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Merge pull request #1814 from gvlproject/genomespace_workflows
Galaxy Workflow support for GenomeSpace
This commit is contained in:
Martin Cech
@@ -6,8 +6,9 @@ define(['utils/utils',
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'mvc/ui/ui-select-content',
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'mvc/ui/ui-select-library',
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'mvc/ui/ui-select-ftp',
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'mvc/ui/ui-select-genomespace',
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'mvc/ui/ui-color-picker'],
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function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, ColorPicker ) {
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function( Utils, Ui, SelectContent, SelectLibrary, SelectFtp, SelectGenomeSpace, ColorPicker ) {
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// create form view
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return Backbone.Model.extend({
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@@ -30,7 +31,8 @@ define(['utils/utils',
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'baseurl' : '_fieldHidden',
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'library_data' : '_fieldLibrary',
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'ftpfile' : '_fieldFtp',
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'upload' : '_fieldUpload'
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'upload' : '_fieldUpload',
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'genomespacefile' : '_fieldGenomeSpace'
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},
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/** Returns an input field for a given field type */
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@@ -216,6 +218,18 @@ define(['utils/utils',
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});
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},
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/** GenomeSpace file select field
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*/
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_fieldGenomeSpace: function( input_def ) {
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var self = this;
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return new SelectGenomeSpace.View({
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id : 'field-' + input_def.id,
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onchange : function() {
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self.app.trigger( 'change' );
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}
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});
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},
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/** Upload file field */
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_fieldUpload: function( input_def ) {
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return new Ui.Upload({
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@@ -0,0 +1,24 @@
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// Provides support for interacting with the GenomeSpace File Browser popup dialogue
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define([], function() {
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// tool form templates
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return {
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openFileBrowser: function( options ) {
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var GS_UI_URL = window.Galaxy.config.genomespace_ui_url;
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var GS_UPLOAD_URL = GS_UI_URL + 'upload/loadUrlToGenomespace.html?getLocation=true'
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var newWin = window.open(GS_UPLOAD_URL, "GenomeSpace File Browser", "height=360px,width=600px");
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successCalBack = options['successCallback'];
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window.addEventListener( "message", function (e) {
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successCalBack(e.data);
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}, false);
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newWin.focus();
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if (options['errorCallback'] != null) newWin.setCallbackOnGSUploadError = config['errorCallback'];
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}
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};
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});
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@@ -0,0 +1,96 @@
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// dependencies
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define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/tool/tool-genomespace'],
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function(Utils, Ui, GenomespaceBrowser) {
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/**
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* GenomeSpace file selector
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*/
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var View = Backbone.View.extend({
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// initialize
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initialize : function(options) {
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// link this
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var self = this;
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// create insert new list element button
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this.browse_button = new Ui.ButtonIcon({
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title : 'Browse',
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icon : 'fa fa-sign-in',
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tooltip : 'Browse GenomeSpace',
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onclick : function() {
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self.browseGenomeSpace();
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}
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});
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// create genomespace filepath textbox
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this.filename_textbox = new Ui.Input();
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// create genomespace token textbox
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this.token_textbox = new Ui.Input({
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type : 'password'
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});
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// create elements
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this.setElement(this._template(options));
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this.$('.ui-gs-browse-button').append(this.browse_button.$el);
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this.$('.ui-gs-filename-textbox').append(this.filename_textbox.$el);
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this.$('.ui-gs-token-textbox').append(this.token_textbox.$el);
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},
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/** Browse GenomeSpace */
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browseGenomeSpace: function(options) {
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var self = this;
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GenomespaceBrowser.openFileBrowser({
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successCallback: function(data) {
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self.value(data.destination + "^" + data.token);
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}
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});
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},
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/** Main Template */
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_template: function(options) {
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return '<div class="ui-gs-select-file">' +
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'<div class="ui-gs-browse-field">' +
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'<span class="ui-gs-browse-button" />' +
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'<span class="ui-gs-filename-textbox" />' +
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'</div>' +
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'<div class="ui-gs-token-field">' +
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'<span class=ui-gs-label"><div class="ui-gs-token-label">Token</div></span>' +
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'<span class="ui-gs-token-textbox" />' +
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'</div>' +
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'</div>';
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},
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/** Return/Set currently selected genomespace filename/token */
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value : function (new_value) {
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// check if new_value is defined
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if (new_value !== undefined) {
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this._setValue(new_value);
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}
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else {
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return this._getValue();
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}
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},
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// get value
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_getValue: function() {
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return this.filename_textbox.value() +
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"^" + this.token_textbox.value();
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},
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// set value
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_setValue: function(new_value) {
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if (new_value) {
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values = new_value.split("^");
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this.filename_textbox.value(values[0]);
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this.token_textbox.value(values[1]);
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}
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},
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});
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return {
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View: View
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}
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});
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@@ -879,6 +879,34 @@
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}
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}
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.ui-gs-select-file {
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.ui-gs-filename-textbox {
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float: right;
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width: ~'calc(100% - 76px)';
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}
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.ui-gs-token-textbox {
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float: right;
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width: ~'calc(100% - 76px)';
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}
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.ui-gs-browse-button {
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float: left;
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.ui-button-icon {
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margin-top: 3px;
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margin-right: 5px;
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}
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}
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.ui-gs-token-label {
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margin-top: 5px;
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margin-left: 32px;
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margin-right: 5px;
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float: left;
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}
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.ui-gs-token-field {
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clear: both;
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padding-top: 5px;
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}
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}
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.ui-select {
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position: relative;
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.icon-dropdown {
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@@ -632,6 +632,10 @@ nglims_config_file = tool-data/nglims.yaml
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# The URL linked by the "Videos" link in the "Help" menu.
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#screencasts_url = https://vimeo.com/galaxyproject
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# Points to the GenomeSpace UI service which will be used by
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# the GenomeSpace importer and exporter tools
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#genomespace_ui_url = https://gsui.genomespace.org/jsui/
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# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well
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# as on the user registration and login forms and in the activation emails.
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#terms_url = None
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@@ -15,8 +15,8 @@
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<tool file="data_source/wormbase.xml" />
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<tool file="data_source/zebrafishmine.xml" />
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<tool file="data_source/eupathdb.xml" />
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<tool file="genomespace/genomespace_file_browser_prod.xml" />
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<tool file="genomespace/genomespace_importer.xml" />
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<tool file="genomespace/genomespace_push.xml" />
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</section>
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<section id="send" name="Send Data">
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<tool file="genomespace/genomespace_exporter.xml" />
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@@ -24,8 +24,8 @@
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<tool file="data_source/zebrafishmine.xml" />
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<tool file="data_source/eupathdb.xml" />
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<tool file="data_source/hbvar.xml" />
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<tool file="genomespace/genomespace_file_browser_prod.xml" />
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<tool file="genomespace/genomespace_importer.xml" />
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<tool file="genomespace/genomespace_push.xml" />
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</section>
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<section id="send" name="Send Data">
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<tool file="genomespace/genomespace_exporter.xml" />
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@@ -382,6 +382,7 @@ class Configuration(object):
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self.wiki_url = kwargs.get('wiki_url', 'https://galaxyproject.org/')
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self.blog_url = kwargs.get('blog_url', None)
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self.screencasts_url = kwargs.get('screencasts_url', None)
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self.genomespace_ui_url = kwargs.get('genomespace_ui_url', 'https://gsui.genomespace.org/jsui/')
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self.library_import_dir = kwargs.get('library_import_dir', None)
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self.user_library_import_dir = kwargs.get('user_library_import_dir', None)
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# Searching data libraries
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@@ -78,3 +78,6 @@ pysam==0.8.4+gx5
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# Chronos client
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chronos-python==0.38.0
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# GenomeSpace dependencies
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python-genomespaceclient==0.1.8
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@@ -45,6 +45,7 @@ class ConfigSerializer(base.ModelSerializer):
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'search_url' : _defaults_to(self.app.config.wiki_url.rstrip("/") + "/search/"),
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'mailing_lists' : _defaults_to(self.app.config.wiki_url.rstrip("/") + "/mailing-lists/"),
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'screencasts_url' : _defaults_to("https://vimeo.com/galaxyproject"),
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'genomespace_ui_url' : _defaults_to(None),
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'citation_url' : _defaults_to(self.app.config.citation_url),
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'support_url' : _defaults_to(self.app.config.support_url),
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'lims_doc_url' : _defaults_to("https://usegalaxy.org/u/rkchak/p/sts"),
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@@ -154,6 +154,8 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
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"gd_phylogenetic_tree",
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"gd_population_structure",
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"gd_prepare_population_structure",
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# Datasources
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"genomespace_importer"
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]
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# Tools that needed galaxy on the PATH in the past but no longer do along
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# with the version at which they were fixed.
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@@ -626,6 +626,20 @@ class FTPFileToolParameter(ToolParameter):
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return d
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class GenomespaceFileToolParameter(ToolParameter):
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"""
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Parameter that takes one of two values.
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"""
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def __init__(self, tool, input_source):
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input_source = ensure_input_source(input_source)
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ToolParameter.__init__(self, tool, input_source)
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self.value = input_source.get('value')
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def get_initial_value(self, trans, other_values):
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return self.value
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class HiddenToolParameter(ToolParameter):
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"""
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Parameter that takes one of two values.
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@@ -2087,6 +2101,7 @@ parameter_types = dict(
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baseurl=BaseURLToolParameter,
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file=FileToolParameter,
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ftpfile=FTPFileToolParameter,
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genomespacefile=GenomespaceFileToolParameter,
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data=DataToolParameter,
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data_collection=DataCollectionToolParameter,
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library_data=LibraryDatasetToolParameter,
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@@ -208,6 +208,27 @@ class FileField(BaseField):
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return unicodify('<input type="file" name="%s%s"%s%s>' % (prefix, self.name, ajax_text, value_text))
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class GenomespaceFileField(BaseField):
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"""
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A genomspace file browser field.
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"""
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def __init__(self, name, value=None):
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self.name = name
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self.value = value or ""
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def get_html(self, prefix=""):
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return unicodify('<script src="https://gsui.genomespace.org/jsui/upload/gsuploadwindow.js"></script>'
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'<input type="text" name="{0}{1}" value="{2}"> '
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'<a href="javascript:gsLocationByGet({{ successCallback: function(config)'
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' {{ selector_name = \'{0}{1}\'; selector = \'input[name=\' + selector_name.replace(\'|\', \'\\\\|\') + \']\';'
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' $(selector).val(config.destination + \'^\' + config.token); }} }});">'
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'Browse</a>'.format(prefix, self.name, escape(str(self.value), quote=True)))
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def to_dict(self):
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return dict(name=self.name,
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token_field=self.token_field)
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class HiddenField(BaseField):
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"""
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A hidden field.
