[33644] | 1 | MongoDB
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| 2 | Installation:
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| 3 | https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
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| 4 | https://docs.mongodb.com/manual/administration/install-on-linux/
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| 5 | https://hevodata.com/blog/install-mongodb-on-ubuntu/
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| 6 | https://www.digitalocean.com/community/tutorials/how-to-install-mongodb-on-ubuntu-16-04
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| 7 | CENTOS (Analytics): https://tecadmin.net/install-mongodb-on-centos/
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| 8 | FROM SOURCE: https://github.com/mongodb/mongo/wiki/Build-Mongodb-From-Source
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| 9 | GUI:
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| 10 | https://robomongo.org/
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| 11 | Robomongo is Robo 3T now
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| 12 |
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| 13 | https://www.tutorialspoint.com/mongodb/mongodb_java.htm
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| 14 | JAR FILE:
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| 15 | http://central.maven.org/maven2/org/mongodb/mongo-java-driver/
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| 16 | https://mongodb.github.io/mongo-java-driver/
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| 17 |
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| 18 |
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| 19 |
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| 20 | https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
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| 21 | http://www.programmersought.com/article/6500308940/
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| 22 |
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| 23 | 52 sudo apt-get install mongodb-clients
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| 24 | 53 mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
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| 25 |
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| 26 | Failed with
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| 27 | Error: HostAndPort: host is empty at src/mongo/shell/mongo.js:148
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| 28 | exception: connect failed
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| 29 |
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| 30 | This is due to a version incompatibility between Client and mongodb Server.
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| 31 | The solution is to follow instructions at http://www.programmersought.com/article/6500308940/
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| 32 | and then https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/
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| 33 | as below:
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| 34 |
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| 35 | 54 sudo apt-get purge mongodb-clients
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| 36 | 55 sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
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| 37 | 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
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| 38 | 57 sudo apt-get update
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| 39 | 58 sudo apt-get install mongodb-clients
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| 40 | 59 mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
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| 41 | (still doesn't work)
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| 42 | 60 sudo apt-get install -y mongodb-org
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| 43 | 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?
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| 44 | 72 sudo service mongod status
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| 45 |
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| 46 | 103 sudo service mongod start
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| 47 | "mongod" stands for mongo-daemon. This runs the mongo db server listening for client connections
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| 48 | 104 sudo service mongod status
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| 49 | 88 sudo service mongod stop
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| 50 |
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| 51 |
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| 52 | DETAILS:
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| 53 |
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| 54 | wharariki:[879]/Scratch/ak19/gs3-extensions/maori-lang-detection>mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
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| 55 |
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| 56 | didn't work with the pwd. Failed with:
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| 57 |
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| 58 | MongoDB shell version: 2.6.10
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| 59 | Enter password:
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| 60 | connecting to: mongodb://mongodb.cms.waikato.ac.nz:27017
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| 61 | 2019-11-04T20:02:47.970+1300 Assertion: 13110:HostAndPort: host is empty
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| 62 | 2019-11-04T20:02:47.970+1300 0x6b75c9 0x659e9f 0x636f69 0x4fa55c 0x501249 0x4fa7f1 0x6006fd 0x5eb869 0x7f7bfbd47d76 0x1f3c10d06362
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| 63 | mongo(_ZN5mongo15printStackTraceERSo+0x39) [0x6b75c9]
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| 64 | mongo(_ZN5mongo10logContextEPKc+0x21f) [0x659e9f]
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| 65 | mongo(_ZN5mongo11msgassertedEiPKc+0xd9) [0x636f69]
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| 66 | mongo(_ZN5mongo16ConnectionString12_fillServersENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x50c) [0x4fa55c]
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| 67 | mongo(_ZN5mongo16ConnectionStringC1ENS0_14ConnectionTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_+0x99) [0x501249]
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| 68 | mongo(_ZN5mongo16ConnectionString5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_+0x201) [0x4fa7f1]
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| 69 | mongo(_ZN5mongo17mongoConsExternalEPNS_7V8ScopeERKN2v89ArgumentsE+0x11d) [0x6006fd]
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| 70 | mongo(_ZN5mongo7V8Scope10v8CallbackERKN2v89ArgumentsE+0xa9) [0x5eb869]
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| 71 | /usr/lib/libv8.so.3.14.5(+0x99d76) [0x7f7bfbd47d76]
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| 72 | [0x1f3c10d06362]
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| 73 | 2019-11-04T20:02:47.971+1300 Error: HostAndPort: host is empty at src/mongo/shell/mongo.js:148
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| 74 | exception: connect failed
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| 75 |
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| 76 |
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| 77 | This is due to a version incompatibility between Client and mongodb Server.
