FIX: uncaught EntityDoesNotExist exceptions

src/main/java/caosdb/server/database/backend/implementation/UnixFileSystem/UnixFileSystemGetFileIterator.java

@@ -22,14 +22,14 @@
  */
 package caosdb.server.database.backend.implementation.UnixFileSystem;
 
+import java.io.File;
+import java.util.Arrays;
+import java.util.Iterator;
 import caosdb.server.FileSystem;
 import caosdb.server.database.access.Access;
 import caosdb.server.database.backend.interfaces.GetFileIteratorImpl;
 import caosdb.server.database.exceptions.TransactionException;
 import caosdb.server.entity.Message;
-import java.io.File;
-import java.util.Arrays;
-import java.util.Iterator;
 
 public class UnixFileSystemGetFileIterator extends UnixFileSystemTransaction
     implements GetFileIteratorImpl {

src/main/java/caosdb/server/jobs/core/InsertFilesInDir.java

@@ -22,6 +22,12 @@
  */
 package caosdb.server.jobs.core;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import caosdb.server.CaosDBException;
 import caosdb.server.CaosDBServer;
 import caosdb.server.FileSystem;
@@ -42,12 +48,6 @@ import caosdb.server.utils.EntityStatus;
 import caosdb.server.utils.FileUtils;
 import caosdb.server.utils.Undoable;
 import caosdb.server.utils.Utils;
-import java.io.File;
-import java.io.IOException;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 @JobAnnotation(
     flag = "InsertFilesInDir",
@@ -262,13 +262,14 @@ public class InsertFilesInDir extends FlagJob {
   }
 
   private boolean shouldBeProcessed(final File sub) throws IOException {
+    if (sub.isFile()) {
       if (this.isNotIncluded(sub)) {
         getContainer()
             .addMessage(
                 new Message(
                     MessageType.Warning,
                     1,
-                  "Not explicitly included directory or file: " + sub.getCanonicalPath()));
+                    "Not explicitly included file: " + sub.getCanonicalPath()));
         return false;
       }
       if (this.isExcluded(sub)) {
@@ -277,9 +278,10 @@ public class InsertFilesInDir extends FlagJob {
                 new Message(
                     MessageType.Warning,
                     2,
-                  "Explicitly excluded directory or file: " + sub.getCanonicalPath()));
+                    "Explicitly excluded file: " + sub.getCanonicalPath()));
         return false;
       }
+    }
     if (sub.isHidden()) {
       getContainer()
           .addMessage(

src/main/java/caosdb/server/transaction/FileStorageConsistencyCheck.java

@@ -22,6 +22,13 @@
  */
 package caosdb.server.transaction;
 
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map.Entry;
+import java.util.TimeZone;
+import org.jdom2.Element;
 import caosdb.datetime.UTCDateTime;
 import caosdb.server.database.DatabaseMonitor;
 import caosdb.server.database.access.Access;
@@ -30,17 +37,11 @@ import caosdb.server.database.backend.transaction.GetFileIterator;
 import caosdb.server.database.backend.transaction.GetFileRecordByPath;
 import caosdb.server.database.backend.transaction.RetrieveAllUncheckedFiles;
 import caosdb.server.database.backend.transaction.SetFileCheckedTimestamp;
+import caosdb.server.database.exceptions.EntityDoesNotExistException;
 import caosdb.server.database.proto.SparseEntity;
 import caosdb.server.entity.Message;
 import caosdb.server.entity.xml.ToElementable;
 import caosdb.server.utils.SHA512;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.TimeZone;
-import org.jdom2.Element;
 
 public class FileStorageConsistencyCheck extends Thread
     implements ToElementable, TransactionInterface {
@@ -81,17 +82,13 @@ public class FileStorageConsistencyCheck extends Thread
         }
 
         final String path = iterator.next();
-        // FIXME this prevents all files with ".thumbnail" from being checked.
-        if (path.contains(".thumbnail")) {
+        // this prevents all thumbnails  from being checked.
+        if (path.contains(".thumbnails/")) {
           continue;
         }
 
+        try {
           final GetFileRecordByPath t = execute(new GetFileRecordByPath(path), this.access);
-
-        if (t.getEntity() == null) {
-          this.results.put(path, FileConsistencyCheck.UNKNOWN_FILE);
-          continue;
-        }
           final int result =
               execute(
                   new FileConsistencyCheck(
@@ -104,6 +101,11 @@ public class FileStorageConsistencyCheck extends Thread
           }
           
           execute(new SetFileCheckedTimestamp(t.getId(), this.ts), this.access);
+        } catch (EntityDoesNotExistException e) {
+          this.results.put(path, FileConsistencyCheck.UNKNOWN_FILE);
+          continue;
+        }
+
       }
 
       // test all remaining file records