromosome label where it will fit; an alternative labeling mechanism // would be nice for small chromosomes. -- var self = this, chrom_arcs = svg.selectAll('g'); chrom_arcs.selectAll('path') .attr('id', function(d) { return 'label-' + d.data.chrom; }); - + chrom_arcs.append("svg:text") .filter(function(d) { return d.endAngle - d.startAngle > self.min_arc_len; @@ -857,12 +861,12 @@ return "rotate(90)"; }; - // FIXME: + // FIXME: // (1) using min_max class below is needed for _update_min_max, which could be improved. // (2) showing config on tick click should be replaced by proper track config icon. // Draw min, max on first chrom only. - var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], + var ticks = this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true) .classed('min_max', true); @@ -872,7 +876,7 @@ var view = new config.ConfigSettingCollectionView({ collection: self.track.get('config') }); - view.render_in_modal('Configure Track'); + view.render_in_modal('Configure Track'); }); }); @@ -951,7 +955,7 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ get_data_bounds: function(data) { - // Set max across dataset by extracting all values, flattening them into a + // Set max across dataset by extracting all values, flattening them into a // single array, and getting third quartile. var values = _.flatten( _.map(data, function(d) { if (d) { @@ -965,8 +969,8 @@ return 0; } }) ); - - // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 + + // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 // for sparsely populated data, so use max in that case. return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ]; } @@ -1068,13 +1072,13 @@ genome : genome, model : vis }); - + // Render vizualization viz_view.render(); - + // setup title $('#center .unified-panel-header-inner').append(galaxy_config.app.viz_config.title + " " + galaxy_config.app.viz_config.dbkey); - + // setup menu var menu = mod_icon_btn.create_icon_buttons_menu([ { @@ -1100,7 +1104,7 @@ { // show saving dialog box Galaxy.modal.show({title: "Saving...", body: "progress" }); - + // send to server $.ajax({ url: galaxy_config.root + "visualization/save", @@ -1132,11 +1136,11 @@ window.location = galaxy_config.root + "visualization/list"; } }], { tooltip_config: { placement: 'bottom' } }); - + // add menu menu.$el.attr("style", "float: right"); $("#center .unified-panel-header-inner").append(menu.$el); - + // manual tooltip config because default gravity is S and cannot be changed $(".menu-button").tooltip( { placement: 'bottom' } ); } diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -580,6 +580,13 @@ # requests. #nginx_upload_path = False +# Galaxy can also use nginx_upload_module to receive files staged out upon job +# completion by remote job runners (i.e. Pulsar) that initiate staging +# operations on the remote end. See the Galaxy nginx documentation for the +# corresponding nginx configuration. +#nginx_upload_job_files_store = False +#nginx_upload_job_files_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 # default though you do need to install node+npm and do an npm install from @@ -960,6 +967,17 @@ # always, onsuccess, never #cleanup_job = always +# For sites where all users in Galaxy match users on the system on which Galaxy +# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the +# actual user instead of as the user running the Galaxy server process. For +# details on these options, see the documentation at: +# +# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster +# +#drmaa_external_runjob_script = scripts/drmaa_external_runner.py +#drmaa_external_killjob_script = scripts/drmaa_external_killer.py +#external_chown_script = scripts/external_chown_script.py + # File to source to set up the environment when running jobs. By default, the # environment in which the Galaxy server starts is used when running jobs # locally, and the environment set up per the DRM's submission method and diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -252,10 +252,7 @@ --></destination><destination id="real_user_cluster" runner="drmaa"> -  - <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> - <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> - <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> + </destination><destination id="dynamic" runner="dynamic"> diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -293,6 +293,8 @@ self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False ) self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False ) self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False ) + self.nginx_upload_job_files_store = kwargs.get( 'nginx_upload_job_files_store', False ) + self.nginx_upload_job_files_path = kwargs.get( 'nginx_upload_job_files_path', False ) if self.nginx_upload_store: self.nginx_upload_store = os.path.abspath( self.nginx_upload_store ) self.object_store = kwargs.get( 'object_store', 'disk' ) @@ -466,7 +468,7 @@ datatypes_config_file=[ 'config/datatypes_conf.xml', 'datatypes_conf.xml', 'config/datatypes_conf.xml.sample' ], external_service_type_config_file=[ 'config/external_service_types_conf.xml', 'external_service_types_conf.xml', 'config/external_service_types_conf.xml.sample' ], job_config_file=[ 'config/job_conf.xml', 'job_conf.xml' ], - job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml' ], + job_metrics_config_file=[ 'config/job_metrics_conf.xml', 'job_metrics_conf.xml','config/job_metrics_conf.xml.sample' ], dependency_resolvers_config_file=[ 'config/dependency_resolvers_conf.xml', 'dependency_resolvers_conf.xml' ], job_resource_params_file=[ 'config/job_resource_params_conf.xml', 'job_resource_params_conf.xml' ], migrated_tools_config=[ 'migrated_tools_conf.xml', 'config/migrated_tools_conf.xml' ], diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -962,12 +962,11 @@ job.set_state( job.states.PAUSED ) self.sa_session.add( job ) - def mark_as_resubmitted( self ): + def mark_as_resubmitted( self, info=None ): job = self.get_job() self.sa_session.refresh( job ) - for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]: - dataset._state = model.Dataset.states.RESUBMITTED - self.sa_session.add( dataset ) + if info is not None: + job.info = info job.set_state( model.Job.states.RESUBMITTED ) self.sa_session.add( job ) self.sa_session.flush() @@ -1251,6 +1250,16 @@ if job.user: job.user.total_disk_usage += bytes + # Emperically, we need to update job.user and + # job.workflow_invocation_step.workflow_invocation in separate + # transactions. Best guess as to why is that the workflow_invocation + # may or may not exist when the job is first loaded by the handler - + # and depending on whether it is or not sqlalchemy orders the updates + # differently and deadlocks can occur (one thread updates user and + # waits on invocation and the other updates invocation and waits on + # user). + self.sa_session.flush() + # fix permissions for path in [ dp.real_path for dp in self.get_mutable_output_fnames() ]: util.umask_fix_perms( path, self.app.config.umask, 0666, self.app.config.gid ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -341,8 +341,8 @@ except: log.exception('Caught exception in runner state handler:') - def mark_as_resubmitted( self, job_state ): - job_state.job_wrapper.mark_as_resubmitted() + def mark_as_resubmitted( self, job_state, info=None ): + job_state.job_wrapper.mark_as_resubmitted( info=info ) if not self.app.config.track_jobs_in_database: job_state.job_wrapper.change_state( model.Job.states.QUEUED ) self.app.job_manager.job_handler.dispatcher.put( job_state.job_wrapper ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/jobs/runners/pulsar.py --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -342,7 +342,12 @@ encoded_job_id = self.app.security.encode_id(job_id) job_key = self.app.security.encode_id( job_id, kind="jobs_files" ) - files_endpoint = "%s/api/jobs/%s/files?job_key=%s" % ( + endpoint_base = "%s/api/jobs/%s?job_key=%s" + if self.app.config.nginx_upload_job_files_path: + endpoint_base = "%s" + \ + self.app.config.nginx_upload_job_files_path + \ + "?job_id=%s&job_key=%s" + files_endpoint = endpoint_base % ( self.galaxy_url, encoded_job_id, job_key diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/jobs/runners/state_handlers/resubmit.py --- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py +++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py @@ -1,4 +1,5 @@ import logging + from galaxy import model @@ -13,31 +14,45 @@ def failure(app, job_runner, job_state): - if getattr( job_state, 'runner_state', None ) and job_state.runner_state in ( job_state.runner_states.WALLTIME_REACHED, job_state.runner_states.MEMORY_LIMIT_REACHED ): - # Intercept jobs that hit the walltime and have a walltime or nonspecific resubmit destination configured + if (getattr(job_state, 'runner_state', None) + and job_state.runner_state in + (job_state.runner_states.WALLTIME_REACHED, + job_state.runner_states.MEMORY_LIMIT_REACHED)): + # Intercept jobs that hit the walltime and have a walltime or + # nonspecific resubmit destination configured for resubmit in job_state.job_destination.get('resubmit'): - if resubmit.get('condition', None) and resubmit['condition'] != job_state.runner_state: - continue # There is a resubmit defined for the destination but its condition is not for walltime_reached - log.info("(%s/%s) Job will be resubmitted to '%s' because %s at the '%s' destination", - job_state.job_wrapper.job_id, - job_state.job_id, - resubmit['destination'], - MESSAGES[job_state.runner_state], - job_state.job_wrapper.job_destination.id ) + if (resubmit.get('condition', None) and resubmit['condition'] != + job_state.runner_state): + # There is a resubmit defined for the destination but + # its condition is not for walltime_reached + continue + log.info("(%s/%s) Job will be resubmitted to '%s' because %s at " + "the '%s' destination", + job_state.job_wrapper.job_id, + job_state.job_id, + resubmit['destination'], + MESSAGES[job_state.runner_state], + job_state.job_wrapper.job_destination.id ) # fetch JobDestination for the id or tag - new_destination = app.job_config.get_destination(resubmit['destination']) + new_destination = app.job_config.get_destination( + resubmit['destination']) # Resolve dynamic if necessary - new_destination = job_state.job_wrapper.job_runner_mapper.cache_job_destination( new_destination ) + new_destination = (job_state.job_wrapper.job_runner_mapper + .cache_job_destination(new_destination)) # Reset job state job = job_state.job_wrapper.get_job() if resubmit.get('handler', None): - log.debug('(%s/%s) Job reassigned to handler %s', job_state.job_wrapper.job_id, job_state.job_id, resubmit['handler']) + log.debug('(%s/%s) Job reassigned to handler %s', + job_state.job_wrapper.job_id, job_state.job_id, + resubmit['handler']) job.set_handler(resubmit['handler']) job_runner.sa_session.add( job ) # Is this safe to do here? job_runner.sa_session.flush() - # Cache the destination to prevent rerunning dynamic after resubmit - job_state.job_wrapper.job_runner_mapper.cached_job_destination = new_destination + # Cache the destination to prevent rerunning dynamic after + # resubmit + job_state.job_wrapper.job_runner_mapper \ + .cached_job_destination = new_destination job_state.job_wrapper.set_job_destination(new_destination) # Clear external ID (state change below flushes the change) job.job_runner_external_id = None @@ -45,5 +60,7 @@ if job.params is None: job.params = {} job_state.runner_state_handled = True - job_runner.mark_as_resubmitted( job_state ) + info = "This job was resubmitted to the queue because %s on its " \ + "compute resource." % MESSAGES[job_state.runner_state] + job_runner.mark_as_resubmitted(job_state, info=info) return diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -700,8 +700,8 @@ setattr( item, key, val ) return val - def deserialize_basestring( self, trans, item, key, val ): - val = self.validate.basestring( key, val ) + def deserialize_basestring( self, trans, item, key, val, convert_none_to_empty=False ): + val = '' if ( convert_none_to_empty and val is None ) else self.validate.basestring( key, val ) return self.default_deserializer( trans, item, key, val ) def deserialize_bool( self, trans, item, key, val ): diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/managers/hdas.py --- a/lib/galaxy/managers/hdas.py +++ b/lib/galaxy/managers/hdas.py @@ -154,8 +154,9 @@ # error here if disallowed - before jobs are stopped #TODO: poss. move to DatasetAssociationManager self.dataset_manager.error_unless_dataset_purge_allowed( trans, hda ) + if trans.user: + trans.user.total_disk_usage -= hda.quota_amount( trans.user ) super( HDAManager, self ).purge( trans, hda, flush=flush ) - if hda.creating_job_associations: job = hda.creating_job_associations[0].job if not job.finished: @@ -195,6 +196,32 @@ break return job + def _job_state_history_query( self, hda ): + """ + Return a query of the job's state history for the job that created this hda. + """ + session = self.app.model.context + JobToOutputDatasetAssociation = model.JobToOutputDatasetAssociation + JobStateHistory = model.JobStateHistory + + # TODO: this does not play well with copied hdas + # NOTE: don't eagerload (JODA will load the hda were using!) + hda_id = hda.id + query = ( session.query( JobToOutputDatasetAssociation, JobStateHistory ) + .filter( JobToOutputDatasetAssociation.dataset_id == hda_id ) + .filter( JobStateHistory.job_id == JobToOutputDatasetAssociation.job_id ) + .enable_eagerloads( False ) ) + return query + + def has_been_resubmitted( self, hda ): + """ + Return True if the hda's job was resubmitted at any point. + """ + job_states = model.Job.states + query = ( self._job_state_history_query( hda ) + .filter( model.JobStateHistory.state == job_states.RESUBMITTED ) ) + return self.app.model.context.query( query.exists() ).scalar() + # .... serialization def get_display_apps( self, trans, hda ): """ @@ -324,7 +351,7 @@ 'history_content_type', 'dataset_id', 'state', 'extension', - 'deleted', 'purged', 'visible', 'resubmitted', + 'deleted', 'purged', 'visible', 