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| 78 | Can find client version above. (2.6.10)
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| 79 | Server version can be found by running the mongo client shell. Doing so without loading a db:
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| 80 |
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| 81 |
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| 82 | wharariki:[880]/Scratch/ak19/gs3-extensions/maori-lang-detection>mongo --shell -nodb
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| 83 | MongoDB shell version: 2.6.10 <<<<<<<<<-------------------<<<< MONGO CLIENT VERSION
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| 84 | type "help" for help
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| 85 | > help
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| 86 | db.help() help on db methods
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| 87 | db.mycoll.help() help on collection methods
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| 88 | sh.help() sharding helpers
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| 89 | rs.help() replica set helpers
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| 90 | help admin administrative help
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| 91 | help connect connecting to a db help
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| 92 | help keys key shortcuts
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| 93 | help misc misc things to know
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| 94 | help mr mapreduce
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| 95 |
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| 96 | show dbs show database names
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| 97 | show collections show collections in current database
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| 98 | show users show users in current database
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| 99 | show profile show most recent system.profile entries with time >= 1ms
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| 100 | show logs show the accessible logger names
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| 101 | show log [name] prints out the last segment of log in memory, 'global' is default
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| 102 | use <db_name> set current database
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| 103 | db.foo.find() list objects in collection foo
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| 104 | db.foo.find( { a : 1 } ) list objects in foo where a == 1
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| 105 | it result of the last line evaluated; use to further iterate
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| 106 | DBQuery.shellBatchSize = x set default number of items to display on shell
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| 107 | exit quit the mongo shell
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| 108 |
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| 109 | > help connect
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| 110 |
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| 111 | Normally one specifies the server on the mongo shell command line. Run mongo --help to see those options.
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| 112 | Additional connections may be opened:
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| 113 |
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| 114 | var x = new Mongo('host[:port]');
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| 115 | var mydb = x.getDB('mydb');
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| 116 | or
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| 117 | var mydb = connect('host[:port]/mydb');
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| 118 |
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| 119 | Note: the REPL prompt only auto-reports getLastError() for the shell command line connection.
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| 120 |
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| 121 | Getting help on connect options:
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| 122 |
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| 123 | > var x = new Mongo('mongodb.cms.waikato.ac.nz:27017');
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| 124 | > var mydb = x.getDB('anupama');
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| 125 |
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| 126 | > mydb.connect.help()
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| 127 | DBCollection help
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| 128 | db.connect.find().help() - show DBCursor help
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| 129 | db.connect.count()
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| 130 | db.connect.copyTo(newColl) - duplicates collection by copying all documents to newColl; no indexes are copied.
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| 131 | db.connect.convertToCapped(maxBytes) - calls {convertToCapped:'connect', size:maxBytes}} command
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| 132 | db.connect.dataSize()
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| 133 | db.connect.distinct( key ) - e.g. db.connect.distinct( 'x' )
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| 134 | db.connect.drop() drop the collection
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| 135 | db.connect.dropIndex(index) - e.g. db.connect.dropIndex( "indexName" ) or db.connect.dropIndex( { "indexKey" : 1 } )
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| 136 | db.connect.dropIndexes()
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| 137 | db.connect.ensureIndex(keypattern[,options]) - options is an object with these possible fields: name, unique, dropDups
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| 138 | db.connect.reIndex()
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| 139 | db.connect.find([query],[fields]) - query is an optional query filter. fields is optional set of fields to return.