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@@ -1 +1 @@
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//# sourceMappingURL=login.bundled.js.map
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@@ -1 +1 @@
|
||||
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|
||||
{"version":3,"sources":["webpack:///login.bundled.js","webpack:///./galaxy/scripts/apps/login.js"],"names":["webpackJsonp","module","exports","__webpack_require__","Backbone","_","jQuery","$","GalaxyApp","_l","Page","window","app","options","bootstrapped","Galaxy","debug","redirect","encodeURI","show_welcome_with_login","params","param","use_panels","location","href","root","LoginPage","View","extend","initialize","page","this","model","Model","title","setElement","_template","render","prop","welcome_url","login_url","Right","call"],"mappings":"AAAAA,cAAc,IAER,SAAUC,EAAQC,EAASC,ICFjC,SAAAC,EAAAC,GAAA,GAAIC,GAASH,EAAS,GAClBI,EAAID,EACJE,EAAYL,EAAS,IAAWK,UAChCC,EAAKN,EAAS,GACdO,EAAOP,EAAS,GAEpBQ,QAAOC,IAAM,SAAcC,EAASC,GAChCH,OAAOI,OAAS,GAAIP,GAAWK,EAASC,GACxCC,OAAOC,MAAO,YACd,IAAIC,GAAWC,UAAWL,EAAQI,SAIlC,KAAKJ,EAAQM,wBAAyB,CAClC,GAAIC,GAASd,EAAOe,OAAQC,WAAa,OAAQL,SAAWA,GAE5D,aADAN,OAAOY,SAASC,KAAOT,OAAOU,KAAO,cAAgBL,GAIzD,GAAIM,GAAYtB,EAASuB,KAAKC,QAC1BC,WAAY,SAAUC,GAClBC,KAAKD,KAAOA,EACZC,KAAKC,MAAQ,GAAI5B,GAAS6B,OAAQC,MAAQzB,EAAI,oBAC9CsB,KAAKI,WAAYJ,KAAKK,cAE1BC,OAAQ,WACJN,KAAKD,KAAKvB,EAAG,gBAAiB+B,KAAM,MAAOzB,EAAQ0B,cAEvDH,UAAY,WACR,GAAII,GAAY3B,EAAQY,KAAO,cAAgBlB,EAAEc,OAASJ,SAAWA,GACrE,OAAO,gBAAkBuB,EAAY,2DAI7CjC,GAAE,WACEQ,OAAOe,KAAO,GAAIpB,GAAKiB,KAAMtB,EAAEuB,OAAQf,GACnC4B,MAAQf,UDQUgB,KAAKxC,EAASC,EAAoB,GAAIA,EAAoB","file":"login.bundled.js","sourcesContent":["webpackJsonp([5],[\n/* 0 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(Backbone, _) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t GalaxyApp = __webpack_require__(51).GalaxyApp,\n\t _l = __webpack_require__(6),\n\t Page = __webpack_require__(52);\n\t\n\twindow.app = function app(options, bootstrapped) {\n\t window.Galaxy = new GalaxyApp(options, bootstrapped);\n\t Galaxy.debug('login app');\n\t var redirect = encodeURI(options.redirect);\n\t\n\t // TODO: remove iframe for user login (at least) and render login page from here\n\t // then remove this redirect\n\t if (!options.show_welcome_with_login) {\n\t var params = jQuery.param({ use_panels: 'True', redirect: redirect });\n\t window.location.href = Galaxy.root + 'user/login?' + params;\n\t return;\n\t }\n\t\n\t var LoginPage = Backbone.View.extend({\n\t initialize: function (page) {\n\t this.page = page;\n\t this.model = new Backbone.Model({ title: _l('Login required') });\n\t this.setElement(this._template());\n\t },\n\t render: function () {\n\t this.page.$('#galaxy_main').prop('src', options.welcome_url);\n\t },\n\t _template: function () {\n\t var login_url = options.root + 'user/login?' + $.param({ redirect: redirect });\n\t return '<iframe src=\"' + login_url + '\" frameborder=\"0\" style=\"width: 100%; height: 100%;\"/>';\n\t }\n\t });\n\t\n\t $(function () {\n\t Galaxy.page = new Page.View(_.extend(options, {\n\t Right: LoginPage\n\t }));\n\t });\n\t};\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(2), __webpack_require__(3)))\n\n/***/ })\n]);\n\n\n// WEBPACK FOOTER //\n// login.bundled.js","var jQuery = require( 'jquery' ),\n $ = jQuery,\n GalaxyApp = require( 'galaxy' ).GalaxyApp,\n _l = require( 'utils/localization' ),\n Page = require( 'layout/page' );\n\nwindow.app = function app( options, bootstrapped ){\n window.Galaxy = new GalaxyApp( options, bootstrapped );\n Galaxy.debug( 'login app' );\n var redirect = encodeURI( options.redirect );\n\n // TODO: remove iframe for user login (at least) and render login page from here\n // then remove this redirect\n if( !options.show_welcome_with_login ){\n var params = jQuery.param({ use_panels : 'True', redirect : redirect });\n window.location.href = Galaxy.root + 'user/login?' + params;\n return;\n }\n\n var LoginPage = Backbone.View.extend({\n initialize: function( page ) {\n this.page = page;\n this.model = new Backbone.Model({ title : _l( 'Login required' ) } );\n this.setElement( this._template() );\n },\n render: function() {\n this.page.$( '#galaxy_main' ).prop( 'src', options.welcome_url );\n },\n _template : function() {\n var login_url = options.root + 'user/login?' + $.param( { redirect : redirect } );\n return '<iframe src=\"' + login_url + '\" frameborder=\"0\" style=\"width: 100%; height: 100%;\"/>';\n }\n });\n\n $(function(){\n Galaxy.page = new Page.View( _.extend( options, {\n Right : LoginPage\n } ) );\n });\n};\n\n\n\n// WEBPACK FOOTER //\n// ./galaxy/scripts/apps/login.js"],"sourceRoot":""}
|
||||
@@ -1,2 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-select-content","mvc/ui/ui-select-library","mvc/ui/ui-select-ftp","mvc/ui/ui-color-picker"],function(a,b,c,d,e,f){return Backbone.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload"},create:function(a){var b=this.types[a.type],c="function"==typeof this[b]?this[b].call(this,a):null;return c||(c=a.options?this._fieldSelect(a):this._fieldText(a),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+a.type+").")),void 0===a.value&&(a.value=null),c.value(a.value),c},_fieldData:function(a){return new c.View({id:"field-"+a.id,extensions:a.extensions,optional:a.optional,multiple:a.multiple,type:a.type,flavor:a.flavor,data:a.options,onchange:a.onchange})},_fieldSelect:function(a){if(a.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=a.data;c||(c=[],_.each(a.options,function(a){c.push({label:a[0],value:a[1]})}));var d=b.Select;switch(a.display){case"checkboxes":d=b.Checkbox;break;case"radio":d=b.Radio;break;case"radiobutton":d=b.RadioButton}return new d.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",multiple:a.multiple,optional:a.optional,onchange:a.onchange,individual:a.individual,searchable:"workflow"!==a.flavor})},_fieldDrilldown:function(a){return a.is_workflow?this._fieldText(a):new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,optional:a.optional,onchange:a.onchange})},_fieldText:function(c){if(c.options&&c.data)if(c.area=c.multiple,a.isEmpty(c.value))c.value=null;else if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}return new b.Input({id:"field-"+c.id,type:c.type,area:c.area,readonly:c.readonly,placeholder:c.placeholder,datalist:c.datalist,onchange:c.onchange})},_fieldSlider:function(a){return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,is_workflow:a.is_workflow,min:a.min,max:a.max,onchange:a.onchange})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:a.onchange})},_fieldColor:function(a){return new f({id:"field-"+a.id,onchange:a.onchange})},_fieldLibrary:function(a){return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:a.onchange})},_fieldFtp:function(a){return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:a.onchange})},_fieldUpload:function(a){return new b.Upload({id:"field-"+a.id,onchange:a.onchange})}})});
|
||||
define(["utils/utils","mvc/ui/ui-misc","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(a,b,c,d,e,f,g){return Backbone.Model.extend({types:{text:"_fieldText",password:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp",upload:"_fieldUpload",genomespacefile:"_fieldGenomeSpace"},create:function(a){var b=this.types[a.type],c="function"==typeof this[b]?this[b].call(this,a):null;return c||(c=a.options?this._fieldSelect(a):this._fieldText(a),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+a.type+").")),void 0===a.value&&(a.value=null),c.value(a.value),c},_fieldData:function(a){return new c.View({id:"field-"+a.id,extensions:a.extensions,optional:a.optional,multiple:a.multiple,type:a.type,flavor:a.flavor,data:a.options,onchange:a.onchange})},_fieldSelect:function(a){if(a.is_workflow)return this._fieldText(a);"data_column"==a.type&&(a.error_text="Missing columns in referenced dataset.");var c=a.data;c||(c=[],_.each(a.options,function(a){c.push({label:a[0],value:a[1]})}));var d=b.Select;switch(a.display){case"checkboxes":d=b.Checkbox;break;case"radio":d=b.Radio;break;case"radiobutton":d=b.RadioButton}return new d.View({id:"field-"+a.id,data:c,error_text:a.error_text||"No options available",multiple:a.multiple,optional:a.optional,onchange:a.onchange,individual:a.individual,searchable:"workflow"!==a.flavor})},_fieldDrilldown:function(a){return a.is_workflow?this._fieldText(a):new b.Drilldown.View({id:"field-"+a.id,data:a.options,display:a.display,optional:a.optional,onchange:a.onchange})},_fieldText:function(c){if(c.options&&c.data)if(c.area=c.multiple,a.isEmpty(c.value))c.value=null;else if($.isArray(c.value)){var d="";for(var e in c.value){if(d+=String(c.value[e]),!c.multiple)break;d+="\n"}c.value=d}return new b.Input({id:"field-"+c.id,type:c.type,area:c.area,readonly:c.readonly,placeholder:c.placeholder,datalist:c.datalist,onchange:c.onchange})},_fieldSlider:function(a){return new b.Slider.View({id:"field-"+a.id,precise:"float"==a.type,is_workflow:a.is_workflow,min:a.min,max:a.max,onchange:a.onchange})},_fieldHidden:function(a){return new b.Hidden({id:"field-"+a.id,info:a.info})},_fieldBoolean:function(a){return new b.RadioButton.View({id:"field-"+a.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:a.onchange})},_fieldColor:function(a){return new g({id:"field-"+a.id,onchange:a.onchange})},_fieldLibrary:function(a){return new d.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:a.onchange})},_fieldFtp:function(a){return new e.View({id:"field-"+a.id,optional:a.optional,multiple:a.multiple,onchange:a.onchange})},_fieldGenomeSpace:function(a){var b=this;return new f.View({id:"field-"+a.id,onchange:function(){b.app.trigger("change")}})},_fieldUpload:function(a){return new b.Upload({id:"field-"+a.id,onchange:a.onchange})}})});