'type', 'url' ]) self.add_view( 'detailed', [ @@ -340,7 +367,8 @@ 'file_ext', 'file_size', 'create_time', 'update_time', - 'metadata', 'meta_files', 'data_type', + 'resubmitted', + 'metadata', 'meta_files', 'data_type', 'peek', #TODO: why is this named uuid!? The hda doesn't have a uuid - it's the underlying dataset's uuid! @@ -388,7 +416,7 @@ 'hda_ldda' : lambda *a: 'hda', # remapped - 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else i.info, + 'info' : lambda t, i, k: i.info.strip() if isinstance( i.info, basestring ) else '', 'misc_info' : lambda t, i, k: self.serializers[ 'info' ]( t, i, k ), 'misc_blurb' : lambda t, i, k: i.blurb, 'genome_build' : lambda t, i, k: i.dbkey, @@ -400,7 +428,7 @@ 'copied_from_history_dataset_association_id' : self.serialize_id, 'copied_from_library_dataset_dataset_association_id': self.serialize_id, - 'resubmitted' : lambda t, i, k: i._state == t.app.model.Dataset.states.RESUBMITTED, + 'resubmitted' : lambda t, i, k: self.hda_manager.has_been_resubmitted( i ), 'meta_files' : self.serialize_meta_files, 'file_path' : self.serialize_file_path, @@ -583,7 +611,8 @@ # remapped 'genome_build' : lambda t, i, k, v: self.deserialize_genome_build( t, i, 'dbkey', v ), - 'misc_info' : lambda t, i, k, v: self.deserialize_basestring( t, i, 'info', v ), + 'misc_info' : lambda t, i, k, v: ( + self.deserialize_basestring( t, i, 'info', v, convert_none_to_empty=True ) ), #TODO: mixin: deletable 'deleted' : self.deserialize_bool, diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/managers/workflows.py --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -569,7 +569,7 @@ for step_index in step_indices: step_dict = supplied_steps[ step_index ] uuid = step_dict.get("uuid", None) - if uuid: + if uuid and uuid != "None": if uuid in discovered_uuids: raise exceptions.DuplicatedIdentifierException("Duplicate step UUID in request.") discovered_uuids.add(uuid) @@ -586,10 +586,9 @@ type-specific functionality from the incoming dicitionary. """ step = model.WorkflowStep() - # TODO: Consider handling position inside module. step.position = step_dict['position'] - if "uuid" in step_dict: + if "uuid" in step_dict and step_dict['uuid'] != "None": step.uuid = step_dict["uuid"] if "label" in step_dict: step.label = step_dict["label"] diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1335,9 +1335,8 @@ DISCARDED = 'discarded', PAUSED = 'paused', SETTING_METADATA = 'setting_metadata', - FAILED_METADATA = 'failed_metadata', - RESUBMITTED = 'resubmitted' ) - # failed_metadata and resubmitted are only valid as DatasetInstance states currently + FAILED_METADATA = 'failed_metadata') + # failed_metadata is only valid as DatasetInstance state currently non_ready_states = ( states.UPLOAD, diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/model/orm/logging_connection_proxy.py --- a/lib/galaxy/model/orm/logging_connection_proxy.py +++ b/lib/galaxy/model/orm/logging_connection_proxy.py @@ -2,7 +2,7 @@ import inspect import os -from galaxy.model.orm import * +from galaxy.model.orm import ConnectionProxy import logging diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -417,13 +417,14 @@ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) default_template = 'tool_form.mako' - def __init__( self, config_file, tool_source, app, guid=None, repository_id=None ): + def __init__( self, config_file, tool_source, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -704,14 +705,15 @@ # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # User interface hints uihints_elem = root.find( "uihints" ) @@ -2433,7 +2435,7 @@ continue # state for subsection/group - group_state = state_inputs[input.name] + group_state = state_inputs.get(input.name, {}) # iterate and update values if input.type == 'repeat': @@ -2444,10 +2446,12 @@ elif input.type == 'conditional': if 'test_param' in tool_dict: test_param = tool_dict['test_param'] - test_param['value'] = jsonify(group_state[test_param['name']]) - if '__current_case__' in group_state: - i = group_state['__current_case__'] - iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, group_state, other_values) + test_param['value'] = jsonify(group_state.get(test_param['name'], None)) + for i in range (len ( tool_dict['cases'] ) ): + current_state = {} + if i == group_state.get('__current_case__', None): + current_state = group_state + iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values) else: # create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options try: @@ -2459,11 +2463,15 @@ input_name = tool_dict.get('name') if input_name: # backup default value - tool_dict['default_value'] = input.get_initial_value(trans, other_values) + try: + tool_dict['default_value'] = input.get_initial_value(trans, other_values) + except Exception: + # get initial value failed due to improper late validation + tool_dict['default_value'] = None + pass # update input value from tool state - if input_name in state_inputs: - tool_dict['value'] = state_inputs[input_name] + tool_dict['value'] = state_inputs.get(input_name, None) # sanitize values sanitize(tool_dict, 'value') @@ -2584,28 +2592,44 @@ # dataset used; parameter should be the analygous dataset in the # current history. history = trans.get_history() - hda_source_dict = {} # Mapping from HDA in history to source HDAs. + + # Create index for hdas. + hda_source_dict = {} for hda in history.datasets: - source_hda = hda.copied_from_history_dataset_association - while source_hda: - if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid: - hda_source_dict[ source_hda.dataset.id ] = hda - source_hda = source_hda.copied_from_history_dataset_association + key = '%s_%s' % (hda.hid, hda.dataset.id) + hda_source_dict[ hda.dataset.id ] = hda_source_dict[ key ] = hda # Ditto for dataset collections. hdca_source_dict = {} for hdca in history.dataset_collections: - source_hdca = hdca.copied_from_history_dataset_collection_association - while source_hdca: - if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid: - hdca_source_dict[ source_hdca.collection.id ] = hdca - source_hdca = source_hdca.copied_from_history_dataset_collection_association + key = '%s_%s' % (hdca.hid, hdca.collection.id) + hdca_source_dict[ hdca.collection.id ] = hdca_source_dict[ key ] = hdca + + # Map dataset or collection to current history + def map_to_history(value): + id = None + source = None + if isinstance(value, trans.app.model.HistoryDatasetAssociation): + id = value.dataset.id + source = hda_source_dict + elif isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation): + id = value.collection.id + source = hdca_source_dict + else: + return None + key = '%s_%s' % (value.hid, id) + if key in source: + return source[ key ] + elif id in source: + return source[ id ] + else: + return None # Unpack unvalidated values to strings, they'll be validated when the # form is submitted (this happens when re-running a job that was # initially run by a workflow) #This needs to be done recursively through grouping parameters - def rerun_callback( input, value, prefixed_name, prefixed_label ): + def mapping_callback( input, value, prefixed_name, prefixed_label ): if isinstance( value, UnvalidatedValue ): try: return input.to_html_value( value.value, trans.app ) @@ -2617,22 +2641,17 @@ if isinstance(value,list): values = [] for val in value: - if isinstance(val, trans.app.model.HistoryDatasetAssociation): - if val.dataset.id in hda_source_dict: - values.append( hda_source_dict[ val.dataset.id ] ) - else: - values.append( val ) + new_val = map_to_history( val ) + if new_val: + values.append( new_val ) + else: + values.append( val ) return values - if isinstance(value, trans.app.model.HistoryDatasetAssociation): - if value.dataset.id in hda_source_dict: - return hda_source_dict[ value.dataset.id ] - if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation): - if value.collection.id in hdca_source_dict: - return hdca_source_dict[ value.collection.id ] + else: + return map_to_history( value ) elif isinstance( input, DataCollectionToolParameter ): - if value.collection.id in hdca_source_dict: - return hdca_source_dict[ value.collection.id ] - visit_input_values( tool_inputs, params, rerun_callback ) + return map_to_history( value ) + visit_input_values( tool_inputs, params, mapping_callback ) def _compare_tool_version( self, trans, job ): """ diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -15,6 +15,7 @@ from galaxy.util import string_as_bool, sanitize_param, unicodify from galaxy.util import listify from galaxy.util.odict import odict +from galaxy.util.expressions import ExpressionContext from sanitize import ToolParameterSanitizer import validation import dynamic_options @@ -802,8 +803,9 @@ self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) def _get_dynamic_options_call_other_values( self, trans, other_values ): - call_other_values = { "__trans__": trans } + call_other_values = ExpressionContext({ "__trans__": trans }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) return call_other_values @@ -1505,8 +1507,9 @@ def _get_options_from_code( self, trans=None, value=None, other_values=None ): assert self.dynamic_options, Exception( "dynamic_options was not specifed" ) - call_other_values = { '__trans__': trans, '__value__': value } + call_other_values = ExpressionContext({ '__trans__': trans, '__value__': value }) if other_values: + call_other_values.parent = other_values.parent call_other_values.update( other_values.dict ) try: return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -978,7 +978,9 @@ if tool_key in val.elems: self._tool_panel[ key ].elems[ tool_key ] = new_tool break - self._tools_by_id[ tool_id ] = new_tool + # (Re-)Register the reloaded tool, this will handle + # _tools_by_id and _tool_versions_by_id + self.register_tool( new_tool ) message = "Reloaded the tool:<br/>" message += "<b>name:</b> %s<br/>" % old_tool.name message += "<b>id:</b> %s<br/>" % old_tool.id diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/util/dbkeys.py --- a/lib/galaxy/util/dbkeys.py +++ b/lib/galaxy/util/dbkeys.py @@ -38,7 +38,7 @@ for dataset in datasets: rval.append( ( dataset.dbkey, "%s (%s) [History]" % ( dataset.name, dataset.dbkey ) ) ) user = trans.user - if user and 'dbkeys' in user.preferences: + if user and hasattr( user, 'preferences' ) and 'dbkeys' in user.preferences: user_keys = loads( user.preferences['dbkeys'] ) for key, chrom_dict in user_keys.iteritems(): rval.append( ( key, "%s (%s) [Custom]" % ( chrom_dict['name'], key ) ) ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/version.py --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "15.03" -VERSION_MINOR = "1" +VERSION_MINOR = "2" VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '') diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/web/framework/webapp.py --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -668,7 +668,8 @@ """ history = None if self.galaxy_session: - history = self.galaxy_session.current_history + if hasattr( self.galaxy_session, 'current_history' ): + history = self.galaxy_session.current_history if not history and util.string_as_bool( create ): history = self.new_history() return history diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -83,9 +83,21 @@ self.__check_job_can_write_to_path( trans, job, path ) # Is this writing an unneeded file? Should this just copy in Python? - input_file = payload.get( "file", payload.get( "__file", None ) ).file + if '__file_path' in payload: + file_path = payload.get( '__file_path' ) + upload_store = trans.app.config.nginx_upload_job_files_store + assert upload_store, ( "Request appears to have been processed by" + " nginx_upload_module but Galaxy is not" + " configured to recognize it" ) + assert file_path.startswith( upload_store ), \ + ( "Filename provided by nginx (%s) is not in correct" + " directory (%s)" % ( file_path, upload_store ) ) + input_file = open( file_path ) + else: + input_file = payload.get( "file", + payload.get( "__file", None ) ).file try: - shutil.copyfile( input_file.name, path ) + shutil.move( input_file.name, path ) finally: input_file.close() return {"message": "ok"} diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -145,7 +145,6 @@ if success: trans.response.set_content_type( 'application/x-gzip' ) download_file = open( tool_tarball ) - os.unlink( tool_tarball ) tarball_path, filename = os.path.split( tool_tarball ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.tgz"' % ( id ) return download_file @@ -332,7 +331,7 @@ # job's previous parameters and incoming parameters. Incoming parameters # have priority. # - original_job = self.hda_manager.creating_job( original_dataset ) + original_job = self.hda_manager.creating_job( trans, original_dataset ) tool = trans.app.toolbox.get_tool( original_job.tool_id ) if not tool or not tool.allow_user_access( trans.user ): return trans.app.model.Dataset.conversion_messages.NO_TOOL diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -106,13 +106,13 @@ pack_scripts() # Close any pooled database connections before forking try: - galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled galaxy model database connections.") try: - galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.tool_shed_install.