Merge branch 'devel_12.0.x' into devel_12.1.x

CHANGELOG

 minerva (12.1.0~beta.0) experimental; urgency=medium
-  * Small improvement: option to remove additional overlays generated by custom 
+  * Small improvement: option to remove additional overlays generated by custom
     semantic zoom
-  * Small improvement: 'Reduced modulation' edge was displayed differently in 
+  * Small improvement: 'Reduced modulation' edge was displayed differently in
     CellDesigner and Minerva
   * Small improvement: user-friendly documentation for plugin URL field
   * Small improvement: plugins have to access information about active submap
@@ -24,6 +24,17 @@ minerva (12.1.0~alpha.0) experimental; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 03 Aug 2018 10:00:00 +0200
 
+minerva (12.0.4) stable; urgency=medium
+  * Bug fix: CellDesigner modifications that are drawn as reaction are handled
+    properly (like catalysis)
+  * Bug fix: Removing of guest (anonymous) account is forbidden - system is
+    unstable after removing such user
+  * Bug fix: Tair database moved to https
+  * Bug fix: Taxnomy database changed html output that resulted in problems
+    with resolving species name to the id
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 12 Sep 2018 17:00:00 +0200
+
 minerva (12.0.3) stable; urgency=medium
   * Bug fix: SBML model annotations caused errors on upload
   * Bug fix: Export of some models to SBML didn't work properly

annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java

@@ -108,7 +108,7 @@ public class TaxonomyBackend extends CachableInterface implements IExternalServi
 			queryTerm = URLEncoder.encode(queryTerm, "UTF-8");
 			String url = "https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?lvl=0&name=" + queryTerm;
 			String page = getWebPageContent(url);
-			Pattern idPattern = Pattern.compile("<em>Taxonomy ID: </em>([0-9]+)");
+			Pattern idPattern = Pattern.compile("Taxonomy ID: ([0-9]+)");
 			Matcher matcher = idPattern.matcher(page);
 			if (!matcher.find()) {
 				logger.warn("Unknown organism: " + term);

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java

@@ -107,7 +107,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
 	 * @return URL to TAIR page about the TAIR entry
 	 */
 	private String getTairUrl(String tairId) {
-		return "http://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
+		return "https://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
 	}
 
 	/**

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

@@ -333,7 +333,11 @@ UsersAdminPanel.prototype.userToTableRow = function (user, row) {
   }
 
   row[5] = "<button name='showEditDialog' data='" + user.getLogin() + "'><i class='fa fa-edit' style='font-size:17px'></i></button>";
-  row[6] = "<button name='removeUser' data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
+  var disabled = "";
+  if (user.getLogin() === "anonymous") {
+    disabled = " disabled ";
+  }
+  row[6] = "<button name='removeUser' " + disabled + " data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
 
   return row;
 };

persist/src/db/12.0.4/fix_db_20180830.sql

+-- empty file to force directory to be commited to git repo

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

@@ -36,6 +36,8 @@ public abstract class BaseController {
       return createErrorResponse("Object not found.", e.getMessage(), new HttpHeaders(), HttpStatus.NOT_FOUND);
     } else if (e instanceof ObjectExistsException) {
       return createErrorResponse("Object already exists.", e.getMessage(), new HttpHeaders(), HttpStatus.CONFLICT);
+    } else if (e instanceof OperationNotAllowedException) {
+      return createErrorResponse("Operation not allowed.", e.getMessage(), new HttpHeaders(), HttpStatus.METHOD_NOT_ALLOWED);
     } else if (e instanceof QueryException) {
       logger.error(e, e);
       return createErrorResponse("Query server error.", e.getMessage(), new HttpHeaders(), HttpStatus.BAD_REQUEST);

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

+package lcsb.mapviewer.api;
+
+/**
+ * Thrown when API operation is not allowed, but operation is valid. This can
+ * happen when user tries to remove default map.
+ * 
+ * @author Piotr Gawron
+ *
+ */
+public class OperationNotAllowedException extends QueryException {
+
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default constructor.
+   * 
+   * @param message
+   *          error message
+   */
+  public OperationNotAllowedException(String message) {
+    super(message);
+  }
+
+  /**
+   * Constructor with error message and parent exception.
+   * 
+   * @param message
+   *          error message
+   * @param reason
+   *          parent exception that caused this one
+   */
+  public OperationNotAllowedException(String message, Exception reason) {
+    super(message, reason);
+  }
+
+}

rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java

@@ -31,6 +31,7 @@ import org.springframework.util.MultiValueMap;
 import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.ObjectExistsException;
 import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.OperationNotAllowedException;
 import lcsb.mapviewer.api.QueryException;
 import lcsb.mapviewer.api.projects.models.publications.PublicationsRestImpl;
 import lcsb.mapviewer.commands.ClearColorModelCommand;
@@ -740,7 +741,7 @@ public class ProjectRestImpl extends BaseRestImpl {
       throws SecurityException, QueryException {
     Project project = getProjectService().getProjectByProjectId(projectId, token);
     if (getConfigurationService().getConfigurationValue(ConfigurationElementType.DEFAULT_MAP).equals(project.getProjectId())) {
-      throw new QueryException("You cannot remove default map");
+      throw new OperationNotAllowedException("You cannot remove default map");
     }
     getProjectService().removeProject(project, path, true, token);
     return getProject(projectId, token);

rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java

@@ -14,7 +14,9 @@ import org.springframework.util.MultiValueMap;
 
 import lcsb.mapviewer.api.BaseRestImpl;
 import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.OperationNotAllowedException;
 import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.MiriamType;
@@ -622,7 +624,9 @@ public class UserRestImpl extends BaseRestImpl {
       throw new SecurityException("Access denied");
     }
     if (user == null) {
-      throw new QueryException("user doesn't exists");
+      throw new ObjectNotFoundException("user doesn't exists");
+    } else if (user.getLogin().equals(Configuration.ANONYMOUS_LOGIN)) {
+      throw new OperationNotAllowedException("guest account cannot be removed");
     }
     getUserService().deleteUser(user);
     return okStatus();