Compatibility with Mongo 3.0?

[tcash21]

Hello,

Trying to connect, authenticate and query but I need to switch away from the admin database once authenticated.

Additionally, even querying against the database is resulting in Read operation failures:
Error in .jcall(rmongo.object@javaMongo, "S", "dbGetQuery", collection, :
com.mongodb.MongoException$Network: Read operation to server dscimemd01/10.9.68.7:27017 failed on database huron

Is this an issue with Mongo 3.0 and the driver included in this package?

Thanks,
Tanya

[tcash21]

I actually just found this closed issue: #31

I'll try installing directly from source since it doesn't look like it's on CRAN yet.

[tcash21]

I'm still unable to authenticate even when using the 0.1.0 version of RMongo.

mongo <- mongoDbConnect(host=host , db=auth.db)
authenticated <- dbAuthenticate(mongo, username, password)
> authenticated
[1] FALSE

When I try to query without authenticating I get this:

Error in .jcall(rmongo.object@javaMongo, "S", "dbGetQuery", collection,  :
com.mongodb.MongoException: not authorized for query on db.collectionName

[tc]

@tcash21 are you sure the user/pass is correct with the permissions? the error message sounds like the permissions aren't correct.

[tcash21]

Yes. We actually wrote a new version with the latest driver and it's working. Will let you know once we're able to release it. Thank you though!

[davesgonechina]

Getting the same error with RMongo 0.1.0 and Mongo 3.0.2:

Error in .jcall(rmongo.object@javaMongo, "[S", "dbShowCollections") :
com.mongodb.MongoException: not authorized for query on admin.system.namespaces

Authentication succeeds if I use local mongo client or pymongo to connect to remote mongodb, but fails in R as well as clients like UMongo. Not sure what I've done wrong.

[tc]

@tcash21 do you have any suggestions for @davesgonechina ?

[svensteudter]

Hi,

I adapted your code such that is able to connect to replica sets with the new authentication method of MongoDB 3.0. Unfortunately I have no experience with the used programming language Scala (and almost no exp. in R). ALso I do not have the time to get the code to a higher quality.

I have not tested, if my changes break anything (which could be the case especially for old authentication methods in my code).

I will publish the patch here and write a few remarks in my next post. So if you, @tc , or anybody else has the time, please feel free to adopt the code snippet and commit it to Github.

Also one remark, although it is not urgent, RMongo uses the Monog Java driver in version 2.13 the 3.0 driver is available for at least half a year now, RMongo is using maven to build this library, it would be cool t update also the driver to 3.0.

[svensteudter]

Index: NAMESPACE
===================================================================
--- NAMESPACE   (revision 17)
+++ NAMESPACE   (revision 18)
@@ -1,5 +1,5 @@
 import('methods')
 import('rJava')
-export('mongoDbConnect', 'mongoDbReplicaSetConnect')
+export('mongoDbConnect', 'mongoDbReplicaSetConnect','mongoDbReplicaSetConnectWithCredentials')
 exportClass('RMongo')
 exportMethods('dbInsertDocument', 'dbAuthenticate', 'dbSetWriteConcern', 'dbShowCollections', 'dbGetQuery', 'dbGetQueryForKeys', 'dbDisconnect', 'dbRemoveQuery', 'dbGetDistinct', 'dbAggregate')
Index: R/rmongo.R
===================================================================
--- R/rmongo.R  (revision 16)
+++ R/rmongo.R  (revision 17)
@@ -16,6 +16,11 @@
   rmongo
 }

+mongoDbReplicaSetConnectWithCredentials <- function(dbName, hosts="127.0.0.1:27017", username, pwd){
+rmongo <- new("RMongo", javaMongo = .jnew("rmongo/RMongo", dbName, hosts, TRUE, username, pwd))
+  rmongo
+}
+
 setGeneric("dbAuthenticate", function(rmongo.object, username, password) standardGeneric("dbAuthenticate"))
 setMethod("dbAuthenticate", signature(rmongo.object="RMongo", username="character", password="character"),
    function(rmongo.object, username, password){
Index: src/r-mongo-scala/src/main/scala/rmongo/RMongo.scala
===================================================================
--- src/r-mongo-scala/src/main/scala/rmongo/RMongo.scala    (revision 16)
+++ src/r-mongo-scala/src/main/scala/rmongo/RMongo.scala    (revision 17)
@@ -10,24 +10,29 @@
 import java.util.logging.Logger
 import java.util.logging.Level