|
||||
//# sourceMappingURL=../../../maps/mvc/form/form-parameters.js.map
|
||||
@@ -0,0 +1,2 @@
|
||||
define([],function(){return{openFileBrowser:function(a){var b=window.Galaxy.config.genomespace_ui_url,c=b+"upload/loadUrlToGenomespace.html?getLocation=true",d=window.open(c,"GenomeSpace File Browser","height=360px,width=600px");successCalBack=a.successCallback,window.addEventListener("message",function(a){successCalBack(a.data)},!1),d.focus(),null!=a.errorCallback&&(d.setCallbackOnGSUploadError=config.errorCallback)}}});
|
||||
//# sourceMappingURL=../../../maps/mvc/tool/tool-genomespace.js.map
|
||||
@@ -0,0 +1,2 @@
|
||||
define(["utils/utils","mvc/ui/ui-misc","mvc/tool/tool-genomespace"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){var c=this;this.browse_button=new b.ButtonIcon({title:"Browse",icon:"fa fa-sign-in",tooltip:"Browse GenomeSpace",onclick:function(){c.browseGenomeSpace()}}),this.filename_textbox=new b.Input,this.token_textbox=new b.Input({type:"password"}),this.setElement(this._template(a)),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)},browseGenomeSpace:function(){var a=this;c.openFileBrowser({successCallback:function(b){a.value(b.destination+"^"+b.token)}})},_template:function(){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>'},value:function(a){return void 0===a?this._getValue():void this._setValue(a)},_getValue:function(){return this.filename_textbox.value()+"^"+this.token_textbox.value()},_setValue:function(a){a&&(values=a.split("^"),this.filename_textbox.value(values[0]),this.token_textbox.value(values[1]))}});return{View:d}});
|
||||
//# sourceMappingURL=../../../maps/mvc/ui/ui-select-genomespace.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -1,334 +1,38 @@
|
||||
#!/usr/bin/env python
|
||||
# Dan Blankenberg
|
||||
from __future__ import print_function
|
||||
|
||||
import base64
|
||||
import argparse
|
||||
import binascii
|
||||
import datetime
|
||||
import hashlib
|
||||
import json
|
||||
import logging
|
||||
import optparse
|
||||
import os
|
||||
import tempfile
|
||||
import sys
|
||||
|
||||
import six
|
||||
from six.moves import http_cookiejar
|
||||
from six.moves.urllib.error import HTTPError
|
||||
from six.moves.urllib.parse import quote, urlencode, urljoin
|
||||
from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen
|
||||
|
||||
log = logging.getLogger("tools.genomespace.genomespace_exporter")
|
||||
|
||||
try:
|
||||
import boto
|
||||
from boto.s3.connection import S3Connection
|
||||
except ImportError:
|
||||
boto = None
|
||||
|
||||
GENOMESPACE_API_VERSION_STRING = "v1.0"
|
||||
GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % (GENOMESPACE_API_VERSION_STRING)
|
||||
DEFAULT_GENOMESPACE_TOOLNAME = 'Galaxy'
|
||||
|
||||
CHUNK_SIZE = 2 ** 20 # 1mb
|
||||
|
||||
# TODO: TARGET_SPLIT_SIZE and TARGET_SIMPLE_PUT_UPLOAD_SIZE are arbitrarily defined
|
||||
# we should programmatically determine these, based upon the current environment
|
||||
TARGET_SPLIT_SIZE = 250 * 1024 * 1024 # 250 mb
|
||||
MIN_MULTIPART_UPLOAD_SIZE = 5 * 1024 * 1024 # 5mb
|
||||
MAX_SIMPLE_PUT_UPLOAD_SIZE = 5 * 1024 * 1024 * 1024 # 5gb
|
||||
TARGET_SIMPLE_PUT_UPLOAD_SIZE = MAX_SIMPLE_PUT_UPLOAD_SIZE / 2
|
||||
|
||||
# Some basic Caching, so we don't have to reload and download everything every time,
|
||||
# especially now that we are calling the parameter's get options method 5 times
|
||||
# (6 on reload) when a user loads the tool interface
|
||||
# For now, we'll use 30 seconds as the cache valid time
|
||||
CACHE_TIME = datetime.timedelta(seconds=30)
|
||||
GENOMESPACE_DIRECTORIES_BY_USER = {}
|
||||
from genomespaceclient import GenomeSpaceClient
|
||||
|
||||
|
||||
def chunk_write(source_stream, target_stream, source_method="read", target_method="write"):
|
||||
source_method = getattr(source_stream, source_method)
|
||||
target_method = getattr(target_stream, target_method)
|
||||
while True:
|
||||
chunk = source_method(CHUNK_SIZE)
|
||||
if chunk:
|
||||
target_method(chunk)
|
||||
else:
|
||||
break
|
||||
def upload_to_genomespace(token, input_file, target_url):
|
||||
token = token or os.environ.get('GS_TOKEN')
|
||||
gs_client = GenomeSpaceClient(token=token)
|
||||
gs_client.copy(input_file, target_url)
|
||||
print("File successfully copied.")
|
||||
|
||||
|
||||
def get_cookie_opener(gs_username, gs_token, gs_toolname=None):
|
||||
""" Create a GenomeSpace cookie opener """
|
||||
cj = http_cookiejar.CookieJar()
|
||||
for cookie_name, cookie_value in [('gs-token', gs_token), ('gs-username', gs_username)]:
|
||||
# create a super-cookie, valid for all domains
|
||||
cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False)
|
||||
cj.set_cookie(cookie)
|
||||
cookie_opener = build_opener(HTTPCookieProcessor(cj))
|
||||
cookie_opener.addheaders.append(('gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME))
|
||||
return cookie_opener
|
||||
def process_args(args):
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument('-i', '--input_file', type=str,
|
||||
help="File to export", required=True)
|
||||
parser.add_argument('-o', '--target_url', type=str,
|
||||
help="GenomeSpace output target folder location", required=True)
|
||||
parser.add_argument('-t', '--token', type=str,
|
||||
help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
|
||||
" If none, the environment variable GS_TOKEN will be respected.", required=False)
|
||||
|
||||
args = parser.parse_args(args[1:])
|
||||
return args
|
||||
|
||||
|
||||
def get_genomespace_site_urls():
|
||||
genomespace_sites = {}
|
||||
for line in urlopen(GENOMESPACE_SERVER_URL_PROPERTIES).read().split('\n'):
|
||||
line = line.rstrip()
|
||||
if not line or line.startswith("#"):
|
||||
continue
|
||||
server, line = line.split('.', 1)
|
||||
if server not in genomespace_sites:
|
||||
genomespace_sites[server] = {}
|
||||
line = line.split("=", 1)
|
||||
genomespace_sites[server][line[0]] = line[1]
|
||||
return genomespace_sites
|
||||
def main():
|
||||
args = process_args(sys.argv)
|
||||
upload_to_genomespace(args.token,
|
||||
binascii.unhexlify(args.input_file).decode('utf-8'),
|
||||
binascii.unhexlify(args.target_url).decode('utf-8'))
|
||||
|
||||
|
||||
def get_directory(url_opener, dm_url, path):
|
||||
url = dm_url
|
||||
i = None
|
||||
dir_dict = {}
|
||||
for i, sub_path in enumerate(path):
|
||||
url = "%s/%s" % (url, sub_path)
|
||||
dir_request = Request(url, headers={'Content-Type': 'application/json', 'Accept': 'application/json'})
|
||||
dir_request.get_method = lambda: 'GET'
|
||||
try:
|
||||
dir_dict = json.loads(url_opener.open(dir_request).read())
|
||||
except HTTPError:
|
||||
# print "e", e, url #punting, assuming lack of permissions at this low of a level...
|
||||
continue
|
||||
break
|
||||
if i is not None:
|
||||
path = path[i + 1:]
|
||||
else:
|
||||
path = []
|
||||
return (dir_dict, path)
|
||||
|
||||
|
||||
def get_default_directory(url_opener, dm_url):
|
||||
return get_directory(url_opener, dm_url, ["%s/defaultdirectory" % (GENOMESPACE_API_VERSION_STRING)])[0]
|
||||
|
||||
|
||||
def get_personal_directory(url_opener, dm_url):
|
||||
return get_directory(url_opener, dm_url, ["%s/personaldirectory" % (GENOMESPACE_API_VERSION_STRING)])[0]
|
||||
|
||||
|
||||
def create_directory(url_opener, directory_dict, new_dir, dm_url):
|
||||
payload = {"isDirectory": True}
|
||||
for dir_slice in new_dir:
|
||||
if dir_slice in ('', '/', None):
|
||||
continue
|
||||
url = '/'.join((directory_dict['url'], quote(dir_slice.replace('/', '_'), safe='')))
|
||||
new_dir_request = Request(url, headers={'Content-Type': 'application/json', 'Accept': 'application/json'}, data=json.dumps(payload))
|
||||
new_dir_request.get_method = lambda: 'PUT'
|
||||
directory_dict = json.loads(url_opener.open(new_dir_request).read())
|
||||
return directory_dict
|
||||
|
||||
|
||||
def get_genome_space_launch_apps(atm_url, url_opener, file_url, file_type):
|
||||
gs_request = Request("%s/%s/webtool/descriptor" % (atm_url, GENOMESPACE_API_VERSION_STRING))
|
||||
gs_request.get_method = lambda: 'GET'
|
||||
opened_gs_request = url_opener.open(gs_request)
|
||||
webtool_descriptors = json.loads(opened_gs_request.read())
|
||||
webtools = []
|
||||
for webtool in webtool_descriptors:
|
||||
webtool_name = webtool.get('name')
|
||||
base_url = webtool.get('baseUrl')
|
||||
use_tool = False
|
||||
for param in webtool.get('fileParameters', []):
|
||||
for format in param.get('formats', []):
|
||||
if format.get('name') == file_type:
|
||||
use_tool = True
|
||||
break
|
||||
if use_tool:
|
||||
file_param_name = param.get('name')
|
||||
# file_name_delimiters = param.get( 'nameDelimiters' )
|
||||
if '?' in base_url:
|
||||
url_delimiter = "&"
|
||||
else:
|
||||
url_delimiter = "?"
