source: other-projects/maori-lang-detection/MoreReading/mongodb.txt@ 33653

MongoDB
Installation:
    https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
        https://docs.mongodb.com/manual/administration/install-on-linux/
    https://hevodata.com/blog/install-mongodb-on-ubuntu/
    https://www.digitalocean.com/community/tutorials/how-to-install-mongodb-on-ubuntu-16-04
    CENTOS (Analytics): https://tecadmin.net/install-mongodb-on-centos/
    FROM SOURCE: https://github.com/mongodb/mongo/wiki/Build-Mongodb-From-Source
GUI:
    https://robomongo.org/
    Robomongo is Robo 3T now

https://www.tutorialspoint.com/mongodb/mongodb_java.htm
JAR FILE:
    http://central.maven.org/maven2/org/mongodb/mongo-java-driver/
    https://mongodb.github.io/mongo-java-driver/



https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
http://www.programmersought.com/article/6500308940/

   52  sudo apt-get install mongodb-clients
   53  mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p

Failed with
    Error: HostAndPort: host is empty at src/mongo/shell/mongo.js:148
    exception: connect failed

This is due to a version incompatibility between Client and mongodb Server.
The solution is to follow instructions at http://www.programmersought.com/article/6500308940/
and then https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
as below:

   54  sudo apt-get purge mongodb-clients
   55  sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
   56  echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/4.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.0.list
   57  sudo apt-get update
   58  sudo apt-get install mongodb-clients
   59  mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
(still doesn't work)
   60  sudo apt-get install -y mongodb-org
The above ensures an up to date mongo client but installs the mongodb server too. Maybe this is the only step that is needed to install up-to-date mongo client and mongodb server?
   72  sudo service mongod status

  103  sudo service mongod start
"mongod" stands for mongo-daemon. This runs the mongo db server listening for client connections
  104  sudo service mongod status
   88  sudo service mongod stop


DETAILS:

wharariki:[879]/Scratch/ak19/gs3-extensions/maori-lang-detection>mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p

didn't work with the pwd. Failed with:

    MongoDB shell version: 2.6.10
    Enter password: 
    connecting to: mongodb://mongodb.cms.waikato.ac.nz:27017
    2019-11-04T20:02:47.970+1300 Assertion: 13110:HostAndPort: host is empty
    2019-11-04T20:02:47.970+1300 0x6b75c9 0x659e9f 0x636f69 0x4fa55c 0x501249 0x4fa7f1 0x6006fd 0x5eb869 0x7f7bfbd47d76 0x1f3c10d06362 
     mongo(_ZN5mongo15printStackTraceERSo+0x39) [0x6b75c9]
     mongo(_ZN5mongo10logContextEPKc+0x21f) [0x659e9f]
     mongo(_ZN5mongo11msgassertedEiPKc+0xd9) [0x636f69]
     mongo(_ZN5mongo16ConnectionString12_fillServersENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x50c) [0x4fa55c]
     mongo(_ZN5mongo16ConnectionStringC1ENS0_14ConnectionTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_+0x99) [0x501249]
     mongo(_ZN5mongo16ConnectionString5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_+0x201) [0x4fa7f1]
     mongo(_ZN5mongo17mongoConsExternalEPNS_7V8ScopeERKN2v89ArgumentsE+0x11d) [0x6006fd]
     mongo(_ZN5mongo7V8Scope10v8CallbackERKN2v89ArgumentsE+0xa9) [0x5eb869]
     /usr/lib/libv8.so.3.14.5(+0x99d76) [0x7f7bfbd47d76]
     [0x1f3c10d06362]
    2019-11-04T20:02:47.971+1300 Error: HostAndPort: host is empty at src/mongo/shell/mongo.js:148
    exception: connect failed


