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Sonotype Nexus Repository/OrientDB can't connect to database

Tags:

orientdb

corrupt

sonatype

Yesterday our nexus repository instance went sideways due to a disk full event. After freeing some space and attempting a restart, nexus is no longer accessible. As a result, the database became corrupted (presumably) and cannot be connected to. When I run the nexus-orient-console.jar to connect, here's what I get:

orientdb> CONNECT plocal:/nexus-data/db/component admin admin        

Connecting to database [plocal:/nexus-data/db/component] with user 'admin'...
2018-08-09 22:04:03:769 WARNI {db=component} Storage 'component' was not closed properly. Will try to recover from write ahead log...
2018-08-09 22:04:03:775 WARNI {db=component} Record com.orientechnologies.orient.core.storage.impl.local.paginated.wal.OCheckpointEndRecord{lsn=LSN{segment=34, position=52}} will be skipped during data restore$ANSI{green {db=component}} Exception during storage data restore
java.lang.NullPointerException
    at com.orientechnologies.orient.core.storage.impl.local.paginated.wal.ODiskWriteAheadLog.cutTill(ODiskWriteAheadLog.java:919)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.makeFullCheckpoint(OAbstractPaginatedStorage.java:3718)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.recoverIfNeeded(OAbstractPaginatedStorage.java:3920)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:294)
    at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.connect(OConsoleDatabaseApp.java:234)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.orientechnologies.common.console.OConsoleApplication.execute(OConsoleApplication.java:405)
    at com.orientechnologies.common.console.OConsoleApplication.executeCommands(OConsoleApplication.java:260)
    at com.orientechnologies.common.console.OConsoleApplication.run(OConsoleApplication.java:131)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.main(OConsoleDatabaseApp.java:145)
    at org.sonatype.nexus.orient.console.Main.main(Main.java:58)
Exception `1FDE0371` in storage `plocal:/nexus-data/db/component`: 2.2.31 (build 285537d2767275f460df32c6a3be01bfff6a517c, branch 2.2.x)
java.lang.NullPointerException
    at com.orientechnologies.orient.core.storage.impl.local.paginated.wal.ODiskWriteAheadLog.cutTill(ODiskWriteAheadLog.java:919)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.makeFullCheckpoint(OAbstractPaginatedStorage.java:3718)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.doClose(OAbstractPaginatedStorage.java:4397)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.close(OAbstractPaginatedStorage.java:580)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:316)
    at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.connect(OConsoleDatabaseApp.java:234)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.orientechnologies.common.console.OConsoleApplication.execute(OConsoleApplication.java:405)
    at com.orientechnologies.common.console.OConsoleApplication.executeCommands(OConsoleApplication.java:260)
    at com.orientechnologies.common.console.OConsoleApplication.run(OConsoleApplication.java:131)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.main(OConsoleDatabaseApp.java:145)
    at org.sonatype.nexus.orient.console.Main.main(Main.java:58)
$ANSI{green {db=component}} Error during storage close
java.lang.NullPointerException
    at com.orientechnologies.orient.core.storage.impl.local.paginated.wal.ODiskWriteAheadLog.cutTill(ODiskWriteAheadLog.java:919)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.makeFullCheckpoint(OAbstractPaginatedStorage.java:3718)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.doClose(OAbstractPaginatedStorage.java:4397)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.close(OAbstractPaginatedStorage.java:580)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:316)
    at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.connect(OConsoleDatabaseApp.java:234)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.orientechnologies.common.console.OConsoleApplication.execute(OConsoleApplication.java:405)
    at com.orientechnologies.common.console.OConsoleApplication.executeCommands(OConsoleApplication.java:260)
    at com.orientechnologies.common.console.OConsoleApplication.run(OConsoleApplication.java:131)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.main(OConsoleDatabaseApp.java:145)
    at org.sonatype.nexus.orient.console.Main.main(Main.java:58)
Exception `260A3A5E` in storage `plocal:/nexus-data/db/component`: 2.2.31 (build 285537d2767275f460df32c6a3be01bfff6a517c, branch 2.2.x)
com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/nexus-data/db/component' with mode=rw
    DB name="component"
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:323)
    at com.orientechnologies.orient.core.db.document.ODatabaseDocumentTx.open(ODatabaseDocumentTx.java:259)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.connect(OConsoleDatabaseApp.java:234)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:498)
    at com.orientechnologies.common.console.OConsoleApplication.execute(OConsoleApplication.java:405)
    at com.orientechnologies.common.console.OConsoleApplication.executeCommands(OConsoleApplication.java:260)
    at com.orientechnologies.common.console.OConsoleApplication.run(OConsoleApplication.java:131)
    at com.orientechnologies.orient.console.OConsoleDatabaseApp.main(OConsoleDatabaseApp.java:145)
    at org.sonatype.nexus.orient.console.Main.main(Main.java:58)
Caused by: java.lang.NullPointerException
    at com.orientechnologies.orient.core.storage.impl.local.paginated.wal.ODiskWriteAheadLog.cutTill(ODiskWriteAheadLog.java:919)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.makeFullCheckpoint(OAbstractPaginatedStorage.java:3718)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.recoverIfNeeded(OAbstractPaginatedStorage.java:3920)
    at com.orientechnologies.orient.core.storage.impl.local.OAbstractPaginatedStorage.open(OAbstractPaginatedStorage.java:294)
    ... 11 more

Error: com.orientechnologies.orient.core.exception.OStorageException: Cannot open local storage '/nexus-data/db/component' with mode=rw
    DB name="component"

Error: java.lang.NullPointerException

Because I am not able to even connect to the database, I haven't been able to attempt the recovery steps suggested here > OrientDB corruption state in Nexus Repository version 3.2.0-01. Is there any way to repair and recover the databases or are we just S.O.L.? Is there any way to start nexus in a safe-mode that ignores database issues?

like image 462
Lance Held Avatar asked Aug 09 '18 22:08

Lance Held

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What is sonatype Nexus repository?

"Nexus is a repository manager. It allows you to proxy, collect, and manage your dependencies so that you are not constantly juggling a collection of JARs. It makes it easy to distribute your software. Internally, you configure your build to publish artifacts to Nexus and they then become available to other developers.

How do I run nexus sonatype?

To use the user interface, fire up a web browser and type in the URL http://localhost:8081/nexus . You should see the user interface as displayed in Figure 3.5, “Application Window”. While we use localhost throughout this book, you may need to use the IP Loopback Address of 127.0.

1 Answers

This thread must fixed our issue. https://groups.google.com/a/glists.sonatype.com/g/nexus-users/c/64W_y9fDGzQ/m/o0FKRgiDAwAJ?pli=1

To summarize, this steps fixed my error (same as you) :

rm /mnt/sonatype-work/nexus3/db/config/*.wal

Then try to start the console and repair the database

At the orientdb prompt run the following:

connect plocal:/mnt/sonatype-work/nexus3/db/confg admin admin
repair database --fix-links
rebuild index *
disconnect 
exit

For Nexus 3.2.1+ it is possible to use the included OrientDB client.

like image 182
YLR Avatar answered Nov 03 '22 22:11

YLR
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