From 6b782ad16d010d6da7808ac7deaecef3ec301b73 Mon Sep 17 00:00:00 2001 From: Nuwan Goonasekera Date: Thu, 1 Mar 2018 21:18:05 +0530 Subject: [PATCH 1/3] Changed GenomeSpace token handling to use manual OpenID association only --- .../scripts/mvc/ui/ui-select-genomespace.js | 51 ++++++++----------- client/galaxy/style/less/ui.less | 16 ++---- tools/genomespace/genomespace_exporter.xml | 12 ++--- tools/genomespace/genomespace_importer.xml | 17 ++++--- tools/genomespace/genomespace_push.xml | 6 +-- 5 files changed, 41 insertions(+), 61 deletions(-) diff --git a/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js b/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js index 61e382f6782..5f63869ea78 100644 --- a/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js @@ -25,16 +25,10 @@ var View = Backbone.View.extend({ // create genomespace filepath textbox this.filename_textbox = new Ui.Input(); - // create genomespace token textbox - this.token_textbox = new Ui.Input({ - type : 'password' - }); - // create elements this.setElement(this._template(options)); - this.$('.ui-gs-browse-button').append(this.browse_button.$el); - this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el); - this.$('.ui-gs-token-textbox').append(this.token_textbox.$el); + this.$(".ui-gs-browse-button").append(this.browse_button.$el); + this.$(".ui-gs-filename-textbox").append(this.filename_textbox.$el); }, /** Browse GenomeSpace */ @@ -42,27 +36,25 @@ var View = Backbone.View.extend({ var self = this; GenomespaceBrowser.openFileBrowser({ successCallback: function(data) { - self.value(data.destination + "^" + data.token); + self.value(`${data.destination}`); } }); }, - + /** Main Template */ _template: function(options) { - return '
' + - '
' + - '' + - '' + - '
' + - '
' + - '
Token
' + - '' + - '
' + - '
'; + return ( + '
' + + '
' + + '' + + '' + + "
" + + "
" + ); }, - - /** Return/Set currently selected genomespace filename/token */ - value : function (new_value) { + + /** Return/Set currently selected genomespace filename */ + value: function(new_value) { // check if new_value is defined if (new_value !== undefined) { this._setValue(new_value); @@ -71,22 +63,19 @@ var View = Backbone.View.extend({ return this._getValue(); } }, - + // get value _getValue: function() { - return this.filename_textbox.value() + - "^" + this.token_textbox.value(); + return `${this.filename_textbox.value()}`; }, - + // set value _setValue: function(new_value) { if (new_value) { - values = new_value.split("^"); - this.filename_textbox.value(values[0]); - this.token_textbox.value(values[1]); + this.filename_textbox.value(new_value); } }, - + }); return { diff --git a/client/galaxy/style/less/ui.less b/client/galaxy/style/less/ui.less index a85e7c58f12..6ac678c4ea1 100644 --- a/client/galaxy/style/less/ui.less +++ b/client/galaxy/style/less/ui.less @@ -884,10 +884,6 @@ float: right; width: ~'calc(100% - 76px)'; } - .ui-gs-token-textbox { - float: right; - width: ~'calc(100% - 76px)'; - } .ui-gs-browse-button { float: left; .ui-button-icon { @@ -895,15 +891,9 @@ margin-right: 5px; } } - .ui-gs-token-label { - margin-top: 5px; - margin-left: 32px; - margin-right: 5px; - float: left; - } - .ui-gs-token-field { - clear: both; - padding-top: 5px; + .ui-gs-browse-field { + height: @input-height-base; + line-height: @line-height-base; } } diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml index 899eb9241ca..70b1d794062 100644 --- a/tools/genomespace/genomespace_exporter.xml +++ b/tools/genomespace/genomespace_exporter.xml @@ -1,10 +1,10 @@ - + - send data to GenomeSpace - #set $token = $genomespace_browser.split('^')[1] or $__user__.preferences.get('genomespace_token', None) - #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid folder via the GenomeSpace browse dialog.') + #set $token = $__user__.preferences.get('genomespace_token', None) + #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.') $token @@ -31,11 +31,9 @@ -This Tool allows you to export data to GenomeSpace. Click the Browse button to select a file to export. The tool will automatically -fetch your GenomeSpace token when you select a file from the export dialog. +This Tool allows you to export data to GenomeSpace. Click the Browse button to select a file to export. -Alternatively, you can be logged in using your GenomeSpace OpenID, and the tool will use this ID if no token is entered. -This allows you to simply paste the filepath into the location box and leave the token empty. +To use this tool, you must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel. Click here_ to refresh your GenomeSpace token. diff --git a/tools/genomespace/genomespace_importer.xml b/tools/genomespace/genomespace_importer.xml index 446de8a4e03..48bd215ac6b 100644 --- a/tools/genomespace/genomespace_importer.xml +++ b/tools/genomespace/genomespace_importer.xml @@ -1,13 +1,18 @@ - + - receive data from GenomeSpace + + + #set $token = $__user__.preferences.get('genomespace_token', None) + #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.') + $token + + -This tool allows you to import data from GenomeSpace. Click the Browse button to select a file to import. The tool will automatically -fetch your GenomeSpace token when you select a file from the import dialog. +This tool allows you to import data from GenomeSpace. Click the Browse button to select a file to import. -Alternatively, you can be logged in using your GenomeSpace OpenID, and the tool will use this ID if no token is entered. -This allows you to simply paste the filepath into the location box and leave the token empty. +To use this tool, you must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel. Click here_ to refresh your GenomeSpace token. diff --git a/tools/genomespace/genomespace_push.xml b/tools/genomespace/genomespace_push.xml index e1a431c3247..ce978e9c6af 100644 --- a/tools/genomespace/genomespace_push.xml +++ b/tools/genomespace/genomespace_push.xml @@ -1,10 +1,10 @@ -