Merge remote-tracking branch 'origin/master' into...

Merge remote-tracking branch 'origin/master' into 911-remove-additional-options-in-copy-from-selecting-annotators-min13-1

CHANGELOG

@@ -30,7 +30,9 @@ minerva (14.0.0~beta.0) unstable; urgency=low
   * Bug fix: creating project with too long name hung (#916)
   * Bug fix: too long user login thrown an error (#915)
   * Bug fix: width of info window adjust to the content size (#903)
-  * Bug fix: list of types when copying from annotators contains only types 
+  * Bug fix: when uploading generic data overlay the type was not updated in
+    case the type was not specified in the input file (#906)
+  * Bug fix: list of types when copying from annotators contains only types
     that are selectable in the dialog (#911)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 21 Aug 2019 21:00:00 +0200

frontend-js/src/main/js/gui/AddOverlayDialog.js

@@ -146,7 +146,6 @@ AddOverlayDialog.prototype.processFile = function (file) {
           var overlay = overlayParser.parse(evt.target.result);
           var nameInput = $("[name='overlay-name']", self.getElement())[0];
           var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
-          var typeSelect = $("[name='overlay-type']", self.getElement());
           if (overlay.getName() !== undefined) {
             nameInput.value = overlay.getName();
           } else {
@@ -163,9 +162,13 @@ AddOverlayDialog.prototype.processFile = function (file) {
           if (overlay.getDescription() !== undefined) {
             descriptionInput.value = overlay.getDescription();
           }
+
           if (overlay.getType() !== undefined) {
-            typeSelect.val(overlay.getType());
+            self.setType(overlay.getType());
+          } else {
+            self.setType("GENERIC");
           }
+
           if (overlayParser.containsMixedNewLineCharacters(evt.target.result)) {
             GuiConnector.warn("Selected file contains new line characters from different operating systems " +
               "(MAC/Windows/Linux). This might cause confusion when reading the file in the editor later on.")
@@ -187,7 +190,7 @@ AddOverlayDialog.prototype.processFile = function (file) {
 
 /**
  *
- * @param {string} fileContent
+ * @param {?null|string} fileContent
  */
 AddOverlayDialog.prototype.setFileContent = function (fileContent) {
   if (typeof fileContent === 'string' || fileContent instanceof String) {
@@ -324,4 +327,24 @@ AddOverlayDialog.prototype.open = function () {
   $(div).dialog("open");
 };
 
+/**
+ *
+ * @param {string} type
+ */
+AddOverlayDialog.prototype.setType = function (type) {
+  var self = this;
+  if (type !== undefined) {
+    var typeSelect = $("[name='overlay-type']", self.getElement());
+    typeSelect.val(type);
+  }
+};
+
+/**
+ *
+ * @return {string}
+ */
+AddOverlayDialog.prototype.getType = function () {
+  var self = this;
+  return $("[name='overlay-type']", self.getElement()).val();
+};
 module.exports = AddOverlayDialog;

frontend-js/src/test/js/gui/AddOverlayDialog-test.js

@@ -10,6 +10,7 @@ var chai = require('chai');
 var assert = chai.assert;
 var logger = require('../logger');
 
+
 describe('AddOverlayDialog', function () {
 
   it('addOverlay', function () {
@@ -57,4 +58,25 @@ describe('AddOverlayDialog', function () {
     });
   });
 
+  describe('processFile', function () {
+    it('set default type', function () {
+      var dialog;
+      return ServerConnector.getProject().then(function (project) {
+        dialog = createDialog(project);
+        return dialog.init();
+      }).then(function () {
+
+        dialog.setType("GENETIC_VARIANT");
+        assert.equal("GENETIC_VARIANT", dialog.getType());
+
+        return helper.stringToBlob("s1\n");
+      }).then(function (file) {
+        return dialog.processFile(file);
+      }).then(function () {
+        assert.equal("GENERIC", dialog.getType());
+      });
+    });
+  });
+
+
 });

frontend-js/src/test/js/gui/admin/AddProjectDialog-test.js

@@ -79,18 +79,10 @@ describe('AddProjectDialog', function () {
 
     it('sbml file', function () {
       var dialog = createDialog();
-      var file;
-
-      return new Promise(function (resolve, reject) {
-        toBlob(fs.createReadStream('testFiles/map/sbml.xml'), function (err, blob) {
-          if (err) return reject(err.message);
-          file = blob;
-          file.name = "sbml.xml";
-          resolve(blob);
-        })
-      }).then(function () {
-        return dialog.init();
-      }).then(function () {
+
+      return dialog.init().then(function () {
+        return helper.fileToBlob('testFiles/map/sbml.xml');
+      }).then(function (file) {
         return dialog.callListeners("onFileUpload", file);
       }).then(function () {
         var converter = dialog.getConverter();
@@ -100,7 +92,6 @@ describe('AddProjectDialog', function () {
     });
     it('invalid zip', function () {
       var dialog = createDialog();
-      var file;
 
       var buf = fs.readFileSync("testFiles/map/invalid-project.zip");
       buf.name = "invalid-project.zip";
@@ -114,18 +105,10 @@ describe('AddProjectDialog', function () {
     });
     it('CellDesigner file', function () {
       var dialog = createDialog();
-      var file;
-
-      return new Promise(function (resolve, reject) {
-        toBlob(fs.createReadStream('testFiles/map/cell_designer.xml'), function (err, blob) {
-          if (err) return reject(err.message);
-          file = blob;
-          file.name = "sbml.xml";
-          resolve(blob);
-        })
-      }).then(function () {
-        return dialog.init();
-      }).then(function () {
+
+      return dialog.init().then(function () {
+        return helper.fileToBlob('testFiles/map/cell_designer.xml');
+      }).then(function (file) {
         return dialog.callListeners("onFileUpload", file);
       }).then(function () {
         var converter = dialog.getConverter();

frontend-js/src/test/js/helper.js

 "use strict";
 
+var Readable = require('stream').Readable;
+var toBlob = require('stream-to-blob');
+
 require("./mocha-config");
 var $ = require('jquery');
 
@@ -643,6 +646,39 @@ Helper.prototype.createGoogleCanvas = function () {
   });
 };
 
+/**
+ *
+ * @param {string} content
+ * @return {Promise<Blob>}
+ */
+Helper.prototype.stringToBlob = function (content) {
+  var stream = new Readable;
+  stream.push(content);
+  stream.push(null);
+
+  return new Promise(function (resolve, reject) {
+    toBlob(stream, function (err, blob) {
+      if (err) return reject(err.message);
+      blob.name = "test.txt";
+      resolve(blob);
+    })
+  });
+};
+
+/**
+ *
+ * @param {string} path
+ * @return {Promise<Blob>}
+ */
+Helper.prototype.fileToBlob = function (path) {
+  var self = this;
+  return self.readFile(path).then(function (content) {
+    return self.stringToBlob(content);
+  }).then(function (blob) {
+    blob.name = require('path').basename(path);
+    return blob;
+  });
+};
 /**
  *
  * @type {number}