|
||||
launch_url = "%s%s%s" % (base_url, url_delimiter, urlencode([(file_param_name, file_url)]))
|
||||
webtools.append((launch_url, webtool_name))
|
||||
break
|
||||
return webtools
|
||||
|
||||
|
||||
def galaxy_code_get_genomespace_folders(genomespace_site='prod', trans=None, value=None, base_url=None, **kwd):
|
||||
if value:
|
||||
if isinstance(value, list):
|
||||
value = value[0] # single select, only 1 value
|
||||
elif not isinstance(value, six.string_types):
|
||||
# unvalidated value
|
||||
value = value.value
|
||||
if isinstance(value, list):
|
||||
value = value[0] # single select, only 1 value
|
||||
|
||||
def recurse_directory_dict(url_opener, cur_options, url):
|
||||
cur_directory = Request(url, headers={'Content-Type': 'application/json', 'Accept': 'application/json, text/plain'})
|
||||
cur_directory.get_method = lambda: 'GET'
|
||||
# get url to upload to
|
||||
try:
|
||||
cur_directory = url_opener.open(cur_directory).read()
|
||||
except HTTPError as e:
|
||||
log.debug('GenomeSpace export tool failed reading a directory "%s": %s' % (url, e))
|
||||
return # bad url, go to next
|
||||
cur_directory = json.loads(cur_directory)
|
||||
directory = cur_directory.get('directory', {})
|
||||
contents = cur_directory.get('contents', [])
|
||||
if directory.get('isDirectory', False):
|
||||
selected = directory.get('path') == value
|
||||
cur_options.append({'name': directory.get('name'), 'value': directory.get('path'), 'options': [], 'selected': selected})
|
||||
for sub_dir in contents:
|
||||
if sub_dir.get('isDirectory', False):
|
||||
recurse_directory_dict(url_opener, cur_options[-1]['options'], sub_dir.get('url'))
|
||||
|
||||
rval = []
|
||||
if trans and trans.user:
|
||||
username = trans.user.preferences.get('genomespace_username', None)
|
||||
token = trans.user.preferences.get('genomespace_token', None)
|
||||
if None not in (username, token):
|
||||
# NB: it is possible, but unlikely for a user to swap GenomeSpace accounts around
|
||||
# in the middle of interacting with tools, so we'll have several layers of caching by ids/values
|
||||
if trans.user in GENOMESPACE_DIRECTORIES_BY_USER:
|
||||
if username in GENOMESPACE_DIRECTORIES_BY_USER[trans.user]:
|
||||
if token in GENOMESPACE_DIRECTORIES_BY_USER[trans.user][username]:
|
||||
cache_dict = GENOMESPACE_DIRECTORIES_BY_USER[trans.user][username][token]
|
||||
if datetime.datetime.now() - cache_dict.get('time_loaded') > CACHE_TIME:
|
||||
# cache too old, need to reload, we'll just kill the whole trans.user
|
||||
del GENOMESPACE_DIRECTORIES_BY_USER[trans.user]
|
||||
else:
|
||||
rval = cache_dict.get('rval')
|
||||
else:
|
||||
del GENOMESPACE_DIRECTORIES_BY_USER[trans.user]
|
||||
else:
|
||||
del GENOMESPACE_DIRECTORIES_BY_USER[trans.user]
|
||||
if not rval:
|
||||
url_opener = get_cookie_opener(username, token, gs_toolname=os.environ.get('GENOMESPACE_TOOLNAME', None))
|
||||
genomespace_site_dict = get_genomespace_site_urls()[genomespace_site]
|
||||
dm_url = genomespace_site_dict['dmServer']
|
||||
# get export root directory
|
||||
# directory_dict = get_default_directory( url_opener, dm_url ).get( 'directory', None ) #This directory contains shares and other items outside of the users home
|
||||
directory_dict = get_personal_directory(url_opener, dm_url).get('directory', None) # Limit export list to only user's home dir
|
||||
if directory_dict is not None:
|
||||
recurse_directory_dict(url_opener, rval, directory_dict.get('url'))
|
||||
# Save the cache
|
||||
GENOMESPACE_DIRECTORIES_BY_USER[trans.user] = {username: {token: {'time_loaded': datetime.datetime.now(), 'rval': rval}}}
|
||||
if not rval:
|
||||
if not base_url:
|
||||
base_url = '..'
|
||||
rval = [{'name': 'Your GenomeSpace token appears to be <strong>expired</strong>, please <a href="%s">reauthenticate</a>.' % (urljoin(base_url, 'user/openid_auth?openid_provider=genomespace&auto_associate=True')), 'value': '', 'options': [], 'selected': False}]
|
||||
return rval
|
||||
|
||||
|
||||
def send_file_to_genomespace(genomespace_site, username, token, source_filename, target_directory, target_filename, file_type, content_type, log_filename, gs_toolname):
|
||||
target_filename = target_filename.replace('/', '-') # Slashes no longer allowed in filenames
|
||||
url_opener = get_cookie_opener(username, token, gs_toolname=gs_toolname)
|
||||
genomespace_site_dict = get_genomespace_site_urls()[genomespace_site]
|
||||
dm_url = genomespace_site_dict['dmServer']
|
||||
# get default directory
|
||||
if target_directory and target_directory[0] == '/':
|
||||
directory_dict, target_directory = get_directory(url_opener, dm_url, ["%s/%s/%s" % (GENOMESPACE_API_VERSION_STRING, 'file', target_directory[1])] + target_directory[2:])
|
||||
directory_dict = directory_dict['directory']
|
||||
else:
|
||||
directory_dict = get_personal_directory(url_opener, dm_url)['directory'] # this is the base for the auto-generated galaxy export directories
|
||||
# what directory to stuff this in
|
||||
target_directory_dict = create_directory(url_opener, directory_dict, target_directory, dm_url)
|
||||
content_length = os.path.getsize(source_filename)
|
||||
input_file = open(source_filename, 'rb')
|
||||
if content_length > TARGET_SIMPLE_PUT_UPLOAD_SIZE:
|
||||
# Determine sizes of each part.
|
||||
split_count = content_length / TARGET_SPLIT_SIZE
|
||||
last_size = content_length - (split_count * TARGET_SPLIT_SIZE)
|
||||
sizes = [TARGET_SPLIT_SIZE] * split_count
|
||||
if last_size:
|
||||
if last_size < MIN_MULTIPART_UPLOAD_SIZE:
|
||||
if sizes:
|
||||
sizes[-1] = sizes[-1] + last_size
|
||||
else:
|
||||
sizes = [last_size]
|
||||
else:
|
||||
sizes.append(last_size)
|
||||
print("Performing multi-part upload in %i parts." % (len(sizes)))
|
||||
# get upload url
|
||||
upload_url = "uploadinfo"
|
||||
upload_url = "%s/%s/%s%s/%s" % (dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], quote(target_filename, safe=''))
|
||||
upload_request = Request(upload_url, headers={'Content-Type': 'application/json', 'Accept': 'application/json'})
|
||||
upload_request.get_method = lambda: 'GET'
|
||||
upload_info = json.loads(url_opener.open(upload_request).read())
|
||||
conn = S3Connection(aws_access_key_id=upload_info['amazonCredentials']['accessKey'],
|
||||
aws_secret_access_key=upload_info['amazonCredentials']['secretKey'],
|
||||
security_token=upload_info['amazonCredentials']['sessionToken'])
|
||||
# Cannot use conn.get_bucket due to permissions, manually create bucket object
|
||||
bucket = boto.s3.bucket.Bucket(connection=conn, name=upload_info['s3BucketName'])
|
||||
mp = bucket.initiate_multipart_upload(upload_info['s3ObjectKey'])
|
||||
for i, part_size in enumerate(sizes, start=1):
|
||||
fh = tempfile.TemporaryFile('wb+')
|
||||
while part_size:
|
||||
if CHUNK_SIZE > part_size:
|
||||
read_size = part_size
|
||||
else:
|
||||
read_size = CHUNK_SIZE
|
||||
chunk = input_file.read(read_size)
|
||||
fh.write(chunk)
|
||||
part_size = part_size - read_size
|
||||
fh.flush()
|
||||
fh.seek(0)
|
||||
mp.upload_part_from_file(fh, i)
|
||||
fh.close()
|
||||
upload_result = mp.complete_upload()
|
||||
else:
|
||||
print('Performing simple put upload.')
|
||||
upload_url = "uploadurl"
|
||||
content_md5 = hashlib.md5()
|
||||
chunk_write(input_file, content_md5, target_method="update")
|
||||
input_file.seek(0) # back to start, for uploading
|
||||
|
||||
upload_params = {'Content-Length': content_length, 'Content-MD5': base64.standard_b64encode(content_md5.digest()), 'Content-Type': content_type}
|
||||
upload_url = "%s/%s/%s%s/%s?%s" % (dm_url, GENOMESPACE_API_VERSION_STRING, upload_url, target_directory_dict['path'], quote(target_filename, safe=''), urlencode(upload_params))
|
||||
new_file_request = Request(upload_url) # , headers = { 'Content-Type': 'application/json', 'Accept': 'application/text' } ) #apparently http://www.genomespace.org/team/specs/updated-dm-rest-api:"Every HTTP request to the Data Manager should include the Accept header with a preference for the media types application/json and application/text." is not correct
|
||||
new_file_request.get_method = lambda: 'GET'
|
||||
# get url to upload to
|
||||
target_upload_url = url_opener.open(new_file_request).read()
|
||||
# upload file to determined url
|
||||
upload_headers = dict(upload_params)
|
||||
# upload_headers[ 'x-amz-meta-md5-hash' ] = content_md5.hexdigest()
|
||||
upload_headers['Accept'] = 'application/json'
|
||||
upload_file_request = Request(target_upload_url, headers=upload_headers, data=input_file)
|
||||
upload_file_request.get_method = lambda: 'PUT'
|
||||
upload_result = urlopen(upload_file_request).read()
|
||||
result_url = "%s/%s" % (target_directory_dict['url'], quote(target_filename, safe=''))
|
||||
# determine available gs launch apps
|
||||
web_tools = get_genome_space_launch_apps(genomespace_site_dict['atmServer'], url_opener, result_url, file_type)
|
||||
if log_filename:
|
||||
log_file = open(log_filename, 'wb')
|
||||
log_file.write("<html><head><title>File uploaded to GenomeSpace from Galaxy</title></head><body>\n")
|
||||
log_file.write('<p>Uploaded <a href="%s">%s/%s</a> to GenomeSpace.</p>\n' % (result_url, target_directory_dict['path'], target_filename))
|
||||
if web_tools:
|
||||
log_file.write("<p>You may open this file directly in the following applications:</p>\n")
|
||||
log_file.write('<p><ul>\n')
|
||||
for web_tool in web_tools:
|
||||
log_file.write('<li><a href="%s">%s</a></li>\n' % (web_tool))
|
||||
log_file.write('</p></ul>\n')
|
||||
else:
|
||||
log_file.write('<p>There are no GenomeSpace applications available for file type: %s</p>\n' % (file_type))
|
||||
log_file.write("</body></html>\n")
|
||||
return upload_result
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
# Parse Command Line
|
||||
parser = optparse.OptionParser()
|
||||
parser.add_option('-s', '--genomespace_site', dest='genomespace_site', action='store', type="string", default=None, help='genomespace_site')
|
||||
parser.add_option('-t', '--token', dest='token', action='store', type="string", default=None, help='token')
|
||||
parser.add_option('-u', '--username', dest='username', action='store', type="string", default=None, help='username')
|
||||
parser.add_option('-d', '--dataset', dest='dataset', action='store', type="string", default=None, help='dataset')
|
||||
parser.add_option('-f', '--filename', dest='filename', action='store', type="string", default=None, help='filename')
|
||||
parser.add_option('-y', '--subdirectory', dest='subdirectory', action='append', type="string", default=None, help='subdirectory')
|
||||
parser.add_option('', '--file_type', dest='file_type', action='store', type="string", default=None, help='file_type')
|
||||
parser.add_option('-c', '--content_type', dest='content_type', action='store', type="string", default=None, help='content_type')
|
||||
parser.add_option('-l', '--log', dest='log', action='store', type="string", default=None, help='log')
|
||||
parser.add_option('', '--genomespace_toolname', dest='genomespace_toolname', action='store', type="string", default=DEFAULT_GENOMESPACE_TOOLNAME, help='value to use for gs-toolname, used in GenomeSpace internal logging')
|
||||
|
||||
(options, args) = parser.parse_args()
|
||||
|
||||
send_file_to_genomespace(options.genomespace_site, options.username, options.token, options.dataset, [binascii.unhexlify(_) for _ in options.subdirectory], binascii.unhexlify(options.filename), options.file_type, options.content_type, options.log, options.genomespace_toolname)
|
||||
if __name__ == "__main__":
|
||||
sys.exit(main())
|
||||
|
||||
@@ -1,54 +1,44 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="GenomeSpace Exporter" id="genomespace_exporter" require_login="True" version="0.0.4">
|
||||
<tool name="GenomeSpace Exporter" id="genomespace_exporter" version="0.0.5">
|
||||
<description> - send data to GenomeSpace</description>
|
||||
<command interpreter="python">genomespace_exporter.py
|
||||
--genomespace_site "prod"
|
||||
#assert $__user__, Exception( 'You must be logged in to use this tool.' )
|
||||
#set $username = $__user__.preferences.get( 'genomespace_username', None )
|
||||
#set $token = $__user__.preferences.get( 'genomespace_token', None )
|
||||
#assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' )
|
||||
<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.')
