fixed log config loading

converter-SBGNML/src/main/resources/log4j2.properties

-rootLogger.level = INFO
-appenders = console
-
-appender.console.type = Console
-appender.console.name = STDOUT
-appender.console.layout.type = PatternLayout
-appender.console.layout.pattern = %d %5p [%t] (%F:%L) - %m%n
-
-rootLogger.appenderRefs = console
-
-rootLogger.appenderRef.console.ref = STDOUT
-
-logger.minerva.name = lcsb
-logger.minerva.level = debug
-logger.minerva-persist.name = lcsb.mapviewer.persist.DbUtils
-logger.minerva-persist.level = info
-logger.minerva-cache.name = lcsb.mapviewer.annotation.cache
-logger.minerva-cache.level = info
-logger.minerva-comparator.name = lcsb.mapviewer.common.Comparator
-logger.minerva-comparator.level = info
-logger.minerva-model.name = lcsb.mapviewer.model
-logger.minerva-model.level = info
-
-logger.springframework.name = org.springframework
-logger.springframework.level = warn
-
-logger.hibernate.name = org.hibernate
-logger.hibernate.level = warn

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

@@ -6,7 +6,6 @@ import java.util.Map;
 
 import javax.servlet.ServletContext;
 
-import lcsb.mapviewer.model.security.Privilege;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;

web/src/main/java/lcsb/mapviewer/web/config/WebAppInitializer.java

@@ -5,23 +5,13 @@ import lcsb.mapviewer.api.SpringRestApiConfig;
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.persist.SpringPersistConfig;
 import lcsb.mapviewer.services.SpringServiceConfig;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
-import org.apache.logging.log4j.core.LoggerContext;
-import org.springframework.security.web.session.HttpSessionEventPublisher;
-import org.springframework.web.context.ContextLoaderListener;
-import org.springframework.web.context.request.RequestContextListener;
-import org.springframework.web.context.support.AnnotationConfigWebApplicationContext;
 import org.springframework.web.servlet.support.AbstractAnnotationConfigDispatcherServletInitializer;
 
 import javax.servlet.*;
-import java.net.URL;
 import java.util.EnumSet;
 
 public class WebAppInitializer extends AbstractAnnotationConfigDispatcherServletInitializer {
 
-  private Logger logger = LogManager.getLogger(WebAppInitializer.class);
-
   @Override
   protected Class<?>[] getRootConfigClasses() {
     return new Class[] {
@@ -47,7 +37,6 @@ public class WebAppInitializer extends AbstractAnnotationConfigDispatcherServlet
 
   @Override
   public void onStartup(ServletContext container) throws ServletException {
-    // FIXME: Does this work? Do we need it?
     assert container.setInitParameter("com.sun.faces.enableMissingResourceLibraryDetection", "true");
     assert container.setInitParameter("primefaces.THEME", "home");
     assert container.setInitParameter("javax.faces.FACELETS_BUFFER_SIZE", "65535");
@@ -57,19 +46,6 @@ public class WebAppInitializer extends AbstractAnnotationConfigDispatcherServlet
     assert container.setInitParameter("javax.faces.DEFAULT_SUFFIX", ".xhtml");
     assert container.setInitParameter("javax.faces.FACELETS_SKIP_COMMENTS", "true");
 
-    // FIXME: Why does this not work?
-//    assert container.setInitParameter("log4jConfigLocation", "/WEB-INF/resources/log4j2.properties");
-
-    // Workaround for above
-    String file = "/WEB-INF/resources/log4j2.properties";
-    try {
-      URL configStream = container.getResource(file);
-      LoggerContext context = (org.apache.logging.log4j.core.LoggerContext) org.apache.logging.log4j.LogManager.getContext(false);
-      context.setConfigLocation(configStream.toURI());
-    } catch (Exception e) {
-      logger.error("Problem with loading log4j configuration: " + file);
-    }
-
     SessionCookieConfig cookieConfig = container.getSessionCookieConfig();
     cookieConfig.setName(Configuration.AUTH_TOKEN);
     cookieConfig.setHttpOnly(false);