project errors and warnings extracted and moved to separate table

model/src/main/java/lcsb/mapviewer/model/Project.java

@@ -7,12 +7,9 @@ import javax.persistence.*;
 import javax.persistence.Entity;
 import javax.persistence.OrderBy;
 
-import org.apache.logging.log4j.core.LogEvent;
 import org.hibernate.annotations.*;
 import org.hibernate.annotations.CascadeType;
 
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.graphics.MapCanvasType;
 import lcsb.mapviewer.model.map.MiriamData;
@@ -61,10 +58,9 @@ public class Project implements Serializable {
    */
   private double progress = 0;
 
-  private String errors = null;
-
-  @Column(columnDefinition = "TEXT")
-  private String warnings;
+  @Cascade({ CascadeType.ALL })
+  @OneToMany(mappedBy = "project", orphanRemoval = true)
+  private Set<ProjectLogEntry> logEntries = new HashSet<>();
 
   @Enumerated(EnumType.STRING)
   private MapCanvasType mapCanvasType = MapCanvasType.OPEN_LAYERS;
@@ -171,14 +167,6 @@ public class Project implements Serializable {
     this.models = models;
   }
 
-  public String getErrors() {
-    return errors;
-  }
-
-  public void setErrors(String errors) {
-    this.errors = errors;
-  }
-
   public String getDirectory() {
     return directory;
   }
@@ -211,62 +199,6 @@ public class Project implements Serializable {
     this.organism = organism;
   }
 
-  public void addWarning(String warning) {
-    if (warning.trim().contains("\n")) {
-      throw new InvalidArgumentException("Warning must be one line of text");
-    }
-    if (warning.trim().equals("")) {
-      return;
-    }
-    if (warnings == null) {
-      warnings = warning.trim();
-    } else {
-      warnings = warnings + "\n" + warning.trim();
-    }
-  }
-
-  public List<String> getWarnings() {
-    List<String> result = new ArrayList<>();
-    if (warnings == null) {
-      return result;
-    }
-    String[] warningsArray = warnings.split("\n");
-    for (String string : warningsArray) {
-      result.add(string);
-    }
-    return result;
-  }
-
-  public void addWarnings(List<String> warnings) {
-    StringBuilder sb = new StringBuilder("");
-    if (this.warnings != null) {
-      sb.append(this.warnings);
-    }
-    for (String string : warnings) {
-      if (string.trim().equals("")) {
-        continue;
-      }
-      if (string.contains("\n")) {
-        throw new InvalidArgumentException("Warning must be one line of text, but found:\n" + string);
-      }
-      if (sb.length() > 0) {
-        sb.append("\n");
-      }
-      sb.append(string.trim());
-    }
-    if (sb.length() != 0) {
-      this.warnings = sb.toString();
-    }
-  }
-
-  public void addLoggingInfo(MinervaLoggerAppender appender) {
-    List<String> warnings = new ArrayList<>();
-    for (LogEvent event : appender.getWarnings()) {
-      warnings.add(event.getMessage().getFormattedMessage().replaceAll("\n", "_NEW_LINE_"));
-    }
-    addWarnings(warnings);
-  }
-
   public boolean isSbgnFormat() {
     return sbgnFormat;
   }
@@ -400,4 +332,24 @@ public class Project implements Serializable {
     this.owner = owner;
   }
 
+  public Set<ProjectLogEntry> getLogEntries() {
+    return logEntries;
+  }
+
+  public void setLogEntries(Set<ProjectLogEntry> logEntries) {
+    this.logEntries = logEntries;
+  }
+
+  public void addLogEntry(ProjectLogEntry entry) {
+    logEntries.add(entry);
+    entry.setProject(this);
+
+  }
+
+  public void addLogEntries(Set<ProjectLogEntry> createLogEntries) {
+    for (ProjectLogEntry projectLogEntry : createLogEntries) {
+      addLogEntry(projectLogEntry);
+    }
+  }
+
 }

