Merge branch 'devel_12.2.x'

CHANGELOG

@@ -38,6 +38,21 @@ minerva (12.3.0~alpha.0) unstable; urgency=low
   * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
     slightly separated from target phenotype (#664)
 
+minerva (12.2.1) stable; urgency=medium
+  * Bug fix: export of reaction colorsi in SBML is properly encoded (COPASI can
+    read colors properly) (#744)
+  * Bug fix: removing active plugin didn't switch plugin tab to the next loaded
+    plugin (#757)
+  * Bug fix: closed submap will not be reopened after page refresh (#763)
+  * Bug fix: comment remove button is disabled for users without proper
+    privileges (#766)
+  * Bug fix: invalid pubmed identifier could break clicking on element
+    containing it (#764, #765, #769)
+  * Bug fix: cache for API queries is explicitly disabled - some queries could
+    be mistakenly cached and the system behaviour might get unstable (#771)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 1 Apr 2019 17:00:00 +0200
+
 minerva (12.2.0) stable; urgency=medium
   * Feature: bug report utility
   * Feature: url GET parameters support all kind of search and selected overlays

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -296,6 +296,7 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     renderInformation.addLocalStyle(style);
     ColorDefinition color = getColorDefinition(node.getLine().getColor());
     style.getGroup().setStroke(color.getId());
+    style.getGroup().setFill(color.getId());
     style.getGroup().setStrokeWidth(node.getLine().getWidth());
     style.getGroup().setStrokeDashArray(strokeToArray(node.getLine().getType().getStroke()));
 

frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js

@@ -4,6 +4,7 @@ var AbstractGuiElement = require('../AbstractGuiElement');
 
 var Functions = require('../../Functions');
 var GuiConnector = require('../../GuiConnector');
+var PrivilegeType = require('../../map/data/PrivilegeType');
 // noinspection JSUnusedLocalSymbols
 var logger = require('../../logger');
 
@@ -16,7 +17,7 @@ var xss = require('xss');
  * @param {Object} params
  * @param {HTMLElement} params.element
  * @param {Configuration} params.configuration
- * @param {Project} [params.project]
+ * @param {Project} params.project
  * @param {ServerConnector} [params.serverConnector]
  *
  * @constructor
@@ -93,7 +94,7 @@ CommentsAdminPanel.prototype._createGui = function () {
  */
 CommentsAdminPanel.prototype.init = function () {
   var self = this;
-  return self.refreshProjects();
+  return self.refreshComments();
 };
 
 /**
@@ -112,6 +113,12 @@ CommentsAdminPanel.prototype.refreshComments = function () {
       data.push(self.commentToTableRow(comments[i]));
     }
     dataTable.clear().rows.add(data).draw();
+    return self.getServerConnector().getLoggedUser();
+  }).then(function (user) {
+    var type = self.getConfiguration().getPrivilegeType(PrivilegeType.EDIT_COMMENTS_PROJECT);
+    if (!user.hasPrivilege(type, self.getProject().getId())) {
+      $("[name='removeComment']", self.getElement()).attr("disabled", true);
+    }
   });
 };
 

frontend-js/src/main/js/gui/admin/EditProjectDialog.js

@@ -33,6 +33,7 @@ var xss = require('xss');
 function EditProjectDialog(params) {
   AbstractGuiElement.call(this, params);
   var self = this;
+  guiUtils.setConfiguration(params.configuration);
   self.setConfiguration(params.configuration);
   self.registerListenerType("onSave");
   $(self.getElement()).addClass("minerva-edit-project-dialog");

frontend-js/src/main/js/gui/leftPanel/GuiUtils.js

@@ -1177,6 +1177,13 @@ GuiUtils.prototype.removeTab = function (abstractGuiElement, panel) {
   } else {
     logger.warn("Cannot find tab for panel: " + panel);
   }
+  var isActive = $(".nav-tabs > li.active", $(abstractGuiElement.getElement())).length > 0;
+  if (!isActive) {
+    var links = $(".nav-tabs > li", $(abstractGuiElement.getElement()));
+    if (links.length > 0) {
+      $("a", $(links[0])).click();
+    }
+  }
 };
 
