Merge pull request #5660 from martenson/merge-genomespace

Merge forward genomespace changes
galaxyproject · Mar 7, 2018 · 300fffe · 300fffe
2 parents fffca43 + cf369e8
commit 300fffe
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Showing 6 changed files with 26 additions and 47 deletions.
diff --git a/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js b/client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
@@ -26,24 +26,18 @@ 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);
     },
 
     /** Browse GenomeSpace */
     browseGenomeSpace: function(options) {
         var self = this;
         GenomespaceBrowser.openFileBrowser({
             successCallback: function(data) {
-                self.value(`${data.destination}^${data.token}`);
+                self.value(data.destination);
             }
         });
     },
@@ -56,15 +50,11 @@ var View = Backbone.View.extend({
             '<span class="ui-gs-browse-button" />' +
             '<span class="ui-gs-filename-textbox" />' +
             "</div>" +
-            '<div class="ui-gs-token-field">' +
-            '<span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span>' +
-            '<span class="ui-gs-token-textbox" />' +
-            "</div>" +
             "</div>"
         );
     },
 
-    /** Return/Set currently selected genomespace filename/token */
+    /** Return/Set currently selected genomespace filename */
     value: function(new_value) {
         // check if new_value is defined
         if (new_value !== undefined) {
@@ -76,15 +66,13 @@ var View = Backbone.View.extend({
 
     // 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) {
-            var values = new_value.split("^");
-            this.filename_textbox.value(values[0]);
-            this.token_textbox.value(values[1]);
+            this.filename_textbox.value(new_value);
         }
         this.options.onchange && this.options.onchange(new_value);
     }

diff --git a/client/galaxy/style/less/ui.less b/client/galaxy/style/less/ui.less
@@ -906,26 +906,16 @@
         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 {
             margin-top: 3px;
             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/static/style/blue/base.css b/static/style/blue/base.css
diff --git a/tools/genomespace/genomespace_exporter.xml b/tools/genomespace/genomespace_exporter.xml
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool name="GenomeSpace Exporter" id="genomespace_exporter" version="0.0.5">
+<tool name="GenomeSpace Exporter" id="genomespace_exporter" require_login="True" version="0.0.6">
     <description> - send data to GenomeSpace</description>
     <environment_variables>
         <environment_variable name="GS_TOKEN">
-            #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
         </environment_variable>
     </environment_variables>
@@ -31,11 +31,9 @@
         <data format="auto" name="output_log" />
     </outputs>
     <help>
-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
@@ -1,13 +1,18 @@
 <?xml version="1.0"?>
-<tool name="GenomeSpace Importer" id="genomespace_importer" require_login="False" version="0.0.5">
+<tool name="GenomeSpace Importer" id="genomespace_importer" require_login="True" version="0.0.6">
     <description> - receive data from GenomeSpace</description>
+    <environment_variables>
+        <environment_variable name="GS_TOKEN">
+            #set $token = $__user__.preferences.get('genomespace_token', None)
+            #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.')
+            $token
+        </environment_variable>
+    </environment_variables>
     <command><![CDATA[
         python $__tool_directory__/genomespace_importer.py
         #set $input_file = $URL.split('^')[0] if '^' in $URL else $URL
-        #set $token = $URL.split('^')[1] if '^' in $URL and $URL.split('^')[1] else $__user__.preferences.get('genomespace_token', None)
 
         #assert $input_file, Exception('You must select a valid input file.')
-        #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID.')
         --json_parameter_file '${output_file1}'
         --galaxy_root $__root_dir__
         --data_conf $__datatypes_config__
@@ -21,11 +26,9 @@
         <data format="auto" name="output_file1" />
     </outputs>
     <help>
-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
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
-<tool name="GenomeSpace Push" id="genomespace_push"  tool_type="data_source" force_history_refresh="True" hidden="True" display_interface="False" require_login="True" version="0.0.1">
+<tool name="GenomeSpace Push" id="genomespace_push"  tool_type="data_source" force_history_refresh="True" hidden="True" display_interface="False" require_login="True" version="0.0.6">
     <description> - Push data from GenomeSpace to Galaxy</description>
     <environment_variables>
         <environment_variable name="GS_TOKEN">
-            #set $token = $__user__.preferences.get( 'genomespace_token', None )
-            #assert $token, Exception('Invalid token. You must be logged into GenomeSpace through OpenID or select a valid file 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
         </environment_variable>
     </environment_variables>