Changeset 4035

Timestamp:

Dec 5, 2007, 9:13:35 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #860: Migration should create File entries even if physical file doesn't exists in BASE 1

File:

• trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java (modified) (1 diff)

trunk/src/clients/migrate/net/sf/basedb/clients/migrate/UploadFileTransfer.java

@@ -259 +259 @@
       // identifier
       String md5 = QUICK_TRANSFER ? fileName : md5sum(location);
-      if (md5 != null)
-      {
-        File file = getFileByMd5(dc, user, md5);
-        if (file == null)
-        {
-          Directory homeDir = user.getHomeDirectory();
-          if (homeDir == null)
-          {
-            log.info("...upload related files");
-            {
-              log.debug("User " + user.getName() + " is missing a home directory");
-            // Something is wrong here homeDir is not null when you
-            // look through the web interface
-            // homeDir = Directory.createHomeDirectory(dc, user,
-            // true);
-            // dc.saveItem(homeDir);
-            }
-          }
-          int prefix = 0;
-          String prefixedFileName = fileName;
-          while (File.exists(dc, homeDir, prefixedFileName))
-          {
-            prefixedFileName = prefix + "_" + fileName;
-            prefix++;
-          }
-          // All files are stored in the users homedirectory
-          file = File.getNew(dc, homeDir);
-          setCommonItemData(dc, file, rs);
-          file.setName(prefixedFileName); // Reset the filename incase
-                          // we've prefixed it in the
-                          // above while loop
-          dc.saveItem(file);
-          log.debug("File item is saved into BASE2");
-          transferFile(file, location, md5);
-          if (createRawBioAssay || createPrintmap) file.setWriteProtected(true);
-          commit(dc);
-          String fileMd5 = file.getMd5();
-          if (fileMd5 != null)
-          {
-            // We assume that each file generates a unique md5sum
-            md5ToIdMap.put(
-                user.getId() + "_" + fileMd5, file.getId());            
-          }
-          if (log.isDebugEnabled())
-          {
-            log.debug("Transfered File: " + file.getName() + "\tBASE1 id(" + rs.getInt(1) + ")");           
-          }         
-        }
-        else
-        {
-          log.info( file.getName() + " already exists");
-        }
-        if (createProtocol)
-        {
-          protocolFileMap.put(rs.getInt(1), file.getId());
-        }
-        if (createImage)
-        {
-          imageFileMap.put(rs.getInt(1), file.getId());
-        }
-        if (createRawBioAssay)
-        {
-          rawBioAssayFileMap.put(rs.getInt(1), file.getId());
-        }
-        if (createPrintmap)
-        {
-          printmapFileMap.put(rs.getInt(1), file.getId());
-        }
-      }
-      else
+      if (md5 == null) 
       {
         log.debug("Couldn't get md5 for file: " + fileName + ":" + rs.getString(ID));
         log.warn("File:" + fileName + " with Base1Id:" + rs.getString(ID) + " will not be uploaded to BASE2");
+        md5 = fileName;
+      }
+
+      File file = getFileByMd5(dc, user, md5);
+      if (file == null)
+      {
+        Directory homeDir = user.getHomeDirectory();
+        if (homeDir == null)
+        {
+          log.info("...upload related files");
+          {
+            log.debug("User " + user.getName() + " is missing a home directory");
+          // Something is wrong here homeDir is not null when you
+          // look through the web interface
+          // homeDir = Directory.createHomeDirectory(dc, user,
+          // true);
+          // dc.saveItem(homeDir);
+          }
+        }
+        int prefix = 0;
+        String prefixedFileName = fileName;
+        while (File.exists(dc, homeDir, prefixedFileName))
+        {
+          prefixedFileName = prefix + "_" + fileName;
+          prefix++;
+        }
+        // All files are stored in the users homedirectory
+        file = File.getNew(dc, homeDir);
+        setCommonItemData(dc, file, rs);
+        file.setName(prefixedFileName); // Reset the filename incase
+                        // we've prefixed it in the
+                        // above while loop
+        dc.saveItem(file);
+        log.debug("File item is saved into BASE2");
+        transferFile(file, location, md5);
+        if (createRawBioAssay || createPrintmap) file.setWriteProtected(true);
+        commit(dc);
+        String fileMd5 = file.getMd5();
+        if (fileMd5 != null)
+        {
+          // We assume that each file generates a unique md5sum
+          md5ToIdMap.put(
+              user.getId() + "_" + fileMd5, file.getId());            
+        }
+        if (log.isDebugEnabled())
+        {
+          log.debug("Transfered File: " + file.getName() + "\tBASE1 id(" + rs.getInt(1) + ")");           
+        }
+      }
+      else
+      {
+        log.info( file.getName() + " already exists");
+      }
+      if (createProtocol)
+      {
+        protocolFileMap.put(rs.getInt(1), file.getId());
+      }
+      if (createImage)
+      {
+        imageFileMap.put(rs.getInt(1), file.getId());
+      }
+      if (createRawBioAssay)
+      {
+        rawBioAssayFileMap.put(rs.getInt(1), file.getId());
+      }
+      if (createPrintmap)
+      {
+        printmapFileMap.put(rs.getInt(1), file.getId());
       }
     }