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled toolshed install model database connections.") if not app.config.is_uwsgi: postfork_setup() diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -852,22 +852,24 @@ status = 'done' try: id = trans.app.security.decode_id( dataset_id ) - history = trans.get_history() user = trans.get_user() hda = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) # Invalid HDA assert hda, 'Invalid history dataset ID' + # Walk up parent datasets to find the containing history + history = trans.get_history() topmost_parent = hda while topmost_parent.parent: topmost_parent = topmost_parent.parent - assert topmost_parent in history.datasets, "Data does not belong to current history" # If the user is anonymous, make sure the HDA is owned by the current session. if not user: - assert trans.galaxy_session.current_history_id == trans.history.id, 'Invalid history dataset ID' + current_history_id = trans.galaxy_session.current_history_id + assert topmost_parent.history.id == current_history_id, 'Data does not belong to current user' # If the user is known, make sure the HDA is owned by the current user. else: - assert topmost_parent.history.user == trans.user, 'Invalid history dataset ID' + assert topmost_parent.history.user == user, 'Data does not belong to current user' + # Ensure HDA is deleted hda.deleted = True # HDA is purgeable @@ -890,8 +892,8 @@ except: log.exception( 'Unable to purge dataset (%s) on purge of HDA (%s):' % ( hda.dataset.id, hda.id ) ) trans.sa_session.flush() - except Exception: - msg = 'HDA purge failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) + except Exception, exc: + msg = 'HDA purge failed (encoded: %s, decoded: %s): %s' % ( dataset_id, id, exc ) log.exception( msg ) trans.log_event( msg ) message = 'Dataset removal from disk failed' diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -605,9 +605,13 @@ except Exception, exc: user_id = str( trans.user.id ) if trans.user else '(anonymous)' - log.exception( 'Error bootstrapping history for user %s: %s', user_id, str( exc ) ) - history_dictionary[ 'error' ] = ( 'An error occurred getting the history data from the server. ' - + 'Please contact a Galaxy administrator if the problem persists.' ) + log.exception( 'Error bootstrapping history for user %s: %s', user_id, exc ) + if isinstance( exc, exceptions.ItemAccessibilityException ): + error_msg = 'You do not have permission to view this history.' + else: + error_msg = ( 'An error occurred getting the history data from the server. ' + + 'Please contact a Galaxy administrator if the problem persists.' ) + return trans.show_error_message( error_msg, use_panels=use_panels ) return trans.fill_template_mako( "history/view.mako", history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner, diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -1136,7 +1136,7 @@ def make_library_uploaded_dataset( self, trans, cntrller, params, name, path, type, library_bunch, in_folder=None ): link_data_only = params.get( 'link_data_only', 'copy_files' ) uuid_str = params.get( 'uuid', None ) - file_type = params.get( 'file_type' ) + file_type = params.get( 'file_type', None ) library_bunch.replace_dataset = None # not valid for these types of upload uploaded_dataset = util.bunch.Bunch() new_name = name @@ -1152,8 +1152,8 @@ uploaded_dataset.type = type uploaded_dataset.ext = None uploaded_dataset.file_type = file_type - uploaded_dataset.dbkey = params.get( 'dbkey' ) - uploaded_dataset.space_to_tab = params.get( 'space_to_tab' ) + uploaded_dataset.dbkey = params.get( 'dbkey', None ) + uploaded_dataset.space_to_tab = params.get( 'space_to_tab', None ) if in_folder: uploaded_dataset.in_folder = in_folder uploaded_dataset.data = upload_common.new_upload( trans, cntrller, uploaded_dataset, library_bunch ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/controllers/tag.py --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -42,7 +42,7 @@ # Apply tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tag.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tag.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=new_tag ) @@ -57,7 +57,7 @@ # Remove tag. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).remove_item_tag( trans, user, item, tag_name.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).remove_item_tag( user, item, tag_name.encode( 'utf-8' ) ) trans.sa_session.flush() # Log. params = dict( item_id=item.id, item_class=item_class, tag=tag_name ) @@ -73,8 +73,8 @@ # Apply tags. item = self._get_item( trans, item_class, trans.security.decode_id( item_id ) ) user = trans.user - self.get_tag_handler( trans ).delete_item_tags( trans, user, item ) - self.get_tag_handler( trans ).apply_item_tags( trans, user, item, new_tags.encode( 'utf-8' ) ) + self.get_tag_handler( trans ).delete_item_tags( user, item ) + self.get_tag_handler( trans ).apply_item_tags( user, item, new_tags.encode( 'utf-8' ) ) trans.sa_session.flush() @web.expose diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -985,7 +985,7 @@ else: # Loading new visualization. dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) - job = self.hda_manager.creating_job( dataset ) + job = self.hda_manager.creating_job( trans, dataset ) viz_config = { 'dataset_id': dataset_id, 'tool_id': job.tool_id, @@ -1017,7 +1017,7 @@ if dataset_id: decoded_id = self.decode_id( dataset_id ) hda = self.hda_manager.get_accessible( trans, decoded_id, trans.user ) - hda = self.hda_manager.error_if_uploading( hda ) + hda = self.hda_manager.error_if_uploading( trans, hda ) else: return trans.show_message( "Phyloviz couldn't find a dataset_id" ) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/reports/buildapp.py --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -70,12 +70,13 @@ webapp = wrap_in_static( webapp, global_conf, **kwargs ) # Close any pooled database connections before forking try: - galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled galaxy model database connections.") # Return return webapp + def wrap_in_middleware( app, global_conf, **local_conf ): """Based on the configuration wrap `app` in a set of common and useful middleware.""" # Merge the global and local configurations diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -134,13 +134,28 @@ # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) - if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, **kwargs ) + # TEST FOR UWSGI -- TODO save this somewhere so we only have to do it once. + is_uwsgi = False + try: + # The uwsgi module is automatically injected by the parent uwsgi + # process and only exists that way. If anything works, this is a + # uwsgi-managed process. + import uwsgi + is_uwsgi = uwsgi.numproc + is_uwsgi = True + except ImportError: + # This is not a uwsgi process, or something went horribly wrong. + pass + if asbool( kwargs.get( 'static_enabled', True) ): + if is_uwsgi: + log.error("Static middleware is enabled in your configuration but this is a uwsgi process. Refusing to wrap in static middleware.") + else: + webapp = wrap_in_static( webapp, global_conf, **kwargs ) # Close any pooled database connections before forking try: - galaxy.webapps.tool_shed.model.mapping.metadata.engine.connection_provider._pool.dispose() + galaxy.webapps.tool_shed.model.mapping.metadata.bind.dispose() except: - pass + log.exception("Unable to dispose of pooled tool_shed model database connections.") # Return return webapp diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -456,8 +456,8 @@ try: exported_workflow_dict = json.loads( workflow_text ) except Exception, e: - log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" \ - % str( relative_path ), str( e ) ) + log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" + % ( str( relative_path ), str( e ) ) ) valid_exported_galaxy_workflow = False if valid_exported_galaxy_workflow and \ 'a_galaxy_workflow' in exported_workflow_dict and \ diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -237,12 +237,19 @@ if invalid: # We're attempting to display a tool in the tool shed that has been determined to have errors, so is invalid. return state + try: + # Attempt to generate the tool state using the standard Galaxy-side code + return tool.new_state( trans ) + except Exception, e: + # Fall back to building tool state as below + log.debug( 'Failed to build tool state for tool "%s" using standard method, will try to fall back on custom method: %s', tool.id, e ) inputs = tool.inputs_by_page[ 0 ] context = ExpressionContext( state.inputs, parent=None ) for input in inputs.itervalues(): try: state.inputs[ input.name ] = input.get_initial_value( trans, context ) except: + # FIXME: not all values should be an empty list state.inputs[ input.name ] = [] return state diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -257,7 +257,7 @@ setAsCurrent : function(){ var history = this, - xhr = jQuery.getJSON( '/history/set_as_current?id=' + this.id ); + xhr = jQuery.getJSON( galaxy_config.root + 'history/set_as_current?id=' + this.id ); xhr.done( function(){ history.trigger( 'set-as-current', history ); @@ -361,7 +361,7 @@ var HistoryCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends HistoryCollection.prototype */{ model : History, - + /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -116,7 +116,7 @@ }, downloadDataset: function(){ - var url = '/api/libraries/datasets/download/uncompressed'; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/uncompressed'; var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, @@ -232,7 +232,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions, is_admin:is_admin}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch dataset permissions.'); @@ -273,7 +273,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#access_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -320,7 +320,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#modify_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -367,7 +367,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#manage_perm'), ajax: { - url: "/api/libraries/datasets/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -413,7 +413,7 @@ self.manageSelectObject = new mod_select.View(manage_select_options); } else { // Non-admins have select with pre-loaded options var template = self.templateAccessSelect(); - $.get( "/api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?scope=available", function( data ) { $('.access_perm').html(template({options:data.roles})); self.accessSelectObject = $('#access_select').select2(); }).fail(function() { @@ -436,7 +436,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -447,7 +447,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -478,7 +478,7 @@ modify_ids.push(modify_roles[i].id); }; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/library/library-folder-view.js --- a/static/scripts/mvc/library/library-folder-view.js +++ b/static/scripts/mvc/library/library-folder-view.js @@ -81,7 +81,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch folder permissions.'); @@ -125,7 +125,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/folders/" + self.id + "/permissions?scope=available", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?scope=available", dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -195,7 +195,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/folders/" + self.id + "/permissions?action=set_permissions", { 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -294,7 +294,7 @@ dataset_ids.push( this.parentElement.parentElement.id ); } } ); - var url = '/api/libraries/datasets/download/' + format; + var url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/download/' + format; var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, @@ -386,7 +386,7 @@ fetchExtAndGenomes: function(){ var that = this; mod_utils.get({ - url : galaxy_config.root + "api/datatypes?extension_only=False", + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/datatypes?extension_only=False", success : function( datatypes ) { for (key in datatypes) { that.list_extensions.push({ @@ -403,7 +403,7 @@ } }); mod_utils.get({ - url: galaxy_config.root + "api/genomes", + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/genomes", success: function( genomes ) { for ( key in genomes ) { that.list_genomes.push({ @@ -689,7 +689,7 @@ for ( var i = history_dataset_ids.length - 1; i >= 0; i-- ) { history_dataset_id = history_dataset_ids[i]; var folder_item = new mod_library_model.Item(); - folder_item.url = '/api/folders/' + this.options.id + '/contents'; + folder_item.url = ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/' + this.options.id + '/contents'; folder_item.set( { 'from_hda_id':history_dataset_id } ); hdas_to_add.push( folder_item ); } @@ -749,7 +749,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&file_type=' + options.file_type + @@ -788,7 +788,7 @@ } return true; } - var promise = $.when( $.post( '/api/libraries/datasets?encoded_folder_id=' + that.id + + var promise = $.when( $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets?encoded_folder_id=' + that.id + '&source=' + options.source + '&path=' + popped_item + '&preserve_dirs=' + options.preserve_dirs + diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/library/library-library-view.js --- a/static/scripts/mvc/library/library-library-view.js +++ b/static/scripts/mvc/library/library-library-view.js @@ -87,7 +87,7 @@ var self = this; if (this.options.fetched_permissions === undefined){ - $.get( "/api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { + $.get( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=current").done(function(fetched_permissions) { self.prepareSelectBoxes({fetched_permissions:fetched_permissions}); }).fail(function(){ mod_toastr.error('An error occurred while attempting to fetch library permissions.'); @@ -134,7 +134,7 @@ placeholder: 'Click to select a role', container: self.$el.find('#' + id), ajax: { - url: "/api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?scope=available&is_library_access=" + is_library_access, dataType: 'json', quietMillis: 100, data: function (term, page) { // page is the one-based page number tracked by Select2 @@ -193,7 +193,7 @@ makeDatasetPrivate: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=make_private").done(function(fetched_permissions) { self.model.set({is_unrestricted:false}); self.showPermissions({fetched_permissions:fetched_permissions}) mod_toastr.success('The dataset is now private to you.'); @@ -204,7 +204,7 @@ removeDatasetRestrictions: function(){ var self = this; - $.post("/api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/datasets/" + self.id + "/permissions?action=remove_restrictions") .done(function(fetched_permissions) { self.model.set({is_unrestricted:true}); self.showPermissions({fetched_permissions:fetched_permissions}) @@ -230,7 +230,7 @@ var manage_ids = this._extractIds(this.manageSelectObject.$el.select2('data')); var modify_ids = this._extractIds(this.modifySelectObject.