Stardog Drop and Restore DB does not work when stardog is configured with LDAP access

earthquakesan · May 15, 2019, 10:10am

Affected stardog version: 6.1.2

Configuration (stardog.properties):

# Default options
query.all.graphs = true
security.named.graphs = true
# Base 64 compatible passwords are a requirement for DataPlatform
password.length.max = 64
password.regex = [\\w+\\/=]+

# Access Logs
logging.access.enabled = true
logging.access.type = text
logging.access.file = /logs/access.log
logging.access.rotation.type = size
logging.access.rotation.limit = 1000000

# Audit Log

# Note, while it is unlikely that both access and audit logging should be enabled, Stardog will not prevent you from
# doing that. But it's strictly superfluous since audit logging is a strict superset of access logging; i.e., the former
# can be created from the latter offline.

# Slow Query Log
logging.slow_query.enabled = true
logging.slow_query.time = 30s
logging.slow_query.type = text

logging.create.failure.fatal = true

backup.location = /backups
export.dir = /export

# LDAP configuration
security.realms = ldap
ldap.provider.url = ldap://example.com:389
ldap.security.principal = cn=username,cn=Users,dc=example,dc=com
ldap.security.credentials = password
ldap.user.dn.template = cn={0},cn=Users,dc=example,dc=com
ldap.group.lookup.string = CN=Groups,dc=example,dc=com
ldap.users.cn = users
ldap.superusers.cn = superusers
ldap.cache.invalidate.time = 1h

There is also sdpass file with the following contents:
::*:username:password

steps to reproduce (initialization script creates stardog database on startup):

$ stardog-admin db list
+-----------+
| Databases |
+-----------+
| stardog   |
+-----------+
$ stardog-admin db create -n stardog2 -v -o versioning.enabled=false preserve.bnode.ids=false --
Successfully created database 'stardog2'.
$ stardog-admin db backup stardog2
Backup of stardog2 saved to /backups/stardog2/2019-05-15 in 00:00:00.029
$ ls /backups/stardog2/2019-05-15
dict.bk  index.bk  metadata.bk  options.bk  version
### Restore with -o flag fails
$ stardog-admin db restore -o /backups/stardog2/2019-05-15
user:internal.devops:read:db:stardog2 exists
### The db is not there anymore
$ stardog-admin db list
+-----------+
| Databases |
+-----------+
| stardog   |
+-----------+
$ stardog-admin db drop stardog2
Database 'stardog2' does not exist.

Stardog Log:

INFO  2019-05-15 12:02:38,865 [stardog-user-1] com.complexible.stardog.docs.db.BitesConnectableFactory:createDocumentStore(133): Creating document store for stardog at file:////data/stardog/docs
INFO  2019-05-15 12:02:38,917 [stardog-user-1] com.complexible.stardog.StardogKernel:write(77): Successfully created database 'stardog'.
INFO  2019-05-15 12:08:07,722 [stardog-user-24] com.complexible.stardog.docs.db.BitesConnectableFactory:createDocumentStore(133): Creating document store for stardog2 at file:////data/stardog2/docs
INFO  2019-05-15 12:08:07,724 [stardog-user-24] com.complexible.stardog.StardogKernel:write(77): Successfully created database 'stardog2'.
INFO  2019-05-15 12:09:00,700 [stardog-user-16] com.complexible.stardog.docs.db.BitesConnectableFactory:createDocumentStore(133): Creating document store for stardog2 at file:////data/stardog2/docs
ERROR 2019-05-15 12:09:00,718 [stardog-user-16] com.complexible.stardog.protocols.http.server.StardogHttpServiceLoader:accept(235): An unexpected exception was handled by the server
com.complexible.stardog.security.ResourceExistsException: user:internal.devops:read:db:stardog2 exists
        at com.complexible.stardog.security.index.IndexAuthorizationManager.add(IndexAuthorizationManager.java:251) ~[stardog-core-security-6.1.2.jar:?]
        at com.complexible.stardog.security.impl.SystemSecurityManagerImpl.add(SystemSecurityManagerImpl.java:285) ~[stardog-core-security-6.1.2.jar:?]
        at com.complexible.stardog.security.index.IndexBackedSystemSecurityManager.add(IndexBackedSystemSecurityManager.java:104) ~[stardog-core-security-6.1.2.jar:?]
        at com.complexible.stardog.security.StardogSecurityManagerImpl.add(StardogSecurityManagerImpl.java:622) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.security.StardogSecurityManagerImpl.addUserPerm(StardogSecurityManagerImpl.java:110) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel$NotifyingSecurityManager.addUserPerm(StardogKernel.java:3889) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.lambda$dbPermissions$10(StardogKernel.java:2153) ~[stardog-6.1.2.jar:?]
        at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90) ~[shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83) ~[shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383) ~[shiro-core-1.2.3.jar:1.2.3]
        at com.complexible.stardog.StardogKernel.dbPermissions(StardogKernel.java:2119) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.internalRestore(StardogKernel.java:1971) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.restore(StardogKernel.java:1872) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.restore(StardogKernel.java:1792) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.protocols.http.server.AdminDatabaseService.restore(AdminDatabaseService.java:138) ~[stardog-protocols-http-server-6.1.2.jar:?]
        at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-6.1.2.jar:?]
        at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.2.3.jar:1.2.3]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_181]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_181]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_181]
ERROR 2019-05-15 12:10:09,915 [stardog-user-11] com.complexible.stardog.protocols.http.server.StardogHttpServiceLoader:accept(235): An unexpected exception was handled by the server
com.complexible.stardog.server.UnknownDatabaseException: Database 'stardog2' does not exist.
        at com.complexible.stardog.server.UnknownDatabaseException.create(UnknownDatabaseException.java:28) ~[stardog-core-shared-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.assertDbExists(StardogKernel.java:2696) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.internalDrop(StardogKernel.java:2219) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.StardogKernel.drop(StardogKernel.java:2207) ~[stardog-6.1.2.jar:?]
        at com.complexible.stardog.protocols.http.server.AdminDatabaseService.dropDatabase(AdminDatabaseService.java:259) ~[stardog-protocols-http-server-6.1.2.jar:?]
        at com.stardog.http.server.undertow.jaxrs.ExtractRoutes.lambda$handleIt$5(ExtractRoutes.java:192) ~[stardog-protocols-http-server-6.1.2.jar:?]
        at org.apache.shiro.subject.support.SubjectRunnable.doRun(SubjectRunnable.java:120) [shiro-core-1.2.3.jar:1.2.3]
        at org.apache.shiro.subject.support.SubjectRunnable.run(SubjectRunnable.java:108) [shiro-core-1.2.3.jar:1.2.3]
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [?:1.8.0_181]
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [?:1.8.0_181]
        at java.lang.Thread.run(Thread.java:748) [?:1.8.0_181]