This is due to a version incompatibility between Client and mongodb Server.
Can find client version above. (2.6.10)
Server version can be found by running the mongo client shell. Doing so without loading a db:


    wharariki:[880]/Scratch/ak19/gs3-extensions/maori-lang-detection>mongo --shell -nodb
    MongoDB shell version: 2.6.10 <<<<<<<<<-------------------<<<< MONGO CLIENT VERSION
    type "help" for help
    > help
        db.help()                    help on db methods
        db.mycoll.help()             help on collection methods
        sh.help()                    sharding helpers
        rs.help()                    replica set helpers
        help admin                   administrative help
        help connect                 connecting to a db help
        help keys                    key shortcuts
        help misc                    misc things to know
        help mr                      mapreduce

        show dbs                     show database names
        show collections             show collections in current database
        show users                   show users in current database
        show profile                 show most recent system.profile entries with time >= 1ms
        show logs                    show the accessible logger names
        show log [name]              prints out the last segment of log in memory, 'global' is default
        use <db_name>                set current database
        db.foo.find()                list objects in collection foo
        db.foo.find( { a : 1 } )     list objects in foo where a == 1
        it                           result of the last line evaluated; use to further iterate
        DBQuery.shellBatchSize = x   set default number of items to display on shell
        exit                         quit the mongo shell

    > help connect

    Normally one specifies the server on the mongo shell command line.  Run mongo --help to see those options.
    Additional connections may be opened:

        var x = new Mongo('host[:port]');
        var mydb = x.getDB('mydb');
      or
        var mydb = connect('host[:port]/mydb');

    Note: the REPL prompt only auto-reports getLastError() for the shell command line connection.

    Getting help on connect options: 

    > var x = new Mongo('mongodb.cms.waikato.ac.nz:27017');
    > var mydb = x.getDB('anupama');

    > mydb.connect.help()
    DBCollection help
        db.connect.find().help() - show DBCursor help
        db.connect.count()
        db.connect.copyTo(newColl) - duplicates collection by copying all documents to newColl; no indexes are copied.
        db.connect.convertToCapped(maxBytes) - calls {convertToCapped:'connect', size:maxBytes}} command
        db.connect.dataSize()
        db.connect.distinct( key ) - e.g. db.connect.distinct( 'x' )
        db.connect.drop() drop the collection
        db.connect.dropIndex(index) - e.g. db.connect.dropIndex( "indexName" ) or db.connect.dropIndex( { "indexKey" : 1 } )
        db.connect.dropIndexes()
        db.connect.ensureIndex(keypattern[,options]) - options is an object with these possible fields: name, unique, dropDups
        db.connect.reIndex()
        db.connect.find([query],[fields]) - query is an optional query filter. fields is optional set of fields to return.
                                                  e.g. db.connect.find( {x:77} , {name:1, x:1} )
        db.connect.find(...).count()
        db.connect.find(...).limit(n)
        db.connect.find(...).skip(n)
        db.connect.find(...).sort(...)
        db.connect.findOne([query])
        db.connect.findAndModify( { update : ... , remove : bool [, query: {}, sort: {}, 'new': false] } )
        db.connect.getDB() get DB object associated with collection
        db.connect.getPlanCache() get query plan cache associated with collection
        db.connect.getIndexes()
        db.connect.group( { key : ..., initial: ..., reduce : ...[, cond: ...] } )
        db.connect.insert(obj)
        db.connect.mapReduce( mapFunction , reduceFunction , <optional params> )
        db.connect.aggregate( [pipeline], <optional params> ) - performs an aggregation on a collection; returns a cursor
        db.connect.remove(query)
        db.connect.renameCollection( newName , <dropTarget> ) renames the collection.
        db.connect.runCommand( name , <options> ) runs a db command with the given name where the first param is the collection name
        db.connect.save(obj)
        db.connect.stats()
        db.connect.storageSize() - includes free space allocated to this collection
        db.connect.totalIndexSize() - size in bytes of all the indexes
        db.connect.totalSize() - storage allocated for all data and indexes
        db.connect.update(query, object[, upsert_bool, multi_bool]) - instead of two flags, you can pass an object with fields: upsert, multi
        db.connect.validate( <full> ) - SLOW
        db.connect.getShardVersion() - only for use with sharding
        db.connect.getShardDistribution() - prints statistics about data distribution in the cluster
        db.connect.getSplitKeysForChunks( <maxChunkSize> ) - calculates split points over all chunks and returns splitter function
        db.connect.getWriteConcern() - returns the write concern used for any operations on this collection, inherited from server/db if set
        db.connect.setWriteConcern( <write concern doc> ) - sets the write concern for writes to the collection
        db.connect.unsetWriteConcern( <write concern doc> ) - unsets the write concern for writes to the collection
    > mydb.version()
    4.0.13 <<<<<<<<<-------------------<<<< MONGODB SERVER VERSION

(Check Mongo server version: https://stackoverflow.com/questions/38160412/how-to-find-the-exact-version-of-installed-mongodb)

Finally we now know the mongodb server version: 4.0.13
This version doesn't work with our mongo client (shell) version of 2.6.10.