$el.select2('data')); - $.post("/api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) + $.post( ( window.galaxy_config ? galaxy_config.root : '/' ) + "api/libraries/" + self.id + "/permissions?action=set_permissions", { 'access_ids[]': access_ids, 'add_ids[]': add_ids, 'manage_ids[]': manage_ids, 'modify_ids[]': modify_ids, } ) .done(function(fetched_permissions){ //fetch dataset again self.showPermissions({fetched_permissions:fetched_permissions}) diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -4,7 +4,7 @@ // LIBRARY RELATED MODELS var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries/', + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/', /** based on show_deleted would this lib show in the list of lib's? * @param {Boolean} show_deleted are we including deleted libraries? @@ -19,7 +19,7 @@ }); var Libraries = Backbone.Collection.extend({ - url: '/api/libraries', + url: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries', model: Library, @@ -84,15 +84,15 @@ // FOLDER RELATED MODELS var Item = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var Ldda = Backbone.Model.extend({ - urlRoot : '/api/libraries/datasets/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/libraries/datasets/' }); var FolderAsModel = Backbone.Model.extend({ - urlRoot: '/api/folders' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders' }); var Folder = Backbone.Collection.extend({ @@ -152,7 +152,7 @@ var FolderContainer = Backbone.Model.extend({ defaults : { folder : new Folder(), - urlRoot : "/api/folders/", + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/folders/', id : "unknown" }, parse : function(obj) { @@ -169,11 +169,11 @@ // TODO UNITE var HistoryItem = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var HistoryContents = Backbone.Collection.extend({ - urlRoot : '/api/histories/', + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/', initialize: function(options){ this.id = options.id; }, @@ -184,11 +184,11 @@ }); var GalaxyHistory = Backbone.Model.extend({ - urlRoot : '/api/histories/' + urlRoot : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories/' }); var GalaxyHistories = Backbone.Collection.extend({ - url : '/api/histories', + url : ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/histories', model : GalaxyHistory }); @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/remote_files' + urlRoot: ( window.galaxy_config ? galaxy_config.root : '/' ) + 'api/remote_files' }); return { diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/mvc/tools/tools-parameters.js --- a/static/scripts/mvc/tools/tools-parameters.js +++ b/static/scripts/mvc/tools/tools-parameters.js @@ -145,6 +145,7 @@ data : options, error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, + optional : input_def.optional, searchable : input_def.searchable, onchange : function() { self.app.trigger('refresh'); diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON("/history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file +define(["mvc/history/history-contents","mvc/base-mvc","utils/localization"],function(h,i,d){var e=Backbone.Model.extend(i.LoggableMixin).extend(i.mixin(i.SearchableModelMixin,{defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:galaxy_config.root+"api/histories",initialize:function(k,l,j){j=j||{};this.logger=j.logger||null;this.log(this+".initialize:",k,l,j);this.log("creating history contents:",l);this.contents=new h.HistoryContents(l||[],{historyId:this.get("id")});this._setUpListeners();this.updateTimeoutId=null},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});if(this.contents){this.listenTo(this.contents,"error",function(){this.trigger.apply(this,["error:contents"].concat(jQuery.makeArray(arguments)))})}this.on("change:id",function(k,j){if(this.contents){this.contents.historyId=j}},this)},errorHandler:function(k,n,j,m,l){this.clearUpdateTimeout()},ownedByCurrUser:function(){if(!Galaxy||!Galaxy.currUser){return false}if(Galaxy.currUser.isAnonymous()||Galaxy.currUser.id!==this.get("user_id")){return false}return true},contentsCount:function(){return _.reduce(_.values(this.get("state_details")),function(j,k){return j+k},0)},searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},checkForUpdates:function(j){if(this.contents.running().length){this.setUpdateTimeout()}else{this.trigger("ready");if(_.isFunction(j)){j.call(this)}}return this},setUpdateTimeout:function(j){j=j||e.UPDATE_DELAY;var k=this;this.clearUpdateTimeout();this.updateTimeoutId=setTimeout(function(){k.refresh()},j);return this.updateTimeoutId},clearUpdateTimeout:function(){if(this.updateTimeoutId){clearTimeout(this.updateTimeoutId);this.updateTimeoutId=null}},refresh:function(k,j){k=k||[];j=j||{};var l=this;j.data=j.data||{};if(k.length){j.data.details=k.join(",")}var m=this.contents.fetch(j);m.done(function(n){l.checkForUpdates(function(){this.fetch()})});return m},_delete:function(j){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},j)},purge:function(j){if(this.get("purged")){return jQuery.when()}return this.save({deleted:true,purged:true},j)},undelete:function(j){if(!this.get("deleted")){return jQuery.when()}return this.save({deleted:false},j)},copy:function(m,k){m=(m!==undefined)?(m):(true);if(!this.id){throw new Error("You must set the history ID before copying it.")}var j={history_id:this.id};if(m){j.current=true}if(k){j.name=k}var l=this,n=jQuery.post(this.urlRoot,j);if(m){return n.then(function(o){var p=new e(o);return p.setAsCurrent().done(function(){l.trigger("copied",l,o)})})}return n.done(function(o){l.trigger("copied",l,o)})},setAsCurrent:function(){var j=this,k=jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+this.id);k.done(function(){j.trigger("set-as-current",j)});return k},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}}));e.UPDATE_DELAY=4000;e.getHistoryData=function c(j,v){v=v||{};var r=v.detailIdsFn||[];var m=v.hdcaDetailIds||[];var s=jQuery.Deferred(),p=null;function k(w){if(j==="current"){return jQuery.getJSON(galaxy_config.root+"history/current_history_json")}return jQuery.ajax(galaxy_config.root+"api/histories/"+j)}function o(w){return w&&w.empty}function q(x){if(o(x)){return[]}if(_.isFunction(r)){r=r(x)}if(_.isFunction(m)){m=m(x)}var w={};if(r.length){w.dataset_details=r.join(",")}if(m.length){w.dataset_collection_details=m.join(",")}return jQuery.ajax(galaxy_config.root+"api/histories/"+x.id+"/contents",{data:w})}var t=v.historyFn||k,u=v.contentsFn||q;var n=t(j);n.done(function(w){p=w;s.notify({status:"history data retrieved",historyJSON:p})});n.fail(function(y,w,x){s.reject(y,"loading the history")});var l=n.then(u);l.then(function(w){s.notify({status:"contents data retrieved",historyJSON:p,contentsJSON:w});s.resolve(p,w)});l.fail(function(y,w,x){s.reject(y,"loading the contents",{history:p})});return s};var f=Backbone.Collection.extend(i.LoggableMixin).extend({model:e,urlRoot:(window.galaxy_config?galaxy_config.root:"/")+"api/histories",initialize:function(k,j){j=j||{};this.log("HistoryCollection.initialize",arguments);this.includeDeleted=j.includeDeleted||false;this.setUpListeners()},setUpListeners:function a(){var j=this;this.on("change:deleted",function(k){this.debug("change:deleted",j.includeDeleted,k.get("deleted"));if(!j.includeDeleted&&k.get("deleted")){j.remove(k)}});this.on("copied",function(k,l){this.unshift(new e(l,[]))})},create:function g(m,k,j,l){var o=this,n=jQuery.getJSON(galaxy_config.root+"history/create_new_current");return n.done(function(p){var q=new e(p,[],j||{});o.unshift(q);o.trigger("new-current")})},toString:function b(){return"HistoryCollection("+this.length+")"}});return{History:e,HistoryCollection:f}}); \ No newline at end of file diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/packed/mvc/library/library-folder-view.js --- a/static/scripts/packed/mvc/library/library-folder-view.js +++ b/static/scripts/packed/mvc/library/library-folder-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch folder permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:"/api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set folder permissions.")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchFolder()}},fetchFolder:function(e){this.options=_.extend(this.options,e);this.model=new c.FolderAsModel({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateFolder();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},shareFolder:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateFolderPermissions();this.$el.html(g({folder:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get((window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch folder permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f]+":"+g[f])}return e},prepareSelectBoxes:function(h){this.options=_.extend(this.options,h);var f=this.options.fetched_permissions;var g=this;var i=this._serializeRoles(f.add_library_item_role_list);var j=this._serializeRoles(f.manage_folder_role_list);var e=this._serializeRoles(f.modify_folder_role_list);g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",i,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",j,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",e,false))},_createSelectOptions:function(e,j,h){var i={minimumInputLength:0,css:j,multiple:true,placeholder:"Click to select a role",container:e.$el.find("#"+j),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+e.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(k,l){return{q:k,page_limit:10,page:l}},results:function(m,l){var k=(l*10)<m.total;return{results:m.roles,more:k}}},formatResult:function f(k){return k.name+" type: "+k.type},formatSelection:function g(k){return k.name},initSelection:function(k,m){var l=[];$(k.val().split(",")).each(function(){var n=this.split(":");l.push({id:n[1],name:n[1]})});m(l)},initialData:h.join(","),dropdownCssClass:"bigdrop"};return i},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var e=this._extractIds(this.addSelectObject.$el.select2("data"));var i=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post((window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+g.id+"/permissions?action=set_permissions",{"add_ids[]":e,"manage_ids[]":i,"modify_ids[]":f,}).done(function(j){g.showPermissions({fetched_permissions:j});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set folder permissions.")})},templateFolder:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateFolderPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#/folders/<%= folder.get("parent_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to the parent folder" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Parent folder</span></button></a>');e.push(" </div>");e.push('<h1>Folder: <%= _.escape(folder.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any folder on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Folder permissions</h2>");e.push("<h4>Roles that can manage permissions on this folder</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this folder.</div>');e.push("<h4>Roles that can add items to this folder</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this folder (folders and datasets).</div>');e.push("<h4>Roles that can modify this folder</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this folder (name, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{FolderView:b}}); \ No newline at end of file diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},renderPaginator:function(h){this.options=_.extend(this.options,h);var g=this.templatePaginator();this.$el.find("#folder_paginator").html(g({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get({url:galaxy_config.root+"api/datatypes?extension_only=False",success:function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)}});e.get({url:galaxy_config.root+"api/genomes",success:function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})}})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets were deleted.")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted. Please make sure you have sufficient permissions.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted. Please make sure you have sufficient permissions.")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},showPageSizePrompt:function(){var g=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));if((g!=null)&&(g==parseInt(g))){Galaxy.libraries.preferences.set({folder_page_size:parseInt(g)});Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></a>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets","click #page_size_prompt":"showPageSizePrompt"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(Galaxy.config.user_library_import_dir!==null||Galaxy.config.allow_library_path_paste!==false||Galaxy.config.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},renderPaginator:function(h){this.options=_.extend(this.options,h);var g=this.templatePaginator();this.$el.find("#folder_paginator").html(g({id:this.options.id,show_page:parseInt(this.options.show_page),page_count:parseInt(this.options.page_count),total_items_count:this.options.total_items_count,items_shown:this.options.items_shown}))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h=(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/datatypes?extension_only=False",success:function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)}});e.get({url:(window.galaxy_config?galaxy_config.root:"/")+"api/genomes",success:function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})}})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"library-genome-select",data:g.list_genomes,container:Galaxy.modal.$el.find("#library_genome_select"),value:"?"});this.select_extension=new a.View({css:"library-extension-select",data:g.list_extensions,container:Galaxy.modal.$el.find("#library_extension_select"),value:"auto"})},importFilesFromGalaxyFolderModal:function(g){var i=this;var h=this.templateBrowserModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Please select folders or files",body:h({}),buttons:{Import:function(){i.importFromJstreePath(i,g)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+i.id,{trigger:true})}});this.renderSelectBoxes();g.disabled_jstree_element="folders";this.renderJstree(g);$("input[type=radio]").change(function(j){if(j.target.value==="jstree-disable-folders"){g.disabled_jstree_element="folders";i.renderJstree(g);$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(j.