Removing LDAP portion of the configuration makes Stardog behave as intended. Here is the working configuration:

# Default options
query.all.graphs = true
security.named.graphs = true
# Base 64 compatible passwords are a requirement for DataPlatform
password.length.max = 64
password.regex = [\\w+\\/=]+

# Access Logs
logging.access.enabled = true
logging.access.type = text
logging.access.file = /logs/access.log
logging.access.rotation.type = size
logging.access.rotation.limit = 1000000

# Audit Log

# Note, while it is unlikely that both access and audit logging should be enabled, Stardog will not prevent you from
# doing that. But it's strictly superfluous since audit logging is a strict superset of access logging; i.e., the former
# can be created from the latter offline.

# Slow Query Log
logging.slow_query.enabled = true
logging.slow_query.time = 30s
logging.slow_query.type = text

logging.create.failure.fatal = true

backup.location = /backups
export.dir = /export

# LDAP configuration

stephen · May 23, 2019, 3:16pm

Hi and welcome! Thanks for the detailed bug report. I'm opening up a ticket to investigate this issue further. In the mean time, you could try doing an explicit stardog-admin db drop before performing the restore, and/or you may need to go into your permissions and explicitly removing any permissions that exist for that db before the restore

earthquakesan · May 24, 2019, 6:07am

Hi Stephen!

The other combination (drop and then restore) also did not work. I had to switch off LDAP for the deployment in the end, did not find a work around.

How do I view/edit permissions for a single DB?

stephen · May 24, 2019, 3:58pm

On the CLI, viewing the db permissions probably isn't the easiest... But if you're using Stardog Studio, you can navigate to the Security tab and sort the tables by resource name. You'll still have to look through each user/role, however

earthquakesan · May 25, 2019, 9:46am

That's not gonna work. I need to do automatic backups/restores of Stardog using ansible playbooks (via CI tool). If permission editing can not be automatized, it's not gonna work for me. My conclusion is that basically, I can not do backups/restores when Stardog is configured with LDAP.

stephen · May 28, 2019, 12:12pm

We're working to reproduce this issue on our side, but having some difficulty. What LDAP are you using where you're seeing this problem?

earthquakesan · May 29, 2019, 7:24am

We use active directory installed on windows server (not office 365). I can try to reproduce it with O365 as well.

If you can give me instructions what I should debug there, I can do it and send you logs.

stephen · May 30, 2019, 7:40pm

Hi Ivan,

For debugging, would you be willing to send us snapshots of your Stardog system database? You can create one for us to read by running the following query against any database on your server:

construct {?s ?p ?o} where
{
    service <db://system> {
        ?s ?p ?o
    }
}

This will produce a turtle file that you can send us. If you're willing, we'd love to have one where your database exists, and then one after you perform a db drop, since you say the "drop and restore" method also didn't work. If you don't want to share the system db publicly (not that there's anything sensitive in it, to my knowledge), you can email it to me directly, <my name> (at) stardog (dot) com

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Stardog Drop and Restore DB does not work when stardog is configured with LDAP access

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