|
||||
$token
|
||||
</environment_variable>
|
||||
</environment_variables>
|
||||
<command>python $__tool_directory__/genomespace_exporter.py
|
||||
#set $target_folder = $genomespace_browser.split('^')[0]
|
||||
#assert $target_folder, Exception('You must select a valid target folder.')
|
||||
|
||||
#import binascii
|
||||
--username "${username}"
|
||||
--token "${token}"
|
||||
--dataset "${input1}"
|
||||
#if $subdirectory:
|
||||
#for $subd in str( $subdirectory ).split( '/' ):
|
||||
#if not $subd:
|
||||
--subdirectory "${ binascii.hexlify( '/' ) }"
|
||||
#else:
|
||||
--subdirectory "${ binascii.hexlify( $subd ) }"
|
||||
#end if
|
||||
#end for
|
||||
#else:
|
||||
--subdirectory "${ binascii.hexlify( 'galaxy_export' ) }"
|
||||
--subdirectory "${ binascii.hexlify( str( $base_url ).split( '://', 1 )[-1] ) }" ##Protocol removed by request
|
||||
#end if
|
||||
--input_file '${ binascii.hexlify(str($input1).encode("utf8")) }'
|
||||
#if $filename:
|
||||
--filename "${ binascii.hexlify( str( $filename ) ) }"
|
||||
--target_url '${ binascii.hexlify(str($target_folder + "/" + str($filename)).encode("utf8") ) }'
|
||||
#else:
|
||||
--filename "${ binascii.hexlify( "Galaxy History Item %s (%s) - %s: %s.%s" % ( $__app__.security.encode_id( $input1.id ), $__app__.security.encode_id( $output_log.id ), $input1.hid, $input1.name, $input1.ext ) ) }"
|
||||
--target_url '${ binascii.hexlify(($target_folder + "/" + "Galaxy History Item %s (%s) - %s: %s.%s" % ($__app__.security.encode_id($input1.id), $__app__.security.encode_id($output_log.id), $input1.hid, $input1.element_identifier.replace("/", "_"), $input1.ext)).encode("utf8")) }'
|
||||
#end if
|
||||
--file_type "${input1.ext}"
|
||||
--content_type "${input1.get_mime()}"
|
||||
--log "${output_log}"
|
||||
--genomespace_toolname="\${GENOMESPACE_TOOLNAME:-Galaxy}"
|
||||
</command>
|
||||
<inputs>
|
||||
<param format="data" name="input1" type="data" label="Send this dataset to GenomeSpace" />
|
||||
<param name="base_url" type="baseurl" />
|
||||
<param name="subdirectory" type="drill_down" display="radio" hierarchy="exact" multiple="False" optional="True" label="Choose Target Directory" dynamic_options="galaxy_code_get_genomespace_folders( genomespace_site = 'prod', trans=__trans__, value=__value__, input_dataset=input1, base_url=base_url )" help="Leave blank to generate automatically"/>
|
||||
<param name="filename" type="text" size="80" label="Filename" help="Leave blank to generate automatically" />
|
||||
<!-- If using this tool through bioblend, the genomespace_browser parameter should contain the path to the GenomeSpaceFile + the security token
|
||||
separated by a ^ as follows: GenomeSpaceFilePath^Token -->
|
||||
<param name="genomespace_browser" type="genomespacefile" label="Choose Target Directory" select_type="FOLDER" />
|
||||
<param name="filename" type="text" label="Filename" help="Leave blank to generate automatically" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="html" name="output_log" />
|
||||
<data format="auto" name="output_log" />
|
||||
</outputs>
|
||||
<help>
|
||||
This Tool allows you to export data to GenomeSpace. You must have logged in using your GenomeSpace OpenID. You can associate your OpenID credentials under the User Preferences panel.
|
||||
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.
|
||||
|
||||
If you are having trouble with this tool, click here_ to refresh your GenomeSpace token before reporting errors.
|
||||
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.
|
||||
You can associate your OpenID credentials under the User Preferences panel.
|
||||
Click here_ to refresh your GenomeSpace token.
|
||||
|
||||
.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
|
||||
</help>
|
||||
<options refresh="True"/>
|
||||
<code file="genomespace_exporter.py" />
|
||||
</tool>
|
||||
|
||||
@@ -1,217 +0,0 @@
|
||||
# Dan Blankenberg
|
||||
import json
|
||||
import optparse
|
||||
import os
|
||||
|
||||
from six.moves import http_cookiejar
|
||||
from six.moves.urllib.parse import unquote_plus, urlencode, urlparse
|
||||
from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen
|
||||
|
||||
from galaxy.datatypes import sniff
|
||||
from galaxy.datatypes.registry import Registry
|
||||
|
||||
GENOMESPACE_API_VERSION_STRING = "v1.0"
|
||||
GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % (GENOMESPACE_API_VERSION_STRING)
|
||||
DEFAULT_GENOMESPACE_TOOLNAME = 'Galaxy'
|
||||
FILENAME_VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
|
||||
|
||||
CHUNK_SIZE = 2**20 # 1mb
|
||||
|
||||
AUTO_GALAXY_EXT = "auto"
|
||||
DEFAULT_GALAXY_EXT = "data"
|
||||
|
||||
# genomespace format identifier is the URL
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = {} # TODO: fix this so it is not a global variable
|
||||
# TODO: we should use a better way to set up this mapping
|
||||
GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
|
||||
'lifes': 'lifes',
|
||||
'cn': 'cn',
|
||||
'GTF': 'gtf',
|
||||
'res': 'res',
|
||||
'xcn': 'xcn',
|
||||
'lowercasetxt': 'lowercasetxt',
|
||||
'bed': 'bed',
|
||||
'CBS': 'cbs',
|
||||
'genomicatab': 'genomicatab',
|
||||
'gxp': 'gxp',
|
||||
'reversedtxt': 'reversedtxt',
|
||||
'nowhitespace': 'nowhitespace',
|
||||
'unknown': 'unknown',
|
||||
'txt': 'txt',
|
||||
'uppercasetxt': 'uppercasetxt',
|
||||
'GISTIC': 'gistic',
|
||||
'GFF': 'gff',
|
||||
'gmt': 'gmt',
|
||||
'gct': 'gct'}
|
||||
|
||||
GENOMESPACE_UNKNOWN_FORMAT_KEY = 'unknown'
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = None
|
||||
|
||||
|
||||
def chunk_write(source_stream, target_stream, source_method="read", target_method="write"):
|
||||
source_method = getattr(source_stream, source_method)
|
||||
target_method = getattr(target_stream, target_method)
|
||||
while True:
|
||||
chunk = source_method(CHUNK_SIZE)
|
||||
if chunk:
|
||||
target_method(chunk)
|
||||
else:
|
||||
break
|
||||
|
||||
|
||||
def get_cookie_opener(gs_username, gs_token, gs_toolname=None):
|
||||
""" Create a GenomeSpace cookie opener """
|
||||
cj = http_cookiejar.CookieJar()
|
||||
for cookie_name, cookie_value in [('gs-token', gs_token), ('gs-username', gs_username)]:
|
||||
# create a super-cookie, valid for all domains
|
||||
cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False)
|
||||
cj.set_cookie(cookie)
|
||||
cookie_opener = build_opener(HTTPCookieProcessor(cj))
|
||||
cookie_opener.addheaders.append(('gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME))
|
||||
return cookie_opener
|
||||
|
||||
|
||||
def get_galaxy_ext_from_genomespace_format_url(url_opener, file_format_url):
|
||||
ext = GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.get(file_format_url, None)
|
||||
if ext is not None:
|
||||
ext = GENOMESPACE_EXT_TO_GALAXY_EXT.get(ext, None)
|
||||
if ext is None:
|
||||
# could check content type, etc here
|
||||
ext = AUTO_GALAXY_EXT
|
||||
return ext
|
||||
|
||||
|
||||
def get_genomespace_site_urls():
|
||||
genomespace_sites = {}
|
||||
for line in urlopen(GENOMESPACE_SERVER_URL_PROPERTIES).read().split('\n'):
|
||||
line = line.rstrip()
|
||||
if not line or line.startswith("#"):
|
||||
continue
|
||||
server, line = line.split('.', 1)
|
||||
if server not in genomespace_sites:
|
||||
genomespace_sites[server] = {}
|
||||
line = line.split("=", 1)
|
||||
genomespace_sites[server][line[0]] = line[1]
|
||||
return genomespace_sites
|
||||
|
||||
|
||||
def set_genomespace_format_identifiers(url_opener, dm_site):
|
||||
gs_request = Request("%s/%s/dataformat/list" % (dm_site, GENOMESPACE_API_VERSION_STRING))
|
||||
gs_request.get_method = lambda: 'GET'
|
||||
opened_gs_request = url_opener.open(gs_request)
|
||||
genomespace_formats = json.loads(opened_gs_request.read())
|
||||
for format in genomespace_formats:
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[format['url']] = format['name']
|
||||
global GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN = dict((x[1], x[0]) for x in GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.items()).get(GENOMESPACE_UNKNOWN_FORMAT_KEY, GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN)
|
||||
|
||||
|
||||
def download_from_genomespace_file_browser(json_parameter_file, genomespace_site, gs_toolname):
|
||||
json_params = json.loads(open(json_parameter_file, 'r').read())
|
||||
datasource_params = json_params.get('param_dict')
|
||||
username = datasource_params.get("gs-username", None)
|
||||
token = datasource_params.get("gs-token", None)
|
||||
assert None not in [username, token], "Missing GenomeSpace username or token."
|
||||
output_filename = datasource_params.get("output", None)
|
||||
dataset_id = json_params['output_data'][0]['dataset_id']
|
||||
hda_id = json_params['output_data'][0]['hda_id']
|
||||
url_opener = get_cookie_opener(username, token, gs_toolname=gs_toolname)
|
||||
# load and set genomespace format ids to galaxy exts
|
||||
genomespace_site_dict = get_genomespace_site_urls()[genomespace_site]
|
||||
set_genomespace_format_identifiers(url_opener, genomespace_site_dict['dmServer'])
|
||||
|
||||
file_url_prefix = "fileUrl"
|
||||
file_type_prefix = "fileFormat"
|
||||
metadata_parameter_file = open(json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb')
|
||||
|
||||
# setup datatypes registry for sniffing
|
||||
datatypes_registry = Registry()
|
||||
datatypes_registry.load_datatypes(root_dir=json_params['job_config']['GALAXY_ROOT_DIR'], config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
|
||||
|
||||
file_numbers = []
|
||||
for name in datasource_params.keys():
|
||||
if name.startswith(file_url_prefix):
|
||||
name = name[len(file_url_prefix):]
|
||||
file_numbers.append(int(name))
|
||||
if not file_numbers:
|
||||
if output_filename:
|
||||
open(output_filename, 'wb') # erase contents of file
|
||||
raise Exception("You must select at least one file to import into Galaxy.")