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| 140 | e.g. db.connect.find( {x:77} , {name:1, x:1} )
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| 141 | db.connect.find(...).count()
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| 142 | db.connect.find(...).limit(n)
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| 143 | db.connect.find(...).skip(n)
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| 144 | db.connect.find(...).sort(...)
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| 145 | db.connect.findOne([query])
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| 146 | db.connect.findAndModify( { update : ... , remove : bool [, query: {}, sort: {}, 'new': false] } )
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| 147 | db.connect.getDB() get DB object associated with collection
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| 148 | db.connect.getPlanCache() get query plan cache associated with collection
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| 149 | db.connect.getIndexes()
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| 150 | db.connect.group( { key : ..., initial: ..., reduce : ...[, cond: ...] } )
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| 151 | db.connect.insert(obj)
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| 152 | db.connect.mapReduce( mapFunction , reduceFunction , <optional params> )
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| 153 | db.connect.aggregate( [pipeline], <optional params> ) - performs an aggregation on a collection; returns a cursor
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| 154 | db.connect.remove(query)
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| 155 | db.connect.renameCollection( newName , <dropTarget> ) renames the collection.
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| 156 | db.connect.runCommand( name , <options> ) runs a db command with the given name where the first param is the collection name
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| 157 | db.connect.save(obj)
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| 158 | db.connect.stats()
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| 159 | db.connect.storageSize() - includes free space allocated to this collection
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| 160 | db.connect.totalIndexSize() - size in bytes of all the indexes
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| 161 | db.connect.totalSize() - storage allocated for all data and indexes
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| 162 | db.connect.update(query, object[, upsert_bool, multi_bool]) - instead of two flags, you can pass an object with fields: upsert, multi
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| 163 | db.connect.validate( <full> ) - SLOW
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| 164 | db.connect.getShardVersion() - only for use with sharding
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| 165 | db.connect.getShardDistribution() - prints statistics about data distribution in the cluster
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| 166 | db.connect.getSplitKeysForChunks( <maxChunkSize> ) - calculates split points over all chunks and returns splitter function
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| 167 | db.connect.getWriteConcern() - returns the write concern used for any operations on this collection, inherited from server/db if set
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| 168 | db.connect.setWriteConcern( <write concern doc> ) - sets the write concern for writes to the collection
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| 169 | db.connect.unsetWriteConcern( <write concern doc> ) - unsets the write concern for writes to the collection
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| 170 | > mydb.version()
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| 171 | 4.0.13 <<<<<<<<<-------------------<<<< MONGODB SERVER VERSION
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| 172 |
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| 173 | (Check Mongo server version: https://stackoverflow.com/questions/38160412/how-to-find-the-exact-version-of-installed-mongodb)
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| 174 |
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| 175 | Finally we now know the mongodb server version: 4.0.13
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| 176 | This version doesn't work with our mongo client (shell) version of 2.6.10.