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();g.disabled_jstree_element="files";i.renderJstree(g)}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var j=g.source||"userdir";var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target="+j+"&format=jstree&disable="+h;this.jstree.fetch({success:function(l,k){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(m){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:l},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){f.error(k.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromJstreePath:function(n,r){var g=$("#jstree_browser").jstree().get_selected(true);var m=this.modal.$el.find(".preserve-checkbox").is(":checked");var o=this.modal.$el.find(".link-checkbox").is(":checked");var j=this.select_extension.value();var p=this.select_genome.value();var k=g[0].type;var q=[];if(g.length<1){f.info("Please select some items first.")}else{this.modal.disableButton("Import");for(var l=g.length-1;l>=0;l--){if(g[l].li_attr.full_path!==undefined){q.push(g[l].li_attr.full_path)}}this.initChainCallControl({length:q.length,action:"adding_datasets"});if(k==="folder"){var h=r.source+"_folder";this.chainCallImportingFolders({paths:q,preserve_dirs:m,link_data:o,source:h,file_type:j,dbkey:p})}else{if(k==="file"){var h=r.source+"_file";this.chainCallImportingUserdirFiles({paths:q,file_type:j,dbkey:p,source:h})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url=(window.galaxy_config?galaxy_config.root:"/")+"api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders(g)})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets were deleted.")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted. Please make sure you have sufficient permissions.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted. Please make sure you have sufficient permissions.")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":this.importFilesFromGalaxyFolderModal({source:"importdir"});break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromGalaxyFolderModal({source:"userdir"});break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},showPageSizePrompt:function(){var g=prompt("How many items per page do you want to see?",Galaxy.libraries.preferences.get("folder_page_size"));if((g!=null)&&(g==parseInt(g))){Galaxy.libraries.preferences.set({folder_page_size:parseInt(g)});Galaxy.libraries.folderListView.render({id:this.options.id,show_page:1})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(Galaxy.config.user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(Galaxy.config.library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/importdir">from Import Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(Galaxy.config.allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <a data-placement="top" title="Add Datasets to Current Folder" style="display:none;" class="btn btn-default add-library-items" href="#folders/<%= id %>/import/history" role="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></a>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(' <span id="folder_paginator" class="library-paginator">');tmpl_array.push(" </span>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="library_extension_select" class="library-extension-select" />');g.push(' Genome: <span id="library_genome_select" class="library-genome-select" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))},templatePaginator:function(){tmpl_array=[];tmpl_array.push(' <ul class="pagination pagination-sm">');tmpl_array.push(" <% if ( ( show_page - 1 ) > 0 ) { %>");tmpl_array.push(" <% if ( ( show_page - 1 ) > page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page - 1 ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/1"><span class="fa fa-angle-double-left"></span></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page - 1 ) %></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(' <li class="active">');tmpl_array.push(' <a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page ) %></a>');tmpl_array.push(" </li>");tmpl_array.push(" <% if ( ( show_page ) < page_count ) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( show_page + 1 ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( show_page ) %>"><% print( show_page + 1 ) %></a></li>');tmpl_array.push(' <li class="disabled"><a href="#folders/<%= id %>/page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>');tmpl_array.push(" <% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" <span>");tmpl_array.push(' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" id="page_size_prompt"><%- items_shown %></a> of <%- total_items_count %> items');tmpl_array.push(" </span>");return _.template(tmpl_array.join(""))},});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 28113eeee212db2eef9cf4304abe9c3b2a92abcd -r bfd4635011e39aa210b2b1498dd65831dd2a365e static/scripts/packed/mvc/library/library-library-view.js --- a/static/scripts/packed/mvc/library/library-library-view.js +++ b/static/scripts/packed/mvc/library/library-library-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchLibrary()}},fetchLibrary:function(e){this.options=_.extend(this.options,e);this.model=new c.Library({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateLibrary();this.$el.html(f({item:this.model}));$("#center [data-toggle]").tooltip()},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_library_role_list.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateLibraryPermissions();this.$el.html(g({library:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch library permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f][1]+":"+g[f][0])}return e},prepareSelectBoxes:function(i){this.options=_.extend(this.options,i);var e=this.options.fetched_permissions;var g=this;var f=this._serializeRoles(e.access_library_role_list);var j=this._serializeRoles(e.add_library_item_role_list);var h=this._serializeRoles(e.manage_library_role_list);var k=this._serializeRoles(e.modify_library_role_list);g.accessSelectObject=new a.View(this._createSelectOptions(this,"access_perm",f,true));g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",j,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",h,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",k,false))},_createSelectOptions:function(f,k,i,e){e=e===true?e:false;var j={minimumInputLength:0,css:k,multiple:true,placeholder:"Click to select a role",container:f.$el.find("#"+k),ajax:{url:"/api/libraries/"+f.id+"/permissions?scope=available&is_library_access="+e,dataType:"json",quietMillis:100,data:function(l,m){return{q:l,page_limit:10,page:m}},results:function(n,m){var l=(m*10)<n.total;return{results:n.roles,more:l}}},formatResult:function g(l){return l.name+" type: "+l.type},formatSelection:function h(l){return l.name},initSelection:function(l,n){var m=[];$(l.val().split(",")).each(function(){var o=this.split(":");m.push({id:o[0],name:o[1]})});n(m)},initialData:i,dropdownCssClass:"bigdrop"};return j},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var i=this._extractIds(this.accessSelectObject.$el.select2("data"));var e=this._extractIds(this.addSelectObject.$el.select2("data"));var j=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post("/api/libraries/"+g.id+"/permissions?action=set_permissions",{"access_ids[]":i,"add_ids[]":e,"manage_ids[]":j,"modify_ids[]":f,}).done(function(k){g.showPermissions({fetched_permissions:k});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set library permissions.")})},templateLibrary:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateLibraryPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');e.push(" </div>");e.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library permissions</h2>");e.push("<h4>Roles that can access the library</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on this library</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');e.push("<h4>Roles that can add items to this library</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');e.push("<h4>Roles that can modify this library</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{LibraryView:b}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,a){var b=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_save_permissions":"savePermissions"},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchLibrary()}},fetchLibrary:function(e){this.options=_.extend(this.options,e);this.model=new c.Library({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{f.render()}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){$(".tooltip").remove();this.options=_.extend(this.options,e);var f=this.templateLibrary();this.$el.html(f({item:this.model}));$("#center [data-toggle]").tooltip()},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_library_role_list.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateLibraryPermissions();this.$el.html(g({library:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i})}).fail(function(){d.error("An error occurred while attempting to fetch library permissions.")})}else{this.prepareSelectBoxes({})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},_serializeRoles:function(g){var e=[];for(var f=0;f<g.length;f++){e.push(g[f][1]+":"+g[f][0])}return e},prepareSelectBoxes:function(i){this.options=_.extend(this.options,i);var e=this.options.fetched_permissions;var g=this;var f=this._serializeRoles(e.access_library_role_list);var j=this._serializeRoles(e.add_library_item_role_list);var h=this._serializeRoles(e.manage_library_role_list);var k=this._serializeRoles(e.modify_library_role_list);g.accessSelectObject=new a.View(this._createSelectOptions(this,"access_perm",f,true));g.addSelectObject=new a.View(this._createSelectOptions(this,"add_perm",j,false));g.manageSelectObject=new a.View(this._createSelectOptions(this,"manage_perm",h,false));g.modifySelectObject=new a.View(this._createSelectOptions(this,"modify_perm",k,false))},_createSelectOptions:function(f,k,i,e){e=e===true?e:false;var j={minimumInputLength:0,css:k,multiple:true,placeholder:"Click to select a role",container:f.$el.find("#"+k),ajax:{url:(window.galaxy_config?galaxy_config.root:"/")+"api/libraries/"+f.id+"/permissions?scope=available&is_library_access="+e,dataType:"json",quietMillis:100,data:function(l,m){return{q:l,page_limit:10,page:m}},results:function(n,m){var l=(m*10)<n.total;return{results:n.roles,more:l}}},formatResult:function g(l){return l.name+" type: "+l.type},formatSelection:function h(l){return l.name},initSelection:function(l,n){var m=[];$(l.val().split(",")).each(function(){var o=this.split(":");m.push({id:o[0],name:o[1]})});n(m)},initialData:i,dropdownCssClass:"bigdrop"};return j},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},_extractIds:function(e){ids_list=[];for(var f=e.length-1;f>=0;f--){ids_list.push(e[f].id)}return ids_list},savePermissions:function(h){var g=this;var i=this._extractIds(this.accessSelectObject.$el.select2("data"));var e=this._extractIds(this.addSelectObject.$el.select2("data"));var j=this._extractIds(this.manageSelectObject.$el.select2("data"));var f=this._extractIds(this.modifySelectObject.$el.select2("data"));$.post((window.galaxy_config?galaxy_config.root:"/")+"api/libraries/"+g.id+"/permissions?action=set_permissions",{"access_ids[]":i,"add_ids[]":e,"manage_ids[]":j,"modify_ids[]":f,}).done(function(k){g.showPermissions({fetched_permissions:k});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set library permissions.")})},templateLibrary:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" </div>");e.push(" <p>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </p>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateLibraryPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#"><button data-toggle="tooltip" data-placement="top" title="Go back to the list of Libraries" class="btn btn-default primary-button" type="button"><span class="fa fa-list"></span> Libraries</span></button></a>');e.push(" </div>");e.push('<h1>Library: <%= _.escape(library.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any library on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% }%>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library permissions</h2>");e.push("<h4>Roles that can access the library</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can access this library. If there are no access roles set on the library it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on this library</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions on this library (includes giving access).</div>');e.push("<h4>Roles that can add items to this library</h4>");e.push('<div id="add_perm" class="add_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can add items to this library (folders and datasets).</div>');e.push("<h4>Roles that can modify this library</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify this library (name, synopsis, etc.).</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))}});return{LibraryView:b}}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/2fd81de68ec1/ Changeset: 2fd81de68ec1 Branch: stable User: natefoo Date: 2015-04-22 19:30:08+00:00 Summary: Update latest_15.03 tag and create v15.03.2 tag. Affected #: 1 file diff -r bfd4635011e39aa210b2b1498dd65831dd2a365e -r 2fd81de68ec10fcfdcc9d031e7ffc59033e56bbc .hgtags --- a/.hgtags +++ b/.hgtags @@ -25,4 +25,5 @@ 5cdf5dc395f16f47e88a5567775dcd21b4906f08 latest_2015.01.13 738f4ad0eb62d5e4bcf0d22a2722ee6c570382b9 v15.03 9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 v15.03.1 -9f40ff3e3fe1f7fed7e055d4269fe83199cf5ed2 latest_15.03 +bfd4635011e39aa210b2b1498dd65831dd2a365e v15.03.2 +bfd4635011e39aa210b2b1498dd65831dd2a365e latest_15.03 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: natefoo: Bump version to 15.03.2
by commits-noreply＠bitbucket.org 22 Apr '15