|
||||
file_numbers.sort()
|
||||
used_filenames = []
|
||||
for file_num in file_numbers:
|
||||
url_key = "%s%i" % (file_url_prefix, file_num)
|
||||
download_url = datasource_params.get(url_key, None)
|
||||
if download_url is None:
|
||||
break
|
||||
filetype_key = "%s%i" % (file_type_prefix, file_num)
|
||||
filetype_url = datasource_params.get(filetype_key, None)
|
||||
galaxy_ext = get_galaxy_ext_from_genomespace_format_url(url_opener, filetype_url)
|
||||
formatted_download_url = "%s?%s" % (download_url, urlencode([('dataformat', filetype_url)]))
|
||||
new_file_request = Request(formatted_download_url)
|
||||
new_file_request.get_method = lambda: 'GET'
|
||||
target_download_url = url_opener.open(new_file_request)
|
||||
filename = None
|
||||
if 'Content-Disposition' in target_download_url.info():
|
||||
# If the response has Content-Disposition, try to get filename from it
|
||||
content_disposition = dict(x.strip().split('=') if '=' in x else (x.strip(), '') for x in target_download_url.info()['Content-Disposition'].split(';'))
|
||||
if 'filename' in content_disposition:
|
||||
filename = content_disposition['filename'].strip("\"'")
|
||||
if not filename:
|
||||
parsed_url = urlparse(download_url)
|
||||
filename = unquote_plus(parsed_url[2].split('/')[-1])
|
||||
if not filename:
|
||||
filename = download_url
|
||||
metadata_dict = None
|
||||
original_filename = filename
|
||||
if output_filename is None:
|
||||
filename = ''.join(c in FILENAME_VALID_CHARS and c or '-' for c in filename)
|
||||
while filename in used_filenames:
|
||||
filename = "-%s" % filename
|
||||
used_filenames.append(filename)
|
||||
output_filename = os.path.join(os.getcwd(), 'primary_%i_%s_visible_%s' % (hda_id, filename, galaxy_ext))
|
||||
|
||||
metadata_dict = dict(type='new_primary_dataset',
|
||||
base_dataset_id=dataset_id,
|
||||
ext=galaxy_ext,
|
||||
filename=output_filename,
|
||||
name="GenomeSpace import on %s" % (original_filename))
|
||||
else:
|
||||
if dataset_id is not None:
|
||||
metadata_dict = dict(type='dataset',
|
||||
dataset_id=dataset_id,
|
||||
ext=galaxy_ext,
|
||||
name="GenomeSpace import on %s" % (filename))
|
||||
output_file = open(output_filename, 'wb')
|
||||
chunk_write(target_download_url, output_file)
|
||||
output_file.close()
|
||||
|
||||
if (galaxy_ext == AUTO_GALAXY_EXT or filetype_url == GENOMESPACE_FORMAT_IDENTIFIER_UNKNOWN) and metadata_dict:
|
||||
# try to sniff datatype
|
||||
try:
|
||||
galaxy_ext = sniff.handle_uploaded_dataset_file(output_filename, datatypes_registry)
|
||||
except:
|
||||
# sniff failed
|
||||
galaxy_ext = original_filename.rsplit('.', 1)[-1]
|
||||
if galaxy_ext not in datatypes_registry.datatypes_by_extension:
|
||||
galaxy_ext = DEFAULT_GALAXY_EXT
|
||||
metadata_dict['ext'] = galaxy_ext
|
||||
|
||||
output_filename = None # only have one filename available
|
||||
|
||||
# write out metadata info
|
||||
if metadata_dict:
|
||||
metadata_parameter_file.write("%s\n" % json.dumps(metadata_dict))
|
||||
|
||||
metadata_parameter_file.close()
|
||||
return True
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = optparse.OptionParser()
|
||||
parser.add_option('-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file')
|
||||
parser.add_option('-s', '--genomespace_site', dest='genomespace_site', action='store', type="string", default=None, help='genomespace_site')
|
||||
parser.add_option('', '--genomespace_toolname', dest='genomespace_toolname', action='store', type="string", default=DEFAULT_GENOMESPACE_TOOLNAME, help='value to use for gs-toolname, used in GenomeSpace internal logging')
|
||||
(options, args) = parser.parse_args()
|
||||
|
||||
download_from_genomespace_file_browser(options.json_parameter_file, options.genomespace_site, options.genomespace_toolname)
|
||||
|
||||
@@ -1,15 +0,0 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="GenomeSpace import" id="genomespace_file_browser_dev" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
|
||||
<description>from file browser (development)</description>
|
||||
<command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "dev" --genomespace_toolname="\${GENOMESPACE_TOOLNAME:-Galaxy}"</command>
|
||||
<inputs action="https://dmdev.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post">
|
||||
<display>go to GenomeSpace Data Manager </display>
|
||||
<param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_dev&runtool_btn=Execute" />
|
||||
<param name="appName" type="hidden" value="Galaxy" />
|
||||
</inputs>
|
||||
<uihints minwidth="800"/>
|
||||
<outputs>
|
||||
<data name="output" format="auto" />
|
||||
</outputs>
|
||||
<options sanitize="False" refresh="True"/>
|
||||
</tool>
|
||||
@@ -1,15 +0,0 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="GenomeSpace import" id="genomespace_file_browser_prod" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
|
||||
<description>from file browser</description>
|
||||
<command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "prod" --genomespace_toolname="\${GENOMESPACE_TOOLNAME:-Galaxy}"</command>
|
||||
<inputs action="https://dm.genomespace.org/datamanager/defaultdirectory" check_values="False" method="post">
|
||||
<display>go to GenomeSpace Data Manager </display>
|
||||
<param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_prod&runtool_btn=Execute" />
|
||||
<param name="appName" type="hidden" value="Galaxy" />
|
||||
</inputs>
|
||||
<uihints minwidth="800"/>
|
||||
<outputs>
|
||||
<data name="output" format="auto" />
|
||||
</outputs>
|
||||
<options sanitize="False" refresh="True"/>
|
||||
</tool>
|
||||
@@ -1,15 +0,0 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="GenomeSpace import" id="genomespace_file_browser_test" tool_type="data_source" add_galaxy_url="False" force_history_refresh="True" version="0.0.1">
|
||||
<description>from file browser (test)</description>
|
||||
<command interpreter="python">genomespace_file_browser.py --json_parameter_file "${output}" --genomespace_site "test" --genomespace_toolname="\${GENOMESPACE_TOOLNAME:-Galaxy}"</command>
|
||||
<inputs action="https://dmtest.genomespace.org:8444/datamanager/defaultdirectory" check_values="False" method="post">
|
||||
<display>go to GenomeSpace Data Manager </display>
|
||||
<param name="appCallbackUrl" type="baseurl" value="/tool_runner?tool_id=genomespace_file_browser_test&runtool_btn=Execute" />
|
||||
<param name="appName" type="hidden" value="Galaxy" />
|
||||
</inputs>
|
||||
<uihints minwidth="800"/>
|
||||
<outputs>
|
||||
<data name="output" format="auto" />
|
||||
</outputs>
|
||||
<options sanitize="False" refresh="True"/>
|
||||
</tool>
|
||||
@@ -1,39 +1,26 @@
|
||||
# Dan Blankenberg
|
||||
|
||||
import argparse
|
||||
import json
|
||||
import optparse
|
||||
import os
|
||||
import shutil
|
||||
import tempfile
|
||||
import sys
|
||||
import uuid
|
||||
|
||||
from six.moves import http_cookiejar
|
||||
from six.moves.urllib.parse import parse_qs, unquote_plus, urlparse
|
||||
from six.moves.urllib.request import build_opener, HTTPCookieProcessor, Request, urlopen
|
||||
from genomespaceclient import GenomeSpaceClient
|
||||
|
||||
import galaxy
|
||||
from galaxy.datatypes import sniff
|
||||
from galaxy.datatypes.registry import Registry
|
||||
|
||||
GENOMESPACE_API_VERSION_STRING = "v1.0"
|
||||
GENOMESPACE_SERVER_URL_PROPERTIES = "https://dm.genomespace.org/config/%s/serverurl.properties" % (GENOMESPACE_API_VERSION_STRING)
|
||||
DEFAULT_GENOMESPACE_TOOLNAME = 'Galaxy'
|
||||
FILENAME_VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
|
||||
|
||||
CHUNK_SIZE = 2**20 # 1mb
|
||||
|
||||
DEFAULT_GALAXY_EXT = "data"
|
||||
|
||||
# genomespace format identifier is the URL
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT = {} # TODO: fix this so it is not a global variable
|
||||
# TODO: we should use a better way to set up this mapping
|
||||
# Mappings for known genomespace formats to galaxy formats
|
||||
GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
|
||||
'lifes': 'lifes',
|
||||
'cn': 'cn',
|
||||
'GTF': 'gtf',
|
||||
'gtf': 'gtf',
|
||||
'res': 'res',
|
||||
'xcn': 'xcn',
|
||||
'lowercasetxt': 'lowercasetxt',
|
||||
'bed': 'bed',
|
||||
'CBS': 'cbs',
|
||||
'cbs': 'cbs',
|
||||
'genomicatab': 'genomicatab',
|
||||
'gxp': 'gxp',
|
||||
'reversedtxt': 'reversedtxt',
|
||||
@@ -41,180 +28,233 @@ GENOMESPACE_EXT_TO_GALAXY_EXT = {'rifles': 'rifles',
|
||||
'unknown': 'unknown',
|
||||
'txt': 'txt',
|
||||
'uppercasetxt': 'uppercasetxt',
|
||||
'GISTIC': 'gistic',
|
||||
'GFF': 'gff',
|
||||
'gistic': 'gistic',
|
||||
'gff': 'gff',
|
||||
'gmt': 'gmt',
|
||||
'gct': 'gct'}
|
||||
|
||||
|
||||
def chunk_write(source_stream, target_stream, source_method="read", target_method="write"):
|
||||
source_method = getattr(source_stream, source_method)
|
||||
target_method = getattr(target_stream, target_method)
|
||||
while True:
|
||||
chunk = source_method(CHUNK_SIZE)
|
||||
if chunk:
|
||||
target_method(chunk)
|
||||
def _prepare_json_list(param_list):
|
||||
"""
|
||||
JSON serialization Support functions for exec_before_job hook
|
||||
"""
|
||||
rval = []
|
||||
for value in param_list:
|
||||
if isinstance(value, dict):
|
||||
rval.append(_prepare_json_param_dict(value))
|
||||
elif isinstance(value, list):
|
||||
rval.append(_prepare_json_list(value))
|
||||
else:
|
||||
break
|
||||
rval.append(str(value))
|
||||
return rval
|
||||
|
||||
|
||||
def get_cookie_opener(gs_username, gs_token, gs_toolname=None):
|
||||
""" Create a GenomeSpace cookie opener """
|
||||
cj = http_cookiejar.CookieJar()
|
||||
for cookie_name, cookie_value in [('gs-token', gs_token), ('gs-username', gs_username)]:
|
||||
# create a super-cookie, valid for all domains
|
||||
cookie = http_cookiejar.Cookie(version=0, name=cookie_name, value=cookie_value, port=None, port_specified=False, domain='', domain_specified=False, domain_initial_dot=False, path='/', path_specified=True, secure=False, expires=None, discard=True, comment=None, comment_url=None, rest={'HttpOnly': None}, rfc2109=False)
|
||||
cj.set_cookie(cookie)
|
||||
cookie_opener = build_opener(HTTPCookieProcessor(cj))
|
||||
cookie_opener.addheaders.append(('gs-toolname', gs_toolname or DEFAULT_GENOMESPACE_TOOLNAME))
|
||||
return cookie_opener
|
||||
|
||||
|
||||
def get_galaxy_ext_from_genomespace_format_url(url_opener, file_format_url, default=DEFAULT_GALAXY_EXT):
|
||||
ext = GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT.get(file_format_url, None)
|
||||
if ext is not None:
|
||||
ext = GENOMESPACE_EXT_TO_GALAXY_EXT.get(ext, None)
|
||||
if ext is None:
|
||||
# could check content type, etc here
|
||||
ext = default
|
||||
return ext
|
||||
|
||||
|
||||
def get_genomespace_site_urls():
|
||||
genomespace_sites = {}
|
||||
for line in urlopen(GENOMESPACE_SERVER_URL_PROPERTIES).read().split('\n'):
|
||||
line = line.rstrip()
|
||||
if not line or line.startswith("#"):
|
||||
continue
|
||||
server, line = line.split('.', 1)
|
||||
if server not in genomespace_sites:
|
||||
genomespace_sites[server] = {}
|
||||
line = line.split("=", 1)
|
||||
genomespace_sites[server][line[0]] = line[1]
|
||||
return genomespace_sites
|
||||
|
||||
|
||||
def set_genomespace_format_identifiers(url_opener, dm_site):
|
||||
gs_request = Request("%s/%s/dataformat/list" % (dm_site, GENOMESPACE_API_VERSION_STRING))
|
||||
gs_request.get_method = lambda: 'GET'
|
||||
opened_gs_request = url_opener.open(gs_request)
|
||||
genomespace_formats = json.loads(opened_gs_request.read())
|
||||
for format in genomespace_formats:
|
||||
GENOMESPACE_FORMAT_IDENTIFIER_TO_GENOMESPACE_EXT[format['url']] = format['name']
|
||||
|
||||
|
||||
def download_from_genomespace_importer(username, token, json_parameter_file, genomespace_site, gs_toolname):
|
||||
json_params = json.loads(open(json_parameter_file, 'r').read())
|
||||
datasource_params = json_params.get('param_dict')
|
||||
assert None not in [username, token], "Missing GenomeSpace username or token."