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| 177 |
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| 178 |
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| 179 | DETAILS OF INSTALLING MONGO-CLIENT AND UPDATING IT, AND INSTALLING MONGODB SERVER:
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| 180 |
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| 181 |
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| 182 | 54 sudo apt-get purge mongodb-clients
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| 183 | 55 sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 9DA31620334BD75D9DCB49F368818C72E52529D4
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| 184 | 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
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| 185 | 57 sudo apt-get update
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| 186 | 58 sudo apt-get install mongodb-clients
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| 187 | 59 mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
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| 188 | 60 sudo apt-get install -y mongodb-org
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| 189 | 61 mongo 'mongodb://mongodb.cms.waikato.ac.nz:27017' -u anupama -p
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| 190 | 62 sudo service apache2 status
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| 191 | 63 sudo service sshd status
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| 192 | 64 sudo service mongodb status
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| 193 | 65 sudo service mongo status
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| 194 | 66 mongod
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| 195 | 67 mongod --help
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| 196 | 68 mongod --help | less
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| 197 | 69 mongod -f /etc/mongod.conf
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| 198 | 70 sudo mongod -f /etc/mongod.conf
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| 199 | 71 less /etc/mongod.conf
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| 200 | 72 sudo service mongod status
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| 201 | 73 sudo service mongod start
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| 202 | 74 sudo service mongod status
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| 203 | 75 ls -l /var/log/mongodb/mongod.log
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| 204 | 76 sudo rm /var/log/mongodb/mongod.log
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| 205 | 77 sudo service mongod status
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| 206 | 78 sudo service mongod start
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| 207 | 79 sudo service mongod status
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| 208 | 80 sudo service mongod stop
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| 209 | 81 ps auxww | grep mongo
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| 210 | 82 sudo service mongod start
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| 211 | 83 sudo service mongod status
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| 212 | 84 ps auxww | grep mongo
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| 213 | 85 sudo dmsg
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| 214 | 86 sudo dmesg
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| 215 | 87 sudo service mongod status
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| 216 | 88 sudo service mongod stop
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| 217 | 89 sudo service mongod start
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| 218 | 90 sudo dmesg
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| 219 | 91 sudo less /var/log/mongodb/mongod.log
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| 220 | 92 ls /var/lib/
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| 221 | 93 ls -ld /var/lib/
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| 222 | 94 ls -l /var/log/mongodb/mongod.log
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| 223 | 95 ls -ld /var/lib/
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| 224 | 96 groups mongodb
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| 225 | 97 less /etc/mongod.conf
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| 226 | 98 sudo less /var/log/mongodb/mongod.log
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| 227 | 99 less /etc/mongod.conf
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| 228 | 100 ls -l /var/lib/mongodb/
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| 229 | 101 sudo chown -R mongodb /var/lib/mongodb/
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| 230 | 102 sudo chgrp -R mongodb /var/lib/mongodb/
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| 231 | 103 sudo service mongod start
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| 232 | 104 sudo service mongod status
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| 233 | 105 history
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| 234 |
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| 235 |
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| 236 |
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| 237 | MONGO DB ROBO 3T
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| 238 | 1. Download "Double Pack" from https://robomongo.org/
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| 239 | 2. Untar its contents. Then untar the tarball in that.
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| 240 | 3. Run:
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| 241 | wharariki:[110]~/Downloads/robo3t-1.3.1-linux-x86_64-7419c406>./bin/robo3t
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| 242 |
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| 243 | ===================
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| 244 | On analytics, vagrant node1, we've installed the mongodb server and client.
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| 245 | We're able to successfully create collections on here.
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| 246 |
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| 247 |
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| 248 | vagrant@node1:~$ mongo
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| 249 | MongoDB shell version v4.2.1
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| 250 | connecting to: mongodb://127.0.0.1:27017/?compressors=disabled&gssapiServiceName=mongodb
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| 251 | Implicit session: session { "id" : UUID("87bb585c-4685-47f6-bf89-a93801daeb2d") }
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| 252 | MongoDB server version: 4.2.1
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| 253 | Server has startup warnings:
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| 254 | 2019-11-04T07:48:14.197+0000 I STORAGE [initandlisten]
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| 255 | 2019-11-04T07:48:14.198+0000 I STORAGE [initandlisten] ** WARNING: Using the XFS filesystem is strongly recommended with the WiredTiger storage engine
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| 256 | 2019-11-04T07:48:14.198+0000 I STORAGE [initandlisten] ** See http://dochub.mongodb.org/core/prodnotes-filesystem
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| 257 | 2019-11-04T07:48:14.624+0000 I CONTROL [initandlisten]
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| 258 | 2019-11-04T07:48:14.624+0000 I CONTROL [initandlisten] ** WARNING: Access control is not enabled for the database.