model/src/main/java/lcsb/mapviewer/model/ProjectLogEntry.java

+package lcsb.mapviewer.model;
+
+import java.io.Serializable;
+
+import javax.persistence.*;
+
+@Entity
+public class ProjectLogEntry implements Serializable {
+
+  private static final long serialVersionUID = 1L;
+
+  @Id
+  @GeneratedValue(strategy = GenerationType.IDENTITY)
+  private int id;
+
+  @ManyToOne(optional = false)
+  private Project project;
+
+  @Column(nullable = false)
+  private String severity;
+
+  @Column(nullable = false)
+  private String type;
+
+  private String objectIdentifier;
+
+  private String objectClass;
+
+  private String mapName;
+
+  @Column(nullable = false)
+  private String content;
+
+  public ProjectLogEntry() {
+
+  }
+
+  public String getContent() {
+    return content;
+  }
+
+  public void setContent(String content) {
+    this.content = content;
+  }
+
+  public String getMapName() {
+    return mapName;
+  }
+
+  public void setMapName(String mapName) {
+    this.mapName = mapName;
+  }
+
+  public String getObjectClass() {
+    return objectClass;
+  }
+
+  public void setObjectClass(String objectClass) {
+    this.objectClass = objectClass;
+  }
+
+  public String getObjectIdentifier() {
+    return objectIdentifier;
+  }
+
+  public void setObjectIdentifier(String objectIdentifier) {
+    this.objectIdentifier = objectIdentifier;
+  }
+
+  public String getSeverity() {
+    return severity;
+  }
+
+  public void setSeverity(String severity) {
+    this.severity = severity;
+  }
+
+  public String getType() {
+    return type;
+  }
+
+  public void setType(String type) {
+    this.type = type;
+  }
+
+  public Project getProject() {
+    return project;
+  }
+
+  public void setProject(Project project) {
+    this.project = project;
+  }
+
+}

model/src/test/java/lcsb/mapviewer/model/ProjectTest.java

@@ -12,8 +12,6 @@ import org.junit.*;
 
 import lcsb.mapviewer.ModelTestFunctions;
 import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.model.*;
@@ -89,9 +87,6 @@ public class ProjectTest extends ModelTestFunctions {
     project.setModels(models);
     assertEquals(models, project.getModels());
 
-    project.setErrors(errors);
-    assertEquals(errors, project.getErrors());
-
     project.setDirectory(directory);
     assertEquals(directory, project.getDirectory());
 
@@ -117,80 +112,4 @@ public class ProjectTest extends ModelTestFunctions {
     assertEquals(creationDate, project.getCreationDate());
   }
 
-  @Test(expected = InvalidArgumentException.class)
-  public void testAddCreationWarning() {
-    Project md = new Project();
-    md.addWarning("text\ntext");
-  }
-
-  @Test
-  public void testAddCreationWarning2() {
-    Project md = new Project();
-    md.addWarning("");
-    List<String> warnings = md.getWarnings();
-    assertEquals(0, warnings.size());
-  }
-
-  @Test
-  public void testAddCreationWarning3() {
-    Project md = new Project();
-    md.addWarning("xqw");
-    List<String> warnings = md.getWarnings();
-    assertEquals(1, warnings.size());
-    assertEquals("xqw", warnings.get(0));
-
-    md.addWarning("WER");
-    warnings = md.getWarnings();
-    assertEquals(2, warnings.size());
-    assertEquals("WER", warnings.get(1));
-  }
-
-  @Test
-  public void testAddCreationWarnings() {
-    List<String> warnings = new ArrayList<>();
-    warnings.add("xqw");
-    warnings.add("aso");
-    warnings.add("");
-    Project project = new Project();
-    project.addWarnings(warnings);
-
-    project.addWarning("WER");
-    warnings = project.getWarnings();
-    assertEquals(3, warnings.size());
-    assertEquals("aso", warnings.get(1));
-
-    project.addWarnings(warnings);
-    warnings = project.getWarnings();
-    assertEquals(6, warnings.size());
-    assertEquals("aso", warnings.get(1));
-  }
-
-  @Test(expected = InvalidArgumentException.class)
-  public void testAddCreationWarnings2() {
-    List<String> warnings = new ArrayList<>();
-    warnings.add("xqw\nwer\nt");
-    Project md = new Project();
-    md.addWarnings(warnings);
-  }
-
-  @Test
-  public void testAddCreationWarnings3() {
-    List<String> warnings = new ArrayList<>();
-    Project md = new Project();
-    md.addWarnings(warnings);
-    assertEquals(0, md.getWarnings().size());
-  }
-
-  @Test
-  public void testAddLoggingInfo() {
-    Project project = new Project();
-    MinervaLoggerAppender appender = MinervaLoggerAppender.createAppender();
-    logger.warn("test");
-    logger.warn("test2");
-    MinervaLoggerAppender.unregisterLogEventStorage(appender);
-
-    project.addLoggingInfo(appender);
-    assertEquals(2, project.getWarnings().size());
-  }
-
 }