|
||||
output_filename = datasource_params.get("output_file1", None)
|
||||
dataset_id = base_dataset_id = json_params['output_data'][0]['dataset_id']
|
||||
hda_id = json_params['output_data'][0]['hda_id']
|
||||
url_opener = get_cookie_opener(username, token, gs_toolname=gs_toolname)
|
||||
# load and set genomespace format ids to galaxy exts
|
||||
genomespace_site_dict = get_genomespace_site_urls()[genomespace_site]
|
||||
set_genomespace_format_identifiers(url_opener, genomespace_site_dict['dmServer'])
|
||||
file_url_name = "URL"
|
||||
metadata_parameter_file = open(json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb')
|
||||
# setup datatypes registry for sniffing
|
||||
datatypes_registry = Registry()
|
||||
datatypes_registry.load_datatypes(root_dir=json_params['job_config']['GALAXY_ROOT_DIR'], config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
|
||||
url_param = datasource_params.get(file_url_name, None)
|
||||
used_filenames = []
|
||||
for download_url in url_param.split(','):
|
||||
using_temp_file = False
|
||||
parsed_url = urlparse(download_url)
|
||||
query_params = parse_qs(parsed_url[4])
|
||||
# write file to disk
|
||||
new_file_request = Request(download_url)
|
||||
new_file_request.get_method = lambda: 'GET'
|
||||
target_download_url = url_opener.open(new_file_request)
|
||||
filename = None
|
||||
if 'Content-Disposition' in target_download_url.info():
|
||||
content_disposition = dict(x.strip().split('=') if '=' in x else (x.strip(), '') for x in target_download_url.info()['Content-Disposition'].split(';'))
|
||||
if 'filename' in content_disposition:
|
||||
filename = content_disposition['filename'].strip("\"'")
|
||||
if not filename:
|
||||
parsed_url = urlparse(download_url)
|
||||
query_params = parse_qs(parsed_url[4])
|
||||
filename = unquote_plus(parsed_url[2].split('/')[-1])
|
||||
if not filename:
|
||||
filename = download_url
|
||||
if output_filename is None:
|
||||
# need to use a temp file here, because we do not know the ext yet
|
||||
using_temp_file = True
|
||||
output_filename = tempfile.NamedTemporaryFile(prefix='tmp-genomespace-importer-').name
|
||||
output_file = open(output_filename, 'wb')
|
||||
chunk_write(target_download_url, output_file)
|
||||
output_file.close()
|
||||
|
||||
# determine file format
|
||||
file_type = None
|
||||
if 'dataformat' in query_params: # this is a converted dataset
|
||||
file_type = query_params['dataformat'][0]
|
||||
file_type = get_galaxy_ext_from_genomespace_format_url(url_opener, file_type)
|
||||
def _prepare_json_param_dict(param_dict):
|
||||
"""
|
||||
JSON serialization Support functions for exec_before_job hook
|
||||
"""
|
||||
rval = {}
|
||||
for key, value in param_dict.iteritems():
|
||||
if isinstance(value, dict):
|
||||
rval[key] = _prepare_json_param_dict(value)
|
||||
elif isinstance(value, list):
|
||||
rval[key] = _prepare_json_list(value)
|
||||
else:
|
||||
try:
|
||||
# get and use GSMetadata object
|
||||
download_file_path = download_url.split("%s/file/" % (genomespace_site_dict['dmServer']), 1)[-1] # FIXME: This is a very bad way to get the path for determining metadata. There needs to be a way to query API using download URLto get to the metadata object
|
||||
metadata_request = Request("%s/%s/filemetadata/%s" % (genomespace_site_dict['dmServer'], GENOMESPACE_API_VERSION_STRING, download_file_path))
|
||||
metadata_request.get_method = lambda: 'GET'
|
||||
metadata_url = url_opener.open(metadata_request)
|
||||
file_metadata_dict = json.loads(metadata_url.read())
|
||||
metadata_url.close()
|
||||
file_type = file_metadata_dict.get('dataFormat', None)
|
||||
if file_type and file_type.get('url'):
|
||||
file_type = file_type.get('url')
|
||||
file_type = get_galaxy_ext_from_genomespace_format_url(url_opener, file_type, default=None)
|
||||
except:
|
||||
pass
|
||||
if file_type is None:
|
||||
# try to sniff datatype
|
||||
try:
|
||||
file_type = sniff.handle_uploaded_dataset_file(output_filename, datatypes_registry)
|
||||
except:
|
||||
pass # sniff failed
|
||||
if file_type is None and '.' in parsed_url[2]:
|
||||
# still no known datatype, fall back to using extension
|
||||
file_type = parsed_url[2].rsplit('.', 1)[-1]
|
||||
file_type = GENOMESPACE_EXT_TO_GALAXY_EXT.get(file_type, file_type)
|
||||
if file_type is None:
|
||||
# use default extension (e.g. 'data')
|
||||
file_type = DEFAULT_GALAXY_EXT
|
||||
rval[key] = str(value)
|
||||
return rval
|
||||
|
||||
# save json info for single primary dataset
|
||||
if dataset_id is not None:
|
||||
|
||||
def exec_before_job(app, inp_data, out_data, param_dict=None, tool=None):
|
||||
"""
|
||||
Galaxy override hook
|
||||
See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccode.3E_tag_set
|
||||
Since only tools with tool_type="data_source" provides functionality for having a JSON param file such as this:
|
||||
https://wiki.galaxyproject.org/Admin/Tools/DataManagers/DataManagerJSONSyntax#Example_JSON_input_to_tool,
|
||||
this hook is used to manually create a similar JSON file.
|
||||
However, this hook does not provide access to GALAXY_DATATYPES_CONF_FILE and GALAXY_ROOT_DIR
|
||||
properties, so these must be passed in as commandline params.
|
||||
"""
|
||||
if param_dict is None:
|
||||
param_dict = {}
|
||||
json_params = {}
|
||||
json_params['param_dict'] = _prepare_json_param_dict(param_dict)
|
||||
json_params['output_data'] = []
|
||||
json_params['job_config'] = dict(GALAXY_DATATYPES_CONF_FILE=param_dict.get('GALAXY_DATATYPES_CONF_FILE'),
|
||||
GALAXY_ROOT_DIR=param_dict.get('GALAXY_ROOT_DIR'),
|
||||
TOOL_PROVIDED_JOB_METADATA_FILE=galaxy.jobs.TOOL_PROVIDED_JOB_METADATA_FILE)
|
||||
json_filename = None
|
||||
for i, (out_name, data) in enumerate(out_data.iteritems()):
|
||||
file_name = data.get_file_name()
|
||||
data_dict = dict(out_data_name=out_name,
|
||||
ext=data.ext,
|
||||
dataset_id=data.dataset.id,
|
||||
hda_id=data.id,
|
||||
file_name=file_name)
|
||||
json_params['output_data'].append(data_dict)
|
||||
if json_filename is None:
|
||||
json_filename = file_name
|
||||
with open(json_filename, 'w') as out:
|
||||
out.write(json.dumps(json_params))
|
||||
|
||||
|
||||
def get_galaxy_ext_from_genomespace_format(format):
|
||||
return GENOMESPACE_EXT_TO_GALAXY_EXT.get(format, None)
|
||||
|
||||
|
||||
def get_galaxy_ext_from_file_ext(filename):
|
||||
if not filename:
|
||||
return None
|
||||
filename = filename.lower()
|
||||
ext = filename.rsplit('.', 1)[-1]
|
||||
return get_galaxy_ext_from_genomespace_format(ext)
|
||||
|
||||
|
||||
def sniff_and_handle_data_type(json_params, output_file):
|
||||
"""
|
||||
The sniff.handle_uploaded_dataset_file() method in Galaxy performs dual
|
||||
functions: it sniffs the filetype and if it's a compressed archive for
|
||||
a non compressed datatype such as fasta, it will be unpacked.
|
||||
"""
|
||||
try:
|
||||
datatypes_registry = Registry()
|
||||
datatypes_registry.load_datatypes(
|
||||
root_dir=json_params['job_config']['GALAXY_ROOT_DIR'],
|
||||
config=json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'])
|
||||
file_type = sniff.handle_uploaded_dataset_file(
|
||||
output_file,
|
||||
datatypes_registry)
|
||||
return file_type
|
||||
except:
|
||||
return None
|
||||
|
||||
|
||||
def determine_output_filename(input_url, metadata, json_params, primary_dataset):
|
||||
"""
|
||||
Determines the output file name. If only a single output file, the dataset name
|
||||
is used. If multiple files are being downloaded, each file is given a unique dataset
|
||||
name
|
||||
"""
|
||||
output_filename = json_params['output_data'][0]['file_name']
|
||||
|
||||
if not primary_dataset or not output_filename:
|
||||
hda_id = json_params['output_data'][0]['hda_id']
|
||||
output_filename = 'primary_%i_%s_visible_%s' % (hda_id, metadata.name, uuid.uuid4())
|
||||
|
||||
return os.path.join(os.getcwd(), output_filename)
|
||||
|
||||
|
||||
def determine_file_type(input_url, output_filename, metadata, json_params, sniffed_type):
|
||||
"""
|
||||
Determine the Galaxy data format for this file.