22 Apr '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d7a9896af111/ Changeset: d7a9896af111 Branch: release_15.03 User: natefoo Date: 2015-04-22 20:05:21+00:00 Summary: Bump version to 15.03.2 Affected #: 1 file diff -r f4f0baa542a89db2d1002a2ff5b119077d2e9de6 -r d7a9896af111d6f86735eb4f2295eee67f7e3527 lib/galaxy/version.py --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "15.03" -VERSION_MINOR = "1" +VERSION_MINOR = "2" VERSION = VERSION_MAJOR + ('.' + VERSION_MINOR if VERSION_MINOR else '') Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 22 Apr '15

22 Apr '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4781746d1979/ Changeset: 4781746d1979 Branch: release_15.03 User: jmchilton Date: 2015-04-21 16:41:33+00:00 Summary: Bugfix: Typo in remap dataset handling in tools. Affected #: 1 file diff -r 57bbbe1463f616f98793a87d6b3ac0d4356825f4 -r 4781746d1979e6b33cf3e8f0177ec88b6cad6d7e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2601,7 +2601,7 @@ hdca_source_dict = {} for hdca in history.dataset_collections: key = '%s_%s' % (hdca.hid, hdca.collection.id) - hdca_source_dict[ hda.collection.id ] = hdca_source_dict[ key ] = hdca + hdca_source_dict[ hdca.collection.id ] = hdca_source_dict[ key ] = hdca # Map dataset or collection to current history def map_to_history(value): https://bitbucket.org/galaxy/galaxy-central/commits/f4f0baa542a8/ Changeset: f4f0baa542a8 Branch: release_15.03 User: dan Date: 2015-04-06 15:29:32+00:00 Summary: Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Affected #: 2 files diff -r 4781746d1979e6b33cf3e8f0177ec88b6cad6d7e -r f4f0baa542a89db2d1002a2ff5b119077d2e9de6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -417,13 +417,14 @@ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) default_template = 'tool_form.mako' - def __init__( self, config_file, tool_source, app, guid=None, repository_id=None ): + def __init__( self, config_file, tool_source, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -704,14 +705,15 @@ # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # User interface hints uihints_elem = root.find( "uihints" ) diff -r 4781746d1979e6b33cf3e8f0177ec88b6cad6d7e -r f4f0baa542a89db2d1002a2ff5b119077d2e9de6 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: 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: 3 new changesets
by commits-noreply＠bitbucket.org 22 Apr '15