-class RMongo(dbName: String, hosts: String, replica: Boolean) {
+class RMongo(dbName: String, hosts: String, replica: Boolean, username: String, pwd: String) {
   val mongoLogger = Logger.getLogger("com.mongodb")
   mongoLogger.setLevel(Level.SEVERE)
   val servers = hosts.split(",").map(_.trim.split(":")).map { a =>
     if (a.size < 2) new ServerAddress(a(0), 27017) else new ServerAddress(a(0), a(1).toInt)
   }.toList
   val this.replica = replica
-  val m = if (!this.replica) new MongoClient(servers(0)) else new MongoClient(servers)
+  val credential = mCreateCredential(username,dbName,pwd)
+  val m = if (!this.replica) new MongoClient(servers(0)) else new MongoClient(servers,List(credential))
   val db = m.getDB(dbName)
   var writeConcern = WriteConcern.NORMAL

-  def this(dbName: String, host: String, port: Int) = this (dbName, host + ":" + port, false)
+  def this(dbName: String, host: String, port: Int) = this (dbName, host + ":" + port, false,"","")

-  def this(dbName: String) = this (dbName, "127.0.0.1:27017", false)
+  def this(dbName: String) = this (dbName, "127.0.0.1:27017", false,"","")

   def dbAuthenticate(username:String, password:String):Boolean = {
     db.authenticate(username, password.toCharArray)
   }
+  
+  def mCreateCredential(userName:String, database:String,password:String):MongoCredential = {
+   MongoCredential.createCredential(username,database,password.toCharArray)
+  }

   def dbSetWriteConcern(w: Int, wtimeout: Int, fsync: Boolean, j: Boolean) {
     writeConcern = new WriteConcern(w, wtimeout, fsync, j)

[svensteudter]

OK,

no idea how to upload patches in a discussion on GIthib. Seems that I would need write rights for uploading a patch file. In my previos post, see above, I posted the content of my patch. The patch should work at least for replica sets with MongoDB 3.0 SCRAM-SHA1 authentictaion.

[tc]

Hi, you can submit this as a pull request. There's a help page on github
about it. It'll make it a lot easier to review
On Thu, Oct 15, 2015 at 3:01 AM svensteudter notifications@github.com
wrote:

OK,

no idea how to upload patches in a discussion on GIthib. Seems that I
would need write rights for uplaoding a patch file. In my previos post, see
above, I posted the content of my patch. The patch should work at least for
replica sets with MongoDB 3.0 SCRAM-SHA1 authentictaion.

—
Reply to this email directly or view it on GitHub
#34 (comment).

[svensteudter]

Hi, not sure if I did the Pull request stuff right (first time), did you receive it?
Btw: added java older with description how to retrieve the source code of the MongoDB Java driver 2.13.0 which should resolve the issue #33.

[tc]

Got the pull request, thanks! will review.

[midunrajendranpandera]

Hi svensteudter,

I am using patch to connect to a replica sets. How would you initialise a host variable when using
mongoDbReplicaSetConnectWithCredentials or
mongoDbReplicaSetConnect

Am stuck here. Can you help.

[midunrajendranpandera]

Hi svensteudter,
Just to update, I was able to authenticate with the change in your script, but dbGetQueryForKeys and dbGetQuery is not working as expected. These two return after merging all the resultant columns in dataframe.
So, I am using your method for authentication and RMongo package for retrieving data .

[svensteudter]

Hi midunrajendranpandera,
could you please provide me with some more detail on your problem? For clarification, the problem I had, was that MongoDB changed the default authentication method used (from MONGDB-CR to SCRAM-SHA1), the way the RMongo package made authentication did not work for MonogDB 3.0.

What I did was changing some code, to adapt it to the new way how a connection and authentication to MongoDB should be done. I ONLY updated this with the focus on connecting to a replica set. That should work. The rest remained unchanged.

If you ar eable to connect and authentciate to a replica seton MongoDB 3.0 with my patch, than my patch is doing what it is intended for, else not.

The way to use it in R should be
mongoDbReplicaSetConnectWithCredentials(dbname,hosts="server1:port1,server2:port2...", username, password)

If there is another bug not related to connecting and authenticating to MongoDB wirh RMongo please open a new issue.