Galaxy Workflow support for GenomeSpace

client/galaxy/scripts/mvc/form/form-parameters.js

@@ -6,8 +6,9 @@ define(['utils/utils',
         'mvc/ui/ui-select-content',
         'mvc/ui/ui-select-library',
         'mvc/ui/ui-select-ftp',
+        'mvc/ui/ui-select-genomespace',
         'mvc/ui/ui-color-picker'],
-    function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker ) {
+    function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker ) {
 
     // create form view
     return Backbone.Model.extend({
@@ -30,7 +31,8 @@ define(['utils/utils',
             'baseurl'           : '_fieldHidden',
             'library_data'      : '_fieldLibrary',
             'ftpfile'           : '_fieldFtp',
-            'upload'            : '_fieldUpload'
+            'upload'            : '_fieldUpload',
+            'genomespacefile'   : '_fieldGenomeSpace'
         },
 
         /** Returns an input field for a given field type */
@@ -216,6 +218,18 @@ define(['utils/utils',
             });
         },
 
+        /** GenomeSpace file select field
+         */
+        _fieldGenomeSpace: function( input_def ) {
+             var self = this;
+             return new SelectGenomeSpace.View({
+                 id          : 'field-' + input_def.id,
+                 onchange    : function() {
+                     self.app.trigger( 'change' );
+                 }
+             });
+         },
+
         /** Upload file field */
         _fieldUpload: function( input_def ) {
             return new Ui.Upload({

client/galaxy/scripts/mvc/tool/tool-genomespace.js

@@ -0,0 +1,24 @@
+// Provides support for interacting with the GenomeSpace File Browser popup dialogue
+define([], function() {
+
+// tool form templates
+return {
+    openFileBrowser: function( options ) {
+        var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;
+        var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true'
+
+        var newWin = window.open(GS_UPLOAD_URL, "GenomeSpace File Browser", "height=360px,width=600px");
+
+        successCalBack = options['successCallback'];
+        window.addEventListener( "message", function (e) {
+             successCalBack(e.data);    
+          }, false);
+
+        newWin.focus();
+
+        if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback'];  
+    }
+
+};
+
+});

client/galaxy/scripts/mvc/ui/ui-select-genomespace.js

@@ -0,0 +1,96 @@
+// dependencies
+define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-genomespace'],
+        function(Utils, Ui, GenomespaceBrowser) {
+
+/**
+ * GenomeSpace file selector
+ */
+var View = Backbone.View.extend({
+    // initialize
+    initialize : function(options) {
+
+        // link this
+        var self = this;
+
+        // create insert new list element button
+        this.browse_button = new Ui.ButtonIcon({
+            title       : 'Browse',
+            icon        : 'fa fa-sign-in',
+            tooltip     : 'Browse GenomeSpace',
+            onclick     : function() {
+                self.browseGenomeSpace();
+            }
+        });
+
+        // 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);
+            }
+        });
+    },
+
+    /** Main Template */
+    _template: function(options) {
+        return  '<div class="ui-gs-select-file">' +
+                    '<div class="ui-gs-browse-field">' +
+                        '<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 */
+    value : function (new_value) {
+        // check if new_value is defined
+        if (new_value !== undefined) {
+            this._setValue(new_value);
+        }
+        else {
+          return this._getValue();
+        }
+    },
+
+    // get value
+    _getValue: function() {
+        return this.filename_textbox.value() +
+            "^" + this.token_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]);
+        }
+    },
+
+});
+
+return {
+    View: View
+}
+
+});

client/galaxy/style/less/ui.less

@@ -879,6 +879,34 @@
     }
 }
 
+.ui-gs-select-file {
+    .ui-gs-filename-textbox {
+        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-select {
     position: relative;
     .icon-dropdown {

config/galaxy.ini.sample

@@ -632,6 +632,10 @@ nglims_config_file = tool-data/nglims.yaml
 # The URL linked by the "Videos" link in the "Help" menu.
 #screencasts_url = https://vimeo.com/galaxyproject
 
+# Points to the GenomeSpace UI service which will be used by
+# the GenomeSpace importer and exporter tools
+#genomespace_ui_url = https://gsui.genomespace.org/jsui/
+
 # The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
 # as on the user registration and login forms and in the activation emails.
 #terms_url = None

config/tool_conf.xml.main

@@ -15,8 +15,8 @@
     <tool file="data_source/wormbase.xml" />
     <tool file="data_source/zebrafishmine.xml" />
     <tool file="data_source/eupathdb.xml" />
-    <tool file="genomespace/genomespace_file_browser_prod.xml" />
     <tool file="genomespace/genomespace_importer.xml" />
+    <tool file="genomespace/genomespace_push.xml" />
   </section>
   <section id="send" name="Send Data">
     <tool file="genomespace/genomespace_exporter.xml" />

