accidentally deleted application-data folder

[Surender Reddy]

Hi 

we are using jira 7.3.3 and we are in a process of upgradation . so we created a clone of dev in different sever and working on that. but accidentally application-data folder is deleted that is home directory of jira. i tried replaceing it with application-data folder from dev environment but its showing error .  instance cannot be recovered.

I am attaching catalina logs when we start jira started. Please help me with this.

package.access : sun.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.jasper.,
org.apache.tomcat.
package.definition : sun.,
java.,
org.apache.catalina.,
org.apache.coyote.,
org.apache.jasper.,
org.apache.naming.,
org.apache.tomcat.
server.loader :
shared.loader :
sun.arch.data.model : 64
sun.boot.library.path : /opt/atlassian/jira/7.3.3/jre/lib/amd64
sun.cpu.endian : little
sun.cpu.isalist :
sun.io.unicode.encoding : UnicodeLittle
sun.java.command : org.apache.catalina.startup.Bootstrap start
sun.java.launcher : SUN_STANDARD
sun.jnu.encoding : UTF-8
sun.management.compiler : HotSpot 64-Bit Tiered Compilers
sun.os.patch.level : unknown
tomcat.util.buf.StringCache.byte.enabled : true
tomcat.util.scan.StandardJarScanFilter.jarsToScan : log4j-web*.jar,
log4j-taglib*.jar,
log4javascript*.jar,
slf4j-taglib*.jar
tomcat.util.scan.StandardJarScanFilter.jarsToSkip : bootstrap.jar,
commons-daemon.jar,
tomcat-juli.jar,
annotations-api.jar,
el-api.jar,
jsp-api.jar,
servlet-api.jar,
websocket-api.jar,
jaspic-api.jar,
catalina.jar,
catalina-ant.jar,
catalina-ha.jar,
catalina-storeconfig.jar,
catalina-tribes.jar,
jasper.jar,
jasper-el.jar,
ecj-*.jar,
tomcat-api.jar,
tomcat-util.jar,
tomcat-util-scan.jar,
tomcat-coyote.jar,
tomcat-dbcp.jar,
tomcat-jni.jar,
tomcat-websocket.jar,
tomcat-i18n-en.jar,
tomcat-i18n-es.jar,
tomcat-i18n-fr.jar,
tomcat-i18n-ja.jar,
tomcat-juli-adapters.jar,
catalina-jmx-remote.jar,
catalina-ws.jar,
tomcat-jdbc.jar,
tools.jar,
commons-beanutils*.jar,
commons-codec*.jar,
commons-collections*.jar,
commons-dbcp*.jar,
commons-digester*.jar,
commons-fileupload*.jar,
commons-httpclient*.jar,
commons-io*.jar,
commons-lang*.jar,
commons-logging*.jar,
commons-math*.jar,
commons-pool*.jar,
jstl.jar,
taglibs-standard-spec-*.jar,
geronimo-spec-jaxrpc*.jar,
wsdl4j*.jar,
ant.jar,
ant-junit*.jar,
aspectj*.jar,
jmx.jar,
h2*.jar,
hibernate*.jar,
httpclient*.jar,
jmx-tools.jar,
jta*.jar,
log4j*.jar,
mail*.jar,
slf4j*.jar,
xercesImpl.jar,
xmlParserAPIs.jar,
xml-apis.jar,
junit.jar,
junit-*.jar,
hamcrest-*.jar,
easymock-*.jar,
cglib-*.jar,
objenesis-*.jar,
ant-launcher.jar,
cobertura-*.jar,
asm-*.jar,
dom4j-*.jar,
icu4j-*.jar,
jaxen-*.jar,
jdom-*.jar,
jetty-*.jar,
oro-*.jar,
servlet-api-*.jar,
tagsoup-*.jar,
xmlParserAPIs-*.jar,
xom-*.jar
user.country : US
user.dir : /opt/atlassian/jira/7.3.3/bin
user.home : /home/jcadmin
user.language : en
user.name : jcadmin
user.timezone : America/New_York