persist/src/main/resources/db/migration/15.0.0/V15.0.1.20191025_3__structured_log.sql

+CREATE SEQUENCE project_log_entry_sequence
+  INCREMENT 1
+  MINVALUE 1
+  MAXVALUE 9223372036854775807
+  START 1
+  CACHE 1;
+
+CREATE TABLE project_log_entry_table
+(
+  id integer NOT NULL DEFAULT nextval('project_log_entry_sequence'::regclass),
+  severity varchar NOT NULL,
+  type varchar NOT NULL,
+  object_identifier varchar,
+  object_class varchar,
+  map_name varchar,
+  project_id integer not null,
+  content text,
+
+  CONSTRAINT project_log_entry_pk PRIMARY KEY (id),
+  CONSTRAINT project_log_entry_project_fk FOREIGN KEY (project_id)
+      REFERENCES project_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION
+)
+WITH (
+  OIDS=FALSE
+);
+
+insert into project_log_entry_table (content, project_id, severity, type) SELECT s.token, id, 'WARNING', 'OTHER' from project_table t, unnest(string_to_array(t.warnings, E'\n')) s(token);
+insert into project_log_entry_table (content, project_id, severity, type) SELECT s.token, id, 'ERROR', 'OTHER' from project_table t, unnest(string_to_array(t.errors, E'\n')) s(token);
+alter table project_table drop column warnings;
+alter table project_table drop column errors;

persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java

@@ -8,6 +8,7 @@ import org.junit.*;
 import org.springframework.beans.factory.annotation.Autowired;
 
 import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectLogEntry;
 import lcsb.mapviewer.model.map.OverviewImage;
 import lcsb.mapviewer.model.map.OverviewModelLink;
 import lcsb.mapviewer.model.map.layout.*;
@@ -201,17 +202,20 @@ public class ProjectDaoTest extends PersistTestFunctions {
   @Test
   public void testCreationWarnings() throws Exception {
     Project project = new Project("test_project_id");
-    project.addWarning("warning A");
-    project.addWarning("warning B");
+    ProjectLogEntry entry = new ProjectLogEntry();
+    entry.setContent("content");
+    entry.setSeverity("WARN");
+    entry.setType("OTHER");
+    project.addLogEntry(entry);
     project.setOwner(userDao.getUserByLogin(ADMIN_BUILT_IN_LOGIN));
-    assertEquals(2, project.getWarnings().size());
+    assertEquals(1, project.getLogEntries().size());
 
     projectDao.add(project);
 
     projectDao.evict(project);
     Project project2 = projectDao.getById(project.getId());
 