|
||||
"""
|
||||
# Use genomespace metadata to map type
|
||||
file_format = metadata.dataFormat.name if metadata.dataFormat else None
|
||||
file_type = get_galaxy_ext_from_genomespace_format(file_format)
|
||||
|
||||
# If genomespace metadata has no identifiable format, attempt to sniff type
|
||||
if not file_type:
|
||||
file_type = sniffed_type
|
||||
|
||||
# Still no type? Attempt to use filename extension to determine a type
|
||||
if not file_type:
|
||||
file_type = get_galaxy_ext_from_file_ext(metadata.name)
|
||||
|
||||
# Nothing works, use default
|
||||
if not file_type:
|
||||
file_type = "data"
|
||||
|
||||
return file_type
|
||||
|
||||
|
||||
def save_result_metadata(output_filename, file_type, metadata, json_params,
|
||||
primary_dataset=False):
|
||||
"""
|
||||
Generates a new job metadata file (typically galaxy.json) with details of
|
||||
all downloaded files, which Galaxy can read and use to display history items
|
||||
and associated metadata
|
||||
"""
|
||||
dataset_id = json_params['output_data'][0]['dataset_id']
|
||||
with open(json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'ab') as metadata_parameter_file:
|
||||
if primary_dataset:
|
||||
metadata_parameter_file.write("%s\n" % json.dumps(dict(type='dataset',
|
||||
dataset_id=dataset_id,
|
||||
ext=file_type,
|
||||
name="GenomeSpace importer on %s" % (filename))))
|
||||
# if using tmp file, move the file to the new file path dir to get scooped up later
|
||||
if using_temp_file:
|
||||
original_filename = filename
|
||||
filename = ''.join(c in FILENAME_VALID_CHARS and c or '-' for c in filename)
|
||||
while filename in used_filenames:
|
||||
filename = "-%s" % filename
|
||||
used_filenames.append(filename)
|
||||
target_output_filename = os.path.join(os.getcwd(), 'primary_%i_%s_visible_%s' % (hda_id, filename, file_type))
|
||||
shutil.move(output_filename, target_output_filename)
|
||||
name="GenomeSpace importer on %s" % (metadata.name))))
|
||||
else:
|
||||
metadata_parameter_file.write("%s\n" % json.dumps(dict(type='new_primary_dataset',
|
||||
base_dataset_id=base_dataset_id,
|
||||
base_dataset_id=dataset_id,
|
||||
ext=file_type,
|
||||
filename=target_output_filename,
|
||||
name="GenomeSpace importer on %s" % (original_filename))))
|
||||
dataset_id = None # only one primary dataset available
|
||||
output_filename = None # only have one filename available
|
||||
metadata_parameter_file.close()
|
||||
return True
|
||||
filename=output_filename,
|
||||
name="GenomeSpace importer on %s" % (metadata.name))))
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
parser = optparse.OptionParser()
|
||||
parser.add_option('-p', '--json_parameter_file', dest='json_parameter_file', action='store', type="string", default=None, help='json_parameter_file')
|
||||
parser.add_option('-s', '--genomespace_site', dest='genomespace_site', action='store', type="string", default=None, help='genomespace_site')
|
||||
parser.add_option('-t', '--token', dest='token', action='store', type="string", default=None, help='token')
|
||||
parser.add_option('-u', '--username', dest='username', action='store', type="string", default=None, help='username')
|
||||
parser.add_option('', '--genomespace_toolname', dest='genomespace_toolname', action='store', type="string", default=DEFAULT_GENOMESPACE_TOOLNAME, help='value to use for gs-toolname, used in GenomeSpace internal logging')
|
||||
(options, args) = parser.parse_args()
|
||||
def download_single_file(gs_client, input_url, json_params,
|
||||
primary_dataset=False):
|
||||
# 1. Get file metadata
|
||||
metadata = gs_client.get_metadata(input_url)
|
||||
|
||||
download_from_genomespace_importer(options.username, options.token, options.json_parameter_file, options.genomespace_site, options.genomespace_toolname)
|
||||
# 2. Determine output file name
|
||||
output_filename = determine_output_filename(input_url, metadata, json_params, primary_dataset)
|
||||
|
||||
# 3. Download file
|
||||
gs_client.copy(input_url, output_filename)
|
||||
|
||||
# 4. Decompress file if compressed and sniff type
|
||||
sniffed_type = sniff_and_handle_data_type(json_params, output_filename)
|
||||
|
||||
# 5. Determine file type from available metadata
|
||||
file_type = determine_file_type(input_url, output_filename, metadata, json_params, sniffed_type)
|
||||
|
||||
# 6. Write job output metadata
|
||||
save_result_metadata(output_filename, file_type, metadata, json_params,
|
||||
primary_dataset=primary_dataset)
|
||||
|
||||
|
||||
def download_from_genomespace_importer(json_parameter_file, root, data_conf, custom_token):
|
||||
with open(json_parameter_file, 'r') as param_file:
|
||||
json_params = json.load(param_file)
|
||||
|
||||
# Add in missing job config properties that could not be set in the exec_before_job hook
|
||||
json_params['job_config']['GALAXY_ROOT_DIR'] = root
|
||||
json_params['job_config']['GALAXY_DATATYPES_CONF_FILE'] = data_conf
|
||||
|
||||
# Extract input_urls and token (format is input_urls^token). If a custom_token is
|
||||
# provided, use that instead.
|
||||
url_with_token = json_params.get('param_dict', {}).get("URL", "")
|
||||
if custom_token:
|
||||
input_urls = url_with_token.split('^')[0]
|
||||
token = custom_token
|
||||
else:
|
||||
input_urls, token = url_with_token.split('^')
|
||||
input_url_list = input_urls.split(",")
|
||||
|
||||
gs_client = GenomeSpaceClient(token=token)
|
||||
|
||||
for idx, input_url in enumerate(input_url_list):
|
||||
download_single_file(gs_client, input_url, json_params,
|
||||
primary_dataset=(idx == 0))
|
||||
|
||||
|
||||
def process_args(args):
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument('-p', '--json_parameter_file', type=str,
|
||||
help="JSON parameter file", required=True)
|
||||
parser.add_argument('-r', '--galaxy_root', type=str,
|
||||
help="Galaxy root dir", required=True)
|
||||
parser.add_argument('-c', '--data_conf', type=str,
|
||||
help="Galaxy data types conf file for mapping file types", required=True)
|
||||
parser.add_argument('-t', '--token', type=str,
|
||||
help="Optional OpenID/GenomeSpace token if not passed in as part of the URL as URLs^Token."
|
||||
" If none, the environment variable GS_TOKEN will be respected.", required=False)
|
||||
|
||||
args = parser.parse_args(args[1:])
|
||||
return args
|
||||
|
||||
|
||||
def main():
|
||||
args = process_args(sys.argv)
|
||||
download_from_genomespace_importer(args.json_parameter_file, args.galaxy_root, args.data_conf, args.token or os.environ.get("GS_TOKEN"))
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
sys.exit(main())
|
||||
|
||||
@@ -1,26 +1,36 @@
|
||||
<?xml version="1.0"?>
|
||||
<tool name="GenomeSpace Importer" id="genomespace_importer" tool_type="data_source" force_history_refresh="True" hidden="True" display_interface="False" require_login="True" version="0.0.2">
|
||||
<tool name="GenomeSpace Importer" id="genomespace_importer" require_login="False" version="0.0.5">
|
||||
<description> - receive data from GenomeSpace</description>
|
||||
<command interpreter="python">genomespace_importer.py
|
||||
--genomespace_site "prod"
|
||||
#assert $__user__, Exception( 'You must be logged in to use this tool.' )
|
||||
#set $username = $__user__.preferences.get( 'genomespace_username', None )
|
||||
#set $token = $__user__.preferences.get( 'genomespace_token', None )
|
||||
#assert None not in ( $username, $token ), Exception( 'You must associate a GenomeSpace OpenID with your account and log in with it.' )
|
||||
--username "${username}"
|
||||
--token "${token}"
|
||||
--json_parameter_file "${output_file1}"
|
||||
--genomespace_toolname="\${GENOMESPACE_TOOLNAME:-Galaxy}"
|
||||
</command>
|
||||
<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__
|
||||
]]></command>
|
||||
<!-- If using this tool through bioblend, the URL parameter should contain the path to the GenomeSpaceFile + the security token
|
||||
separated by a ^ as follows: GenomeSpaceFilePath^Token -->
|
||||
<inputs check_values="False">
|
||||
<!-- <param name="file_name" type="text" value="" /> -->
|
||||
<param name="URL" type="hidden" value="" />
|
||||
<param name="URL" type="genomespacefile" label="Choose Input File from GenomeSpace" select_type="FILE" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="auto" name="output_file1" />
|
||||
</outputs>
|
||||
<help>
|
||||
some help text here...
|
||||
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.
|
||||
|
||||
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.
|
||||
You can associate your OpenID credentials under the User Preferences panel.
|
||||
Click here_ to refresh your GenomeSpace token.
|
||||
|
||||
.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
|
||||
</help>
|
||||
<code file="genomespace_importer.py"/>
|
||||
<options sanitize="False" refresh="True"/>
|
||||
</tool>
|
||||
|
||||
@@ -0,0 +1,36 @@
|
||||
<?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">
|
||||
<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.' )
|
||||
$token
|
||||
</environment_variable>
|
||||
</environment_variables>
|
||||
<command interpreter="python">genomespace_importer.py
|
||||
#set $input_file = $URL.split("^")[0] if "^" in $URL else $URL
|
||||
|
||||
#assert $input_file, Exception( 'You must select a valid input file.' )
|
||||
--json_parameter_file '${output_file1}'
|
||||
--galaxy_root $__root_dir__
|
||||
--data_conf $__datatypes_config__
|
||||
</command>
|
||||
<!-- If using this tool through bioblend, the URL parameter should contain a comma separated list of GenomeSpace URLs -->
|
||||
<inputs check_values="False">
|
||||
<param name="URL" type="genomespacefile" label="Choose Input File from GenomeSpace" select_type="FILE" />
|
||||
</inputs>
|
||||
<outputs>
|
||||
<data format="auto" name="output_file1" />
|
||||
</outputs>
|
||||
<help>
|
||||
This tool is a variant of the genomespace_importer which behaves like a data_source and allows you to pull data from GenomeSpace.
|
||||
The URL parameter must contain a comma separated list of files to pull from GenomeSpace.
|
||||
The user must be logged into GenomeSpace through OpenID so that the authentication token can be obtained.
|
||||
You can associate your OpenID credentials under the User Preferences panel.
|
||||
Click here_ to refresh your GenomeSpace token.
|
||||
|
||||
.. _here: ${static_path}/../user/openid_auth?openid_provider=genomespace&auto_associate=True
|
||||
</help>
|
||||
<options sanitize="False" refresh="True"/>
|
||||
</tool>
|
||||
Reference in New Issue
Block a user