22 Apr '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/74f9d06223e4/ Changeset: 74f9d06223e4 Branch: release_14.08 User: dan Date: 2015-04-22 19:36:36+00:00 Summary: Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version. Affected #: 2 files diff -r de9d5f65c15eb5a5a6b61d72d0dbbaf105ea2ccb -r 74f9d06223e40395e9b991171ab4aa21eec73b2e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1062,13 +1062,14 @@ default_tool_action = DefaultToolAction dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) - def __init__( self, config_file, root, app, guid=None, repository_id=None ): + def __init__( self, config_file, root, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -1303,14 +1304,15 @@ # "module" if it has one. Allows us to reuse code files, etc. self.code_namespace = dict() self.hook_map = {} - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # Load any tool specific options (optional) self.options = dict( sanitize=True, refresh=False ) for option_elem in root.findall("options"): diff -r de9d5f65c15eb5a5a6b61d72d0dbbaf105ea2ccb -r 74f9d06223e40395e9b991171ab4aa21eec73b2e lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: https://bitbucket.org/galaxy/galaxy-central/commits/9eaf8d97dfef/ Changeset: 9eaf8d97dfef Branch: release_14.10 User: dan Date: 2015-04-22 19:40:55+00:00 Summary: Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version Affected #: 2 files diff -r a2fad44da847abfe5c39ffdf82f10f6e4be3d1e3 -r 9eaf8d97dfef5577825c921a86df74e8dadb2134 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1179,13 +1179,14 @@ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) default_template = 'tool_form.mako' - def __init__( self, config_file, root, app, guid=None, repository_id=None ): + def __init__( self, config_file, root, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -1420,14 +1421,15 @@ # "module" if it has one. Allows us to reuse code files, etc. self.code_namespace = dict() self.hook_map = {} - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # Load any tool specific options (optional) self.options = dict( sanitize=True, refresh=False ) for option_elem in root.findall("options"): diff -r a2fad44da847abfe5c39ffdf82f10f6e4be3d1e3 -r 9eaf8d97dfef5577825c921a86df74e8dadb2134 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: https://bitbucket.org/galaxy/galaxy-central/commits/8586ba87fdfe/ Changeset: 8586ba87fdfe Branch: release_15.01 User: dan Date: 2015-04-22 19:42:50+00:00 Summary: Fix for abitrary code execution in the ToolShed when uploaded tools reference a <code file=...>. Release 14.08..15.01 version Affected #: 2 files diff -r 7a09c05aed7a3ca0cb64edb0e5e331d59028d86e -r 8586ba87fdfe4a3d9f3088ddb07f4466c53d3945 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1238,13 +1238,14 @@ dict_collection_visible_keys = ( 'id', 'name', 'version', 'description' ) default_template = 'tool_form.mako' - def __init__( self, config_file, root, app, guid=None, repository_id=None ): + def __init__( self, config_file, root, app, guid=None, repository_id=None, allow_code_files=True ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is self.config_file = config_file self.tool_dir = os.path.dirname( config_file ) self.app = app self.repository_id = repository_id + self._allow_code_files = allow_code_files #setup initial attribute values self.inputs = odict() self.stdio_exit_codes = list() @@ -1485,14 +1486,15 @@ # "module" if it has one. Allows us to reuse code files, etc. self.code_namespace = dict() self.hook_map = {} - for code_elem in root.findall("code"): - for hook_elem in code_elem.findall("hook"): - for key, value in hook_elem.items(): - # map hook to function - self.hook_map[key] = value - file_name = code_elem.get("file") - code_path = os.path.join( self.tool_dir, file_name ) - execfile( code_path, self.code_namespace ) + if self._allow_code_files: + for code_elem in root.findall("code"): + for hook_elem in code_elem.findall("hook"): + for key, value in hook_elem.items(): + # map hook to function + self.hook_map[key] = value + file_name = code_elem.get("file") + code_path = os.path.join( self.tool_dir, file_name ) + execfile( code_path, self.code_namespace ) # Load any tool specific options (optional) self.options = dict( sanitize=True, refresh=False ) for option_elem in root.findall("options"): diff -r 7a09c05aed7a3ca0cb64edb0e5e331d59028d86e -r 8586ba87fdfe4a3d9f3088ddb07f4466c53d3945 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -292,7 +292,7 @@ def load_tool_from_config( self, repository_id, full_path ): try: - tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id, allow_code_files=False ) valid = True error_message = None except KeyError, e: 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