 /**

frontend-js/src/main/js/map/CustomMap.js

@@ -42,6 +42,7 @@ function CustomMap(options) {
   this.registerListenerType("onHideOverlay");
   this.registerListenerType("onBackgroundOverlayChange");
   this.registerListenerType("onSubmapOpen");
+  this.registerListenerType("onSubmapClose");
 
   // @type {boolean[]}
   this._selectedOverlays = [];
@@ -134,9 +135,14 @@ CustomMap.prototype.init = function () {
  * Create submaps.
  */
 CustomMap.prototype.createSubmaps = function () {
-  this.submaps = [];
-  for (var i = 1; i < this.getProject().getModels().length; i++) {
-    this.submaps.push(new Submap(this, this.getProject().getModels()[i]));
+  var self = this;
+  self.submaps = [];
+  for (var i = 1; i < self.getProject().getModels().length; i++) {
+    var submap = new Submap(self, self.getProject().getModels()[i]);
+    submap.addListener("onClose", function (event) {
+      return self.callListeners("onSubmapClose", {mapId: event.object.getId()});
+    });
+    self.submaps.push(submap);
   }
 };
 

frontend-js/src/main/js/map/data/PrivilegeType.js

@@ -37,6 +37,8 @@ PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
 PrivilegeType.ADD_MAP = 'ADD_MAP';
 PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
 PrivilegeType.LAYOUT_MANAGEMENT = 'LAYOUT_MANAGEMENT';
+PrivilegeType.EDIT_COMMENTS_PROJECT = 'EDIT_COMMENTS_PROJECT';
+
 
 /**
  *

frontend-js/src/main/js/minerva.js

@@ -372,6 +372,9 @@ function addUrlChangeListenersToCustomMap(customMap) {
   customMap.addListener("onSubmapOpen", function (event) {
     GuiConnector.setUrlParam("submap", event.arg.mapId.toString());
   });
+  customMap.addListener("onSubmapClose", function (event) {
+    GuiConnector.setUrlParam("submap", undefined);
+  });
   var onCenterChangedHandler = function (event) {
     if (event.object.getId() !== customMap.getId()) {
       GuiConnector.setUrlParam("submap", event.object.getId().toString());

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

@@ -14,11 +14,13 @@ var assert = chai.assert;
 
 describe('CommentsAdminPanel', function () {
   function createDialog() {
-    return ServerConnector.getConfiguration().then(function (configuration) {
+    return ServerConnector.getProject().then(function (project) {
       return new CommentsAdminPanel({
         element: testDiv,
-        configuration: configuration,
-        customMap: null
+        configuration: helper.getConfiguration(),
+        customMap: null,
+        project: project,
+        serverConnector: ServerConnector
       });
     });
   }
@@ -75,4 +77,29 @@ describe('CommentsAdminPanel', function () {
       });
     });
   });
+
+  describe('remove comment', function () {
+    it('admin can remove', function () {
+      helper.loginAsAdmin();
+      var dialog;
+      return createDialog().then(function (result) {
+        dialog = result;
+        return dialog.init();
+      }).then(function () {
+        assert.ok($("[name='removeComment']").is(':enabled'));
+        return dialog.destroy();
+      });
+    });
+    it('anonymous cannot remove', function () {
+      var dialog;
+      return createDialog().then(function (result) {
+        dialog = result;
+        return dialog.init();
+      }).then(function () {
+        assert.ok($("[name='removeComment']").is(':disabled'));
+        return dialog.destroy();
+      });
+    });
+  });
+
 });

frontend-js/src/test/js/minerva-test.js

@@ -6,6 +6,7 @@ var Promise = require("bluebird");
 
 var minerva = require('../../main/js/minerva');
 var ConfigurationType = require('../../main/js/ConfigurationType');
+var GuiConnector = require('../../main/js/GuiConnector');
 var SecurityError = require('../../main/js/SecurityError');
 var ServerConnectorMock = require('./ServerConnector-mock');
 var Point = require('../../main/js/map/canvas/Point');
@@ -340,7 +341,7 @@ describe('minerva global', function () {
   it('plugin onFocus functionality', function () {
     helper.setUrl("http://test/?search=s1");
 
