#1

deploy.sh

+mvn package  -Dmaven.test.skip && cd target/ && unzip ids.server-1.8.0-patched-distro.zip && cd ids.server && cp ../../*properties . && python setup install && cd .. && cd ..
+
+

run.properties

+# General properties
+icat.url = https://icat.esrf.fr
+
+
+plugin.zipMapper.class = org.icatproject.ids.storage.esrf.ZipMapper
+
+# Properties for main storage
+plugin.main.class = org.icatproject.ids.storage.esrf.MainFileStorage
+plugin.main.dir = /data/icat/main
+plugin.main.icat.url = https://icat.esrf.fr
+plugin.main.icat.user = admin
+plugin.main.icat.password = 1dM!n
+plugin.main.icat.auth = db
+
+cache.dir = /data/icat/cache
+
+# Ids server settings
+preparedCount = 10000
+processQueueIntervalSeconds = 5
+rootUserNames = root
+sizeCheckIntervalSeconds = 60
+reader = db username admin password 1dM!n
+!readOnly = true
+maxIdsInQuery = 1000
+
+# Properties for archive storage
+plugin.archive.class = org.icatproject.ids.storage.esrf.ArchiveFileStorage
+plugin.archive.dir = /data/iti/restored
+plugin.archive.queue_out_tmp = /data/iti/outq/tmp
+plugin.archive.queue_out_wait = /data/iti/outq/wait
+plugin.archive.restoration_time_out = 86400
+
+writeDelaySeconds = 60
+startArchivingLevel1024bytes = 5000000
+stopArchivingLevel1024bytes =  4000000
+storageUnit = dataset
+tidyBlockSize = 500
+
+# File checking properties
+filesCheck.parallelCount = 0
+filesCheck.gapSeconds = 5
+filesCheck.lastIdFile = /tmp/ids/lastIdFile
+filesCheck.errorLog = /tmp/ids/errorLog
+
+# Link properties
+linkLifetimeSeconds = 3600
+
+# JMS Logging
+log.list = READ WRITE INFO LINK MIGRATE PREPARE
+
+# JMS - uncomment and edit if needed
+!jms.topicConnectionFactory = java:comp/DefaultJMSConnectionFactory

setup.properties

+# Glassfish
+secure         = false
+container      = Glassfish
+home           = /opt2/glassfish4
+port           = 4848
+
+# Any libraries needed (space separated list of jars in domain's lib/applibs
+libraries=ids.storage_esrf-1.8.0.jar

src/main/java/org/icatproject/ids/IdsBean.java

@@ -217,22 +217,25 @@ public class IdsBean {
 						String entryName = zipMapper.getFullEntryName(dsInfo, dfInfo);
 						InputStream stream = null;
 						try {
-							zos.putNextEntry(new ZipEntry(entryName));
-							if (new File( dfInfo.getDfLocation()).exists()){
+							//System.out.println("Main path: " + mainStorage.getPath(dfInfo.getDfLocation(), dfInfo.getCreateId(), dfInfo.getModId()));
+							
+							if (new File( dfInfo.getDfLocation()).exists() || mainStorage.exists(dsInfo)){
+								zos.putNextEntry(new ZipEntry(entryName));
 								stream = mainStorage.get(dfInfo.getDfLocation(), dfInfo.getCreateId(), dfInfo.getModId());
 								int length;
 								while ((length = stream.read(bytes)) >= 0) {
 									zos.write(bytes, 0, length);
 								}
+								zos.closeEntry();
 							}
 							else{
 								System.out.println("File does not exist: " + dfInfo.getDfLocation());
 								missingFiles.add(dfInfo.getDfLocation());
 							}
 						} catch (ZipException e) {
+							e.printStackTrace();
 							logger.debug("Skipped duplicate");
 						}
-						zos.closeEntry();
 						if (stream != null) {							
 							stream.close();
 						}