-    assertEquals(2, project2.getWarnings().size());
+    assertEquals(1, project2.getLogEntries().size());
 
     projectDao.delete(project2);
   }

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

@@ -102,8 +102,7 @@ public class ProjectRestImpl extends BaseRestImpl {
     result.put("directory", project.getDirectory());
     result.put("progress", project.getProgress());
     result.put("notifyEmail", project.getNotifyEmail());
-    result.put("warnings", project.getWarnings().size() > 0);
-    result.put("errors", project.getErrors() != null && !project.getErrors().isEmpty());
+    result.put("logEntries", project.getLogEntries().size() > 0);
     result.put("name", project.getName());
     result.put("owner", project.getOwner().getLogin());
     result.put("projectId", project.getProjectId());
@@ -579,29 +578,30 @@ public class ProjectRestImpl extends BaseRestImpl {
   }
 
   private List<LogEntry> getEntries(Project project, String level) {
-    List<LogEntry> result = new ArrayList<>();
-    int id = 0;
-    for (String s : project.getWarnings()) {
-      if (!s.isEmpty()) {
-        if (level.equalsIgnoreCase("warning") || level.equals("")) {
-          result.add(new LogEntry(id, s, "WARNING"));
-        }
-        id++;
-      }
-    }
-    String errors = project.getErrors();
-    if (errors == null) {
-      errors = "";
-    }
-    for (String s : errors.split("\n")) {
-      if (!s.isEmpty()) {
-        if (level.equalsIgnoreCase("error") || level.equals("")) {
-          result.add(new LogEntry(id, s, "ERROR"));
-        }
-        id++;
-      }
-    }
-    return result;
+    throw new NotImplementedException();
+//    List<LogEntry> result = new ArrayList<>();
+//    int id = 0;
+//    for (String s : project.getWarnings()) {
+//      if (!s.isEmpty()) {
+//        if (level.equalsIgnoreCase("warning") || level.equals("")) {
+//          result.add(new LogEntry(id, s, "WARNING"));
+//        }
+//        id++;
+//      }
+//    }
+//    String errors = project.getErrors();
+//    if (errors == null) {
+//      errors = "";
+//    }
+//    for (String s : errors.split("\n")) {
+//      if (!s.isEmpty()) {
+//        if (level.equalsIgnoreCase("error") || level.equals("")) {
+//          result.add(new LogEntry(id, s, "ERROR"));
+//        }
+//        id++;
+//      }
+//    }
+//    return result;
   }
 
   private Comparator<LogEntry> getComparatorForColumn(LogSortColumn sortColumnEnum, String sortOrder)

rest-api/src/test/java/lcsb/mapviewer/api/projects/ProjectRestImplTest.java

@@ -20,6 +20,7 @@ import com.google.gson.Gson;
 import lcsb.mapviewer.api.*;
 import lcsb.mapviewer.converter.zip.*;
 import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectLogEntry;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.persist.dao.ProjectDao;
@@ -211,7 +212,7 @@ public class ProjectRestImplTest extends RestTestFunctions {
       project.addModel(model);
       project.setOwner(userDao.getUserByLogin(ADMIN_BUILT_IN_LOGIN));
       project.setProjectId(model.getName());
-      project.addWarning("some warning");
+      project.addLogEntry(new ProjectLogEntry());
     }
     IModelService mockModelService = Mockito.mock(IModelService.class);
     Mockito.when(mockModelService.getLastModelByProjectId(anyString())).thenReturn(model);

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -22,14 +22,14 @@ import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.commands.*;
 import lcsb.mapviewer.common.*;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.*;
 import lcsb.mapviewer.converter.graphics.DrawingException;
 import lcsb.mapviewer.converter.graphics.MapGenerator;
 import lcsb.mapviewer.converter.graphics.MapGenerator.MapGeneratorParams;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
 import lcsb.mapviewer.converter.zip.ZipEntryFile;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.*;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.layout.*;
@@ -378,7 +378,7 @@ public class ProjectService implements IProjectService {
               analyzeAnnotations(originalModel, params);
             }
             MinervaLoggerAppender.unregisterLogEventStorage(appender);
-            project.addLoggingInfo(appender);
+            project.addLogEntries(createLogEntries(appender));
 
