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MAUSDocumentCacheConfiguration » History » Revision 14

Revision 13 (Rogers, Chris, 15 May 2012 09:28) → Revision 14/15 (Rogers, Chris, 15 May 2012 09:28)

h1. How to configure MongoDB as a document cache 

 {{>toc}} 

 MAUS can use the MongoDB (http://www.mongodb.org/) document-oriented database to cache spills that have been transformed until they are ready to be merged. A MongoDB server holds 0 or more databases. Each database holds 1 or more collections and each collection 0 or more documents. MongoDB is schema free - the documents can be all of the same structure or of different structures. 

 h2. Set up MongoDB  

 MongoDB can be installed using @yum@ as follows. 

  * Log in as a super-user by using @sudo su -@ or @su@. 
  * Edit @/etc/yum.repos.d/10gen.repo@ and add the lines 
 <pre> 
 [10gen] 
 name=10gen Repository 
 baseurl=http://downloads-distro.mongodb.org/repo/redhat/os/i686 
 gpgcheck=0 
 </pre> 
  * Run  
 <pre> 
 $ yum install mongo-10gen 
  ... 
  mongo-10gen           i686           2.0.1-mongodb_1             10gen            28 M 
  ... 
 $ yum install mongo-10gen-server 
  ... 
  mongo-10gen-server         i686         2.0.1-mongodb_1            10gen         5.4 M 
 ... 
 </pre> 
  * Start the server 
 <pre> 
 $ /sbin/service mongod start 
 Starting mongod: forked process: 4357 
                                                            [    OK    ] 
 all output going to: /var/log/mongo/mongod.log 
 $ /sbin/service mongod status 
 mongod (pid 4357) is running... 
 </pre> 
 (as an alternative to @service mongod@ you can use @/etc/init.d/mongod@) 

 By default MongoDB is available on http://localhost:27017/. 

 h2. Set up pymngo  

 pymongo(http://api.mongodb.org/python/current/) provides a Python API to MongoDB. pymongo is automatically downloaded and installed when you build MAUS.  

 h2. Set up MongoDB connection 

 By default MAUS is set up to use a MongoDB database running locally.  

 If you need to change this, or make other configuration changes, then the supported configuration parameters are as follows: 

  * Document store class name. This mandatory parameter specifies the MAUS Python module that handles interaction with MongoDB. The parameter and value needs to be: 
 <pre> 
 doc_store_class="MongoDBDocumentStore.MongoDBDocumentStore" 
 </pre> 
  * MongoDB host. This optional parameter specifies the MongoDB host. If omitted then the default of @localhost@ is used. To override this value do: 
 <pre> 
 mongodb_host="maus.org.uk" 
 </pre> 
  * MongoDB port. This optional parameter specifies the MongoDB port. If omitted then the default of @27017@ is used. To override this value do: 
 <pre> 
 mongodb_port=12345 
 </pre> 
  * MongoDB database name. This optional parameter specifies the database within MongoDB to use. If omotted then the default of @mausdb@ is used. To override this value do: 
 <pre> 
 mongodb_database_name="someotherdbname"  
 </pre> 
  ** Note that if the database is not present in MongoDB it will be created automatically. 
  * MongoDB collection name. This optional parameter specifies the collection within the MongoDB database to use. If omotted then the default of @spills@ is used. To override this value do: 
 <pre> 
 mongodb_collection_name="someothercollectionname"  
 </pre> 
  ** Note that if the database is not present in MongoDB it will be created automatically. 

 h2. Run a quick test 

 Run the MAUS MongoDB integration tests: 
 <pre> 
 $ python tests/integration/test_docstore/test_MongoDBDocumentStore.py 
 ............ 
 ---------------------------------------------------------------------- 
 Ran 12 tests in 76.781s 

 OK 
 </pre> 

 h2. Clear Mongo Database Cache 

 Mongo can encounter weird problems with data corruption, for example if the machine on which it is running crashes (power outage, etc). All existing data can be wiped from the database by doing (as root) 
 <pre> 
 $ /sbin/service mongod stop 
 $ rm /var/lib/mongo/* 
 $ /sbin/service mongod start 
 $ /sbin/service mongod status 
 </pre> 

 As mongo is only used as a transient database, this is probably a safe operation.