DETAILS OF INSTALLING MONGO-CLIENT AND UPDATING IT, AND INSTALLING MONGODB SERVER:


   54  sudo apt-get purge mongodb-clients
   55  sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
   56  echo "deb [ arch=amd64,arm64 ] https://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/4.0 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-4.0.list
   57  sudo apt-get update
   58  sudo apt-get install mongodb-clients
   59  mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
   60  sudo apt-get install -y mongodb-org
   61  mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
   62  sudo service apache2 status
   63  sudo service sshd status
   64  sudo service mongodb status
   65  sudo service mongo status
   66  mongod
   67  mongod --help
   68  mongod --help | less
   69  mongod -f /etc/mongod.conf 
   70  sudo mongod -f /etc/mongod.conf 
   71  less /etc/mongod.conf 
   72  sudo service mongod status
   73  sudo service mongod start
   74  sudo service mongod status
   75  ls -l  /var/log/mongodb/mongod.log 
   76  sudo rm  /var/log/mongodb/mongod.log 
   77  sudo service mongod status
   78  sudo service mongod start
   79  sudo service mongod status
   80  sudo service mongod stop
   81  ps auxww | grep mongo
   82  sudo service mongod start
   83  sudo service mongod status
   84  ps auxww | grep mongo
   85  sudo dmsg
   86  sudo dmesg
   87  sudo service mongod status
   88  sudo service mongod stop
   89  sudo service mongod start
   90  sudo dmesg
   91  sudo less  /var/log/mongodb/mongod.log 
   92  ls /var/lib/
   93  ls -ld /var/lib/
   94  ls -l  /var/log/mongodb/mongod.log 
   95  ls -ld /var/lib/
   96  groups mongodb
   97  less /etc/mongod.conf 
   98  sudo less  /var/log/mongodb/mongod.log 
   99  less /etc/mongod.conf 
  100  ls -l /var/lib/mongodb/
  101  sudo chown -R mongodb /var/lib/mongodb/
  102  sudo chgrp -R mongodb /var/lib/mongodb/
  103  sudo service mongod start
  104  sudo service mongod status
  105  history



MONGO DB ROBO 3T
1. Download "Double Pack" from https://robomongo.org/
2. Untar its contents. Then untar the tarball in that.
3. Run:
    wharariki:[110]~/Downloads/robo3t-1.3.1-linux-x86_64-7419c406>./bin/robo3t

===================
On analytics, vagrant node1, we've installed the mongodb server and client.
We're able to successfully create collections on here.


vagrant@node1:~$ mongo
MongoDB shell version v4.2.1
connecting to: mongodb://127.0.0.1:27017/?compressors=disabled&gssapiServiceName=mongodb
Implicit session: session { "id" : UUID("87bb585c-4685-47f6-bf89-a93801daeb2d") }
MongoDB server version: 4.2.1
Server has startup warnings: 
2019-11-04T07:48:14.197+0000 I  STORAGE  [initandlisten] 
2019-11-04T07:48:14.198+0000 I  STORAGE  [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
2019-11-04T07:48:14.198+0000 I  STORAGE  [initandlisten] **          See http://dochub.mongodb.org/core/prodnotes-filesystem
2019-11-04T07:48:14.624+0000 I  CONTROL  [initandlisten] 
2019-11-04T07:48:14.624+0000 I  CONTROL  [initandlisten] ** WARNING: Access control is not enabled for the database.
2019-11-04T07:48:14.624+0000 I  CONTROL  [initandlisten] **          Read and write access to data and configuration is unrestricted.
2019-11-04T07:48:14.624+0000 I  CONTROL  [initandlisten] 
---
Enable MongoDB's free cloud-based monitoring service, which will then receive and display
metrics about your deployment (disk utilization, CPU, operation statistics, etc).

The monitoring data will be available on a MongoDB website with a unique URL accessible to you
and anyone you share the URL with. MongoDB may use this information to make product
improvements and to suggest MongoDB products and deployment options to you.