[galaxyproject/usegalaxy-playbook] df33f1: Update Main Pulsar
by GitHub 22 Apr '15

22 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: df33f13029bfbddf6a9530dcb741f758cf6b9aa5 https://github.com/galaxyproject/usegalaxy-playbook/commit/df33f13029bfbddf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: M production/group_vars/pulsarservers.yml Log Message: ----------- Update Main Pulsar Commit: df4a9bb43b7449f1406260e85c8d2e6f574b22cb https://github.com/galaxyproject/usegalaxy-playbook/commit/df4a9bb43b7449f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-22 (Wed, 22 Apr 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2015PostersDue.png A files/galaxy/common/static/welcome_img/GCC2015Scholarships.png M stage/group_vars/toolshedservers.yml M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Merge branch 'master' of github.com:galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/2c468f8f2495...…

1 0

[galaxyproject/usegalaxy-playbook] 2c468f: update TTS
by GitHub 21 Apr '15

21 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2c468f8f2495dd88109a1f750e7b304b271c26cb https://github.com/galaxyproject/usegalaxy-playbook/commit/2c468f8f2495dd88… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS

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[galaxyproject/usegalaxy-playbook] 2ee595: Added GCC2015 Scholarships slide
by GitHub 21 Apr '15

21 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2ee595800192fa7a202cf002ec48bd70decf1139 https://github.com/galaxyproject/usegalaxy-playbook/commit/2ee595800192fa7a… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2015Scholarships.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Added GCC2015 Scholarships slide

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[galaxyproject/usegalaxy-playbook] 5260cd: Swapped poster abstracts due slide in for talk abs...
by GitHub 21 Apr '15

21 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5260cd9ae712392abf173579d224657d5ccf4c07 https://github.com/galaxyproject/usegalaxy-playbook/commit/5260cd9ae712392a… Author: Dave Clements <clements(a)Clements-Galaxy.local> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: A files/galaxy/common/static/welcome_img/GCC2015PostersDue.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Swapped poster abstracts due slide in for talk abstracts due slide.

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[galaxyproject/usegalaxy-playbook] 33b39a: Reenable Stampede on Main
by GitHub 21 Apr '15

21 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 33b39a41c95da135b5a02f119b26d541d11d3c2e https://github.com/galaxyproject/usegalaxy-playbook/commit/33b39a41c95da135… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Reenable Stampede on Main

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[galaxyproject/usegalaxy-playbook] b6cf73: Use absolute path to display site files (fixes war...
by GitHub 21 Apr '15

21 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b6cf73d1bc2d5acaebc9490dcc39fef72f030a7e https://github.com/galaxyproject/usegalaxy-playbook/commit/b6cf73d1bc2d5aca… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-21 (Tue, 21 Apr 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Use absolute path to display site files (fixes warnings under Pulsar).

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[galaxyproject/usegalaxy-playbook] 1be70d: Integrated tool panel update from Test
by GitHub 20 Apr '15

20 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1be70d633396e57c55ecc1d39eb15ca8f41385e9 https://github.com/galaxyproject/usegalaxy-playbook/commit/1be70d633396e57c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml Log Message: ----------- Integrated tool panel update from Test Commit: b198b80789638623b3c8f73ff5907f2404350faf https://github.com/galaxyproject/usegalaxy-playbook/commit/b198b80789638623… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase varscan memory to 16GB Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/578c429426ec...…

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[galaxyproject/usegalaxy-playbook] 578c42: update TTS, include sentry_dsn config from vault
by GitHub 20 Apr '15

20 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 578c429426ecfb11447c7097b4eaec55837a1a5a https://github.com/galaxyproject/usegalaxy-playbook/commit/578c429426ecfb11… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS, include sentry_dsn config from vault

1 0

[galaxyproject/usegalaxy-playbook] 249c34: adding sentry entry for TTS
by GitHub 20 Apr '15

20 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 249c34b7aeb0322916a5b8b901373bf932d12750 https://github.com/galaxyproject/usegalaxy-playbook/commit/249c34b7aeb03229… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-04-20 (Mon, 20 Apr 2015) Changed paths: M stage/secret_vars/toolshedservers.yml Log Message: ----------- adding sentry entry for TTS

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commit/galaxy-central: 44 new changesets
by commits-noreply＠bitbucket.org 20 Apr '15

20 Apr '15

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[galaxyproject/usegalaxy-playbook] b5768f: update TTS config
by GitHub 17 Apr '15

17 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b5768fb2d3238552dfb045f974e33590ec093068 https://github.com/galaxyproject/usegalaxy-playbook/commit/b5768fb2d3238552… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M stage/group_vars/toolshedservers.yml Log Message: ----------- update TTS config

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[galaxyproject/usegalaxy-playbook] d164d7: Fix log archival cron jobs.
by GitHub 17 Apr '15

17 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d164d700b94e5da2444e188d164482fe95875807 https://github.com/galaxyproject/usegalaxy-playbook/commit/d164d700b94e5da2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M roles/usegalaxy_admin/tasks/main.yml Log Message: ----------- Fix log archival cron jobs.

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[galaxyproject/usegalaxy-playbook] aebfe1: Enable nginx upload for job files.
by GitHub 17 Apr '15

17 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aebfe1c548b38dbb2c86a2b49c85a64b0b3412bd https://github.com/galaxyproject/usegalaxy-playbook/commit/aebfe1c548b38dbb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- Enable nginx upload for job files.

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[galaxyproject/usegalaxy-playbook] 8a9c35: Reenable rodeo
by GitHub 17 Apr '15

17 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8a9c357a3d20693a621962b5ad9b36722842474e https://github.com/galaxyproject/usegalaxy-playbook/commit/8a9c357a3d20693a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-04-17 (Fri, 17 Apr 2015) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Reenable rodeo

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[galaxyproject/ansible-galaxy] b88864: Add a flag to force vcs checkout (defaulting to no...
by GitHub 16 Apr '15

16 Apr '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: b8886463194ed66c22c2a810956b84b2ed551638 https://github.com/galaxyproject/ansible-galaxy/commit/b8886463194ed66c22c2… Author: Enis Afgan <afgane(a)gmail.com> Date: 2015-04-16 (Thu, 16 Apr 2015) Changed paths: M README.md M defaults/main.yml M tasks/clone.yml Log Message: ----------- Add a flag to force vcs checkout (defaulting to no)

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