-    var globalObject, plugin, callbackCalled=false;
+    var globalObject, plugin, callbackCalled = false;
     return ServerConnectorMock.getProject().then(function (project) {
       var options = helper.createCustomMapOptions(project);
       plugin = new ProxyAccessPlugin();
@@ -361,4 +362,29 @@ describe('minerva global', function () {
   });
 
 
+  describe("close submap", function () {
+    it("check if url parameters changed", function () {
+      var data;
+      var map;
+      var submapId = 16729;
+      var submapParameter;
+      var projectId = "complex_model_with_submaps";
+      return ServerConnectorMock.getProject(projectId).then(function (project) {
+        var options = helper.createCustomMapOptions(project);
+        options.setDebug(true);
+        return minerva.create(options);
+      }).then(function (result) {
+        data = result;
+        map = result.customMap;
+        return map.openSubmap(submapId);
+      }).then(function () {
+        submapParameter = GuiConnector.getParams["submap"];
+        return map.getSubmapById(submapId).close();
+      }).then(function () {
+        assert.notEqual(GuiConnector.getParams["submap"], submapParameter, "Submap parameter should change after submap was closed");
+        return data.destroy();
+      })
+    });
+  });
+
 });

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -19,6 +19,7 @@ import javax.xml.transform.TransformerFactoryConfigurationError;
 import javax.xml.transform.stream.StreamResult;
 import javax.xml.transform.stream.StreamSource;
 
+import org.apache.commons.lang3.math.NumberUtils;
 import org.apache.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.io.ClassPathResource;
@@ -121,11 +122,15 @@ public abstract class BaseRestImpl {
         }
       }
       if (MiriamType.PUBMED.equals(annotation.getDataType())) {
-        try {
-          Article article = pubmedParser.getPubmedArticleById(annotation.getResource());
-          result.put("article", article);
-        } catch (PubmedSearchException e) {
-          logger.error("Problem with accessing info about pubmed", e);
+        if (NumberUtils.isDigits(annotation.getResource())) {
+          try {
+            Article article = pubmedParser.getPubmedArticleById(annotation.getResource());
+            result.put("article", article);
+          } catch (PubmedSearchException e) {
+            logger.error("Problem with accessing info about pubmed", e);
+          }
+        } else {
+          logger.error("Invalid pubmed identifier: " + annotation.getResource());
         }
       }
       result.put("type", annotation.getDataType().name());

rest-api/src/test/java/lcsb/mapviewer/api/BaseRestImplTest.java

@@ -84,4 +84,21 @@ public class BaseRestImplTest extends RestTestFunctions {
     }
   }
 
+  @Test
+  public void testCreateAnnotationWithNonNumericValues() throws Exception {
+    BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
+    controller.setMiriamConnector(mc);
+    controller.setPubmedParser(pubmedParser);
+    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED, "28255955PG"));
+    assertNotNull(response);
+  }
+
+  @Test
+  public void testCreateAnnotationWithEmptyValue() throws Exception {
+    BaseRestImpl controller = Mockito.mock(BaseRestImpl.class, CALLS_REAL_METHODS);
+    controller.setMiriamConnector(mc);
+    controller.setPubmedParser(pubmedParser);
+    Map<String, Object> response = controller.createAnnotation(new MiriamData(MiriamType.PUBMED, ""));
+    assertNotNull(response);
+  }
 }

web/src/main/java/lcsb/mapviewer/web/bean/utils/ApiAccessControlFilter.java

@@ -13,7 +13,7 @@ import javax.servlet.http.HttpServletResponse;
 import org.apache.log4j.Logger;
 
 /**
- * This filter enables x-frames from another domain if necessary.
+ * This filter disables caching for API queries.
  * 
  * @author Piotr Gawron
  *
@@ -33,7 +33,12 @@ public class ApiAccessControlFilter implements Filter {
   public void doFilter(ServletRequest req, ServletResponse res, FilterChain chain)
       throws IOException, ServletException {
     HttpServletResponse response = (HttpServletResponse) res;
+    //caching on Safari
     response.addHeader("Vary", "*");
+    // generic cache prevent mechanism
+    response.addHeader("Cache-Control", "no-cache, no-store, must-revalidate");
+    response.addHeader("Pragma", "no-cache");
+    response.addHeader("Expires", "0");
     chain.doFilter(req, response);
   }