diff --git a/CHANGELOG b/CHANGELOG
index ea66d7c7d92a1daa90d8d4ad57564f10d91ef139..96e84cde4cb6ce660be1cf998ec271dd98fd36d8 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,7 +1,7 @@
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
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
index 22962ff9eb49703b93d97d6d3916cbba831bd507..5ab139112cd4630eb1ea13dcd46443ab1829a8ef 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/TaxonomyBackend.java
+++ b/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);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index 91850ea93b6edd63f90aa6c0f7d81089a4088880..0d52689155610ed6bed70551d3d05a54bd348478 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/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;
}
/**
diff --git a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
index 5332f39c23749f849e7f56e5676dd83552bb6201..b5bb5b2b8804c69480bc545357cd8a3ce3c15fa4 100644
--- a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
+++ b/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;
};
diff --git a/persist/src/db/12.0.4/fix_db_20180830.sql b/persist/src/db/12.0.4/fix_db_20180830.sql
new file mode 100644
index 0000000000000000000000000000000000000000..a33b6ad89d4881c84fb355b8c56d309760e66b70
--- /dev/null
+++ b/persist/src/db/12.0.4/fix_db_20180830.sql
@@ -0,0 +1 @@
+-- empty file to force directory to be commited to git repo
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
index d93c477c3d665b6f1da088aa16b316806ebb2985..7bc7a6182d8300741589675c677f06342c3be029 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseController.java
+++ b/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);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/OperationNotAllowedException.java b/rest-api/src/main/java/lcsb/mapviewer/api/OperationNotAllowedException.java
new file mode 100644
index 0000000000000000000000000000000000000000..b013109551afbd0ef1f8dc1d748cd429bc2684a8
--- /dev/null
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/OperationNotAllowedException.java
@@ -0,0 +1,39 @@
+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);
+ }
+
+}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
index 317f1afedeffa7d6e665dae8249f84cee12801df..b0d4cee6b5a1daaa65835f322cb113bcb8e89719 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/ProjectRestImpl.java
+++ b/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);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index 069b94fa576559ebd0505b02c523496e46c3f0a5..43398352563d06ba223e5fb2396f8f39f72629be 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/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();