config/tool_conf.xml.sample

@@ -24,8 +24,8 @@
     <tool file="data_source/zebrafishmine.xml" />
     <tool file="data_source/eupathdb.xml" />
     <tool file="data_source/hbvar.xml" />
-    <tool file="genomespace/genomespace_file_browser_prod.xml" />
     <tool file="genomespace/genomespace_importer.xml" />
+    <tool file="genomespace/genomespace_push.xml" />
   </section>
   <section id="send" name="Send Data">
     <tool file="genomespace/genomespace_exporter.xml" />

lib/galaxy/config.py

@@ -382,6 +382,7 @@ def __init__(self, **kwargs):
         self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
         self.blog_url = kwargs.get('blog_url', None)
         self.screencasts_url = kwargs.get('screencasts_url', None)
+        self.genomespace_ui_url = kwargs.get('genomespace_ui_url', 'https://gsui.genomespace.org/jsui/')
         self.library_import_dir = kwargs.get('library_import_dir', None)
         self.user_library_import_dir = kwargs.get('user_library_import_dir', None)
         # Searching data libraries

lib/galaxy/dependencies/pinned-requirements.txt

@@ -78,3 +78,6 @@ pysam==0.8.4+gx5
 
 # Chronos client
 chronos-python==0.38.0
+
+# GenomeSpace dependencies
+python-genomespaceclient==0.1.8

lib/galaxy/managers/configuration.py

@@ -45,6 +45,7 @@ def _defaults_to(default):
             'search_url'                        : _defaults_to(self.app.config.wiki_url.rstrip("/") + "/search/"),
             'mailing_lists'                     : _defaults_to(self.app.config.wiki_url.rstrip("/") + "/mailing-lists/"),
             'screencasts_url'                   : _defaults_to("https://vimeo.com/galaxyproject"),
+            'genomespace_ui_url'                : _defaults_to(None),
             'citation_url'                      : _defaults_to(self.app.config.citation_url),
             'support_url'                       : _defaults_to(self.app.config.support_url),
             'lims_doc_url'                      : _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),

lib/galaxy/tools/__init__.py

@@ -154,6 +154,8 @@
     "gd_phylogenetic_tree",
     "gd_population_structure",
     "gd_prepare_population_structure",
+    # Datasources
+    "genomespace_importer"
 ]
 # Tools that needed galaxy on the PATH in the past but no longer do along
 # with the version at which they were fixed.

lib/galaxy/tools/parameters/basic.py

@@ -626,6 +626,20 @@ def to_dict(self, trans, other_values=None):
         return d
 
 
+class GenomespaceFileToolParameter(ToolParameter):
+    """
+    Parameter that takes one of two values.
+    """
+
+    def __init__(self, tool, input_source):
+        input_source = ensure_input_source(input_source)
+        ToolParameter.__init__(self, tool, input_source)
+        self.value = input_source.get('value')
+
+    def get_initial_value(self, trans, other_values):
+        return self.value
+
+
 class HiddenToolParameter(ToolParameter):
     """
     Parameter that takes one of two values.
@@ -2087,6 +2101,7 @@ def to_dict(self, trans, other_values=None):
     baseurl=BaseURLToolParameter,
     file=FileToolParameter,
     ftpfile=FTPFileToolParameter,
+    genomespacefile=GenomespaceFileToolParameter,
     data=DataToolParameter,
     data_collection=DataCollectionToolParameter,
     library_data=LibraryDatasetToolParameter,

lib/galaxy/web/form_builder.py

@@ -208,6 +208,27 @@ def get_html(self, prefix=""):
         return unicodify('<input type="file" name="%s%s"%s%s>' % (prefix, self.name, ajax_text, value_text))
 
 
+class GenomespaceFileField(BaseField):
+    """
+    A genomspace file browser field.
+    """
+    def __init__(self, name, value=None):
+        self.name = name
+        self.value = value or ""
+
+    def get_html(self, prefix=""):
+        return unicodify('<script src="https://gsui.genomespace.org/jsui/upload/gsuploadwindow.js"></script>'
+                         '<input type="text" name="{0}{1}" value="{2}">&nbsp;'
+                         '<a href="javascript:gsLocationByGet({{ successCallback: function(config)'
+                         ' {{ selector_name = \'{0}{1}\'; selector = \'input[name=\' + selector_name.replace(\'|\', \'\\\\|\') + \']\';'
+                         ' $(selector).val(config.destination + \'^\' + config.token); }} }});">'
+                         'Browse</a>'.format(prefix, self.name, escape(str(self.value), quote=True)))
+
+    def to_dict(self):
+        return dict(name=self.name,
+                    token_field=self.token_field)
+
+
 class HiddenField(BaseField):
     """
     A hidden field.