2018-11-28 15:58:43,418 JIRA-Bootstrap INFO [c.a.j.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from /var/atlassian/application-data/jira/7.3.3/dbconfig.xml
28-Nov-2018 15:58:43.488 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler [https-jsse-nio-8443]
2018-11-28 15:58:43,686 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] Running JIRA startup checks.
2018-11-28 15:58:43,687 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.
28-Nov-2018 15:58:43.805 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
28-Nov-2018 15:58:43.823 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 6490 ms
2018-11-28 15:58:44,920 JIRA-Bootstrap ERROR [c.a.jira.startup.LauncherContextListener] Unable to start JIRA.
com.google.common.util.concurrent.UncheckedExecutionException: java.lang.RuntimeException: Unable to obtain a connection from the underlying connection pool
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2203)
at com.google.common.cache.LocalCache.get(LocalCache.java:3937)
at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3941)
at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4824)
at com.google.common.cache.LocalCache$LocalLoadingCache.getUnchecked(LocalCache.java:4830)
at org.ofbiz.core.entity.GenericDelegator.getGenericDelegator(GenericDelegator.java:107)
at com.atlassian.core.ofbiz.CoreFactory.getGenericDelegator(CoreFactory.java:34)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.configureOfbiz(DatabaseConfigurationManagerImpl.java:215)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:295)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseConfigured(DatabaseConfigurationManagerImpl.java:199)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:134)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:103)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:101)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:149)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.RuntimeException: Unable to obtain a connection from the underlying connection pool
at org.ofbiz.core.entity.jdbc.interceptors.connection.ConnectionTracker.trackConnection(ConnectionTracker.java:60)
at org.ofbiz.core.entity.transaction.JNDIFactory.trackConnection(JNDIFactory.java:253)
at org.ofbiz.core.entity.transaction.JNDIFactory.getJndiConnection(JNDIFactory.java:224)
at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:147)
at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136)
at org.ofbiz.core.entity.ConnectionFactory$1.getConnection(ConnectionFactory.java:52)
at org.ofbiz.core.entity.jdbc.DatabaseUtil.getConnection(DatabaseUtil.java:133)
at org.ofbiz.core.entity.jdbc.DatabaseUtil.getTableNames(DatabaseUtil.java:904)
at org.ofbiz.core.entity.jdbc.DatabaseUtil.checkDb(DatabaseUtil.java:167)
at org.ofbiz.core.entity.jdbc.DatabaseUtil.checkDb(DatabaseUtil.java:145)
at org.ofbiz.core.entity.GenericDAO.checkDb(GenericDAO.java:1475)
at org.ofbiz.core.entity.GenericHelperDAO.checkDataSource(GenericHelperDAO.java:270)
at org.ofbiz.core.entity.GenericDelegator.initialiseAndCheckDatabase(GenericDelegator.java:238)
at org.ofbiz.core.entity.GenericDelegator.<init>(GenericDelegator.java:169)
at org.ofbiz.core.entity.GenericDelegator$1.load(GenericDelegator.java:93)
at org.ofbiz.core.entity.GenericDelegator$1.load(GenericDelegator.java:90)
at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
... 15 more
Caused by: java.sql.SQLException: Cannot create PoolableConnectionFactory (ORA-28000: the account is locked
)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2303)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.createDataSource(BasicDataSource.java:2043)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1543)
at org.ofbiz.core.entity.transaction.JNDIFactory$2.call(JNDIFactory.java:257)
at org.ofbiz.core.entity.jdbc.interceptors.connection.ConnectionTracker.trackConnection(ConnectionTracker.java:54)
... 35 more
Caused by: java.sql.SQLException: ORA-28000: the account is locked

at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:450)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:392)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:385)
at oracle.jdbc.driver.T4CTTIfun.processError(T4CTTIfun.java:938)
at oracle.jdbc.driver.T4CTTIfun.receive(T4CTTIfun.java:655)
at oracle.jdbc.driver.T4CTTIfun.doRPC(T4CTTIfun.java:249)
at oracle.jdbc.driver.T4CTTIoauthenticate.doOAUTH(T4CTTIoauthenticate.java:416)
at oracle.jdbc.driver.T4CTTIoauthenticate.doOAUTH(T4CTTIoauthenticate.java:825)
at oracle.jdbc.driver.T4CConnection.logon(T4CConnection.java:596)
at oracle.jdbc.driver.PhysicalConnection.<init>(PhysicalConnection.java:715)
at oracle.jdbc.driver.T4CConnection.<init>(T4CConnection.java:385)
at oracle.jdbc.driver.T4CDriverExtension.getConnection(T4CDriverExtension.java:30)
at oracle.jdbc.driver.OracleDriver.connect(OracleDriver.java:564)
at org.apache.tomcat.dbcp.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at org.apache.tomcat.dbcp.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:257)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.validateConnectionFactory(BasicDataSource.java:2313)
at org.apache.tomcat.dbcp.dbcp2.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:2299)
... 40 more
2018-11-28 15:58:44,932 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 460 MiB. Committed: 1406 MiB. Max: 10202 MiB
Non-heap memory : Used: 47 MiB. Committed: 49 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 507 MiB. Committed: 1455 MiB. Max: 11466 MiB
---------------------------------------------------------------------------------

[Nic Brough -Adaptavist-]

But what about the standard backups you should be taking regularly?

[Alexis Wilke]

As a side note, I install version 8.2.3 today and my atlassian-data folder disappeared!

It now gets moved to /var/atlassian/atlassian-data

I was pretty surprised to not see the folder anymore as I was looking for the backup folder...

[Surender Reddy]

before the files are missing we are not ready for upgrade. we just started to reach the space for backup . so no backup is taken . when i copy the file var/attlasian/aplication from dev and replaced before its not showing jira in  browser but not its not allowing me to login to the accout. 

[Nic Brough -Adaptavist-]

That makes it more difficult again, but it is possible to recover a complete Jira from a backup of the database and a copy of the attachments.  Do you have those?  (Database backup literally means a backup of the data, using the db tools to do it, not the xml copy)

[Surender Reddy]

ok   i dont have any backup all export folder is also deleted .

[Nic Brough -Adaptavist-]

I'm afraid you have destroyed your installation.  Just copying bits from other installations is not going to be good enough.

Your best option is to install a new clean copy of Jira, of exactly the same version, then import the data from the backup you took at the beginning of the process.