             if (params.isCacheModel()) {
               cacheData(originalModel, params);
@@ -406,7 +406,11 @@ public class ProjectService implements IProjectService {
             outOfMemoryBuffer = null;
             logger.error("Out of memory", oome);
             if (project != null) {
-              project.setErrors("Out of memory: " + oome.getMessage());
+              ProjectLogEntry entry = new ProjectLogEntry();
+              entry.setType("OUT_OF_MEMORY");
+              entry.setSeverity("ERROR");
+              entry.setContent("Out of memory: " + oome.getMessage());
+              project.addLogEntry(entry);
             }
             updateProjectStatus(project, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
           } finally {
@@ -602,9 +606,15 @@ public class ProjectService implements IProjectService {
           // we need to get the project from db, because session where
           // originalProject was retrieved is broken
           Project project = getProjectByProjectId(originalProject.getProjectId());
-          String errorMessage = "Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
-              + "\nMore information can be found in log file.";
-          project.setErrors(errorMessage + "\n" + project.getErrors());
+
+          ProjectLogEntry entry = new ProjectLogEntry();
+          entry.setType("OTHER");
+          entry.setSeverity("ERROR");
+          entry.setContent("Severe problem with removing object. Underlaying eror:\n" + exception.getMessage()
+              + "\nMore information can be found in log file.");
+
+          project.addLogEntry(entry);
+
           project.setStatus(ProjectStatus.FAIL);
           projectDao.update(project);
         } finally {
@@ -1061,10 +1071,15 @@ public class ProjectService implements IProjectService {
 
         try {
           Project project = getProjectByProjectId(params.getProjectId());
-          String errorMessage = "Problem with uploading to database. "
+
+          ProjectLogEntry entry = new ProjectLogEntry();
+          entry.setType("DATABASE_PROBLEM");
+          entry.setSeverity("ERROR");
+          entry.setContent("Problem with uploading to database. "
               + "You might violated some unhandled constraints or you run out of memory. Underlaying eror:\n"
-              + e.getMessage() + "\nMore information can be found in log file.";
-          project.setErrors(errorMessage);
+              + e.getMessage() + "\nMore information can be found in log file.");
+
+          project.addLogEntry(entry);
           project.setStatus(ProjectStatus.FAIL);
           projectDao.update(project);
         } catch (Exception e) {
@@ -1091,7 +1106,11 @@ public class ProjectService implements IProjectService {
     logger.error("Problem with uploading project " + params.getProjectId(), e);
     Project p = projectDao.getProjectByProjectId(params.getProjectId());
     if (p != null) {
-      p.setErrors("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
+      ProjectLogEntry entry = new ProjectLogEntry();
+      entry.setType("OTHER");
+      entry.setSeverity("ERROR");
+      entry.setContent("Problem with uploading map: " + e.getMessage() + ". More details can be found in log file.");
+      p.addLogEntry(entry);
     }
     updateProjectStatus(p, ProjectStatus.FAIL, IProgressUpdater.MAX_PROGRESS, params);
 
@@ -1148,4 +1167,8 @@ public class ProjectService implements IProjectService {
     return project;
   }
 
+  private Set<ProjectLogEntry> createLogEntries(MinervaLoggerAppender appender) {
+    throw new NotImplementedException();
+  }
+
 }

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

@@ -14,8 +14,7 @@ import org.springframework.stereotype.Component;
 
 import lcsb.mapviewer.common.Configuration;
 import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.ProjectStatus;
+import lcsb.mapviewer.model.*;
 import lcsb.mapviewer.model.map.layout.ReferenceGenome;
 import lcsb.mapviewer.model.user.ConfigurationElementType;
 import lcsb.mapviewer.services.interfaces.*;
@@ -136,18 +135,15 @@ public class StartupBean {
     try {
       for (Project project : projectService.getAllProjects()) {
         if (!ProjectStatus.DONE.equals(project.getStatus()) && !ProjectStatus.FAIL.equals(project.getStatus())) {
-          String errors = project.getErrors();
-          if (errors == null || errors.trim().isEmpty()) {
-            errors = "";
-          } else {