To enable free monitoring, run the following command: db.enableFreeMonitoring()
To permanently disable this reminder, run the following command: db.disableFreeMonitoring()
---

> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB
> use db ateacrawldata
2019-11-05T05:24:20.155+0000 E  QUERY    [js] Error: [db ateacrawldata] is not a valid database name :
Mongo.prototype.getDB@src/mongo/shell/mongo.js:51:12
getDatabase@src/mongo/shell/session.js:913:28
DB.prototype.getSiblingDB@src/mongo/shell/db.js:22:12
shellHelper.use@src/mongo/shell/utils.js:803:10
shellHelper@src/mongo/shell/utils.js:790:15
@(shellhelp2):1:1
> db.createCollection('webpages');
{ "ok" : 1 }
> db.webpages.drop();
... ^C

> db.webpages.drop();
true
> use ateacrawldata
switched to db ateacrawldata
> db.createCollection('webpages');
{ "ok" : 1 }
> show collections
webpages
> db.createCollection('websites');
{ "ok" : 1 }
> 

------------------------

Ask Clint to rename "anupama" database to "ateacrawldata" database following the instructions at:
    https://stackoverflow.com/questions/9201832/how-do-you-rename-a-mongodb-database
I don't have permissions to do this.
Nor do I have permissions to create Mongo collections within a new database that I create, like ateacrawldata.
I only seem to have rights to the "anupama" database.



-----------------------

MONGODB QUERIES:

db.getCollection('webpages').find({"isMRI": true, "singleSentences.langCode": "mri"})
db.getCollection('webpages').find({"singleSentences": { $elemMatch: {"langCode":"mri"} } }, {"singleSentences.$": "mri"})
db.getCollection('Webpages').find({"isMRI": true, "singleSentences": { $elemMatch: {"langCode":"eng"} } }, {"singleSentences.$": "eng"}) [single English lang sentence]
db.getCollection('Webpages').find({"containsMRI": true, "singleSentences": { $elemMatch: {"langCode":"mri"} } }, {"singleSentences.$": "mri"}) [gets 1st sentence of docs which have sentences containing MRI]


READING

mongodb java convert class
https://www.quora.com/What-are-the-ways-of-converting-a-Java-object-to-a-MongoDB-document-and-vice-versa
https://stackoverflow.com/questions/39320825/pojo-to-org-bson-document-and-vice-versa
X https://mongodb.github.io/morphia/
https://stackoverflow.com/questions/10170506/inserting-java-object-to-mongodb-collection-using-java
X https://www.google.com/search?q=morphia+example&oq=morphia+example&aqs=chrome.0.0l6.4223j0j9&sourceid=chrome&ie=UTF-8
https://www.baeldung.com/mongodb-morphia
X https://web.archive.org/web/20171117121335/http://mongodb.github.io/morphia/1.3/getting-started/
=> https://morphia.dev/1.4/getting-started/quick-tour/
https://github.com/MorphiaOrg/morphia/tree/master/docs/reference


mongodb querying
https://docs.mongodb.com/manual/tutorial/query-embedded-documents/
https://docs.mongodb.com/manual/tutorial/query-arrays/
https://www.google.com/search?q=mongodb+find+subdocument&oq=mongodb+find+&aqs=chrome.0.69i59j69i57j0l4.7607j1j8&sourceid=chrome&ie=UTF-8
https://stackoverflow.com/questions/25586901/how-to-find-document-and-single-subdocument-matching-given-criterias-in-mongodb
https://stackoverflow.com/questions/21113543/mongodb-get-subdocument
https://stackoverflow.com/questions/36948856/find-subdocuments-in-mongo
https://docs.mongodb.com/v3.0/reference/operator/projection/positional/#proj._S_
https://www.google.com/search?q=mongodb+query+tutorial&oq=mongodb+query+tutorial&aqs=chrome..69i57j0l2j69i60l3.4719j0j7&sourceid=chrome&ie=UTF-8
https://blog.exploratory.io/an-introduction-to-mongodb-query-for-beginners-bd463319aa4c
https://docs.mongodb.com/manual/reference/method/db.collection.find/
https://docs.mongodb.com/manual/reference/method/db.collection.find/#find-projection