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| 259 | 2019-11-04T07:48:14.624+0000 I CONTROL [initandlisten] ** Read and write access to data and configuration is unrestricted.
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| 260 | 2019-11-04T07:48:14.624+0000 I CONTROL [initandlisten]
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| 261 | ---
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| 262 | Enable MongoDB's free cloud-based monitoring service, which will then receive and display
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| 263 | metrics about your deployment (disk utilization, CPU, operation statistics, etc).
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| 264 |
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| 265 | The monitoring data will be available on a MongoDB website with a unique URL accessible to you
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| 266 | and anyone you share the URL with. MongoDB may use this information to make product
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| 267 | improvements and to suggest MongoDB products and deployment options to you.
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| 268 |
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| 269 | To enable free monitoring, run the following command: db.enableFreeMonitoring()
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| 270 | To permanently disable this reminder, run the following command: db.disableFreeMonitoring()
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| 271 | ---
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| 272 |
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| 273 | > show dbs
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| 274 | admin 0.000GB
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| 275 | config 0.000GB
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| 276 | local 0.000GB
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| 277 | > use db ateacrawldata
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| 278 | 2019-11-05T05:24:20.155+0000 E QUERY [js] Error: [db ateacrawldata] is not a valid database name :
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| 279 | Mongo.prototype.getDB@src/mongo/shell/mongo.js:51:12
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| 280 | getDatabase@src/mongo/shell/session.js:913:28
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| 281 | DB.prototype.getSiblingDB@src/mongo/shell/db.js:22:12
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| 282 | shellHelper.use@src/mongo/shell/utils.js:803:10
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| 283 | shellHelper@src/mongo/shell/utils.js:790:15
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| 284 | @(shellhelp2):1:1
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| 285 | > db.createCollection('webpages');
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| 286 | { "ok" : 1 }
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[33646] | 287 | > db.webpages.drop();
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[33644] | 288 | ... ^C
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| 289 |
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| 290 | > db.webpages.drop();
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| 291 | true
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| 292 | > use ateacrawldata
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| 293 | switched to db ateacrawldata
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| 294 | > db.createCollection('webpages');
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| 295 | { "ok" : 1 }
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| 296 | > show collections
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| 297 | webpages
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| 298 | > db.createCollection('websites');
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| 299 | { "ok" : 1 }
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| 300 | >
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| 301 |
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| 302 | ------------------------
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| 303 |
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| 304 | Ask Clint to rename "anupama" database to "ateacrawldata" database following the instructions at:
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| 305 | https://stackoverflow.com/questions/9201832/how-do-you-rename-a-mongodb-database
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| 306 | I don't have permissions to do this.
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| 307 | Nor do I have permissions to create Mongo collections within a new database that I create, like ateacrawldata.
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| 308 | I only seem to have rights to the "anupama" database.
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| 309 |
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| 310 |
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[33646] | 311 |
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| 312 | -----------------------
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| 313 |
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| 314 | MONGODB QUERIES:
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| 315 |
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| 316 | db.getCollection('webpages').find({"isMRI": true, "singleSentences.langCode": "mri"})
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| 317 | db.getCollection('webpages').find({"singleSentences": { $elemMatch: {"langCode":"mri"} } }, {"singleSentences.$": "mri"})
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[33653] | 318 | db.getCollection('Webpages').find({"isMRI": true, "singleSentences": { $elemMatch: {"langCode":"eng"} } }, {"singleSentences.$": "eng"}) [single English lang sentence]
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| 319 | db.getCollection('Webpages').find({"containsMRI": true, "singleSentences": { $elemMatch: {"langCode":"mri"} } }, {"singleSentences.$": "mri"}) [gets 1st sentence of docs which have sentences containing MRI]
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[33646] | 320 |
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| 321 |
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| 322 | READING
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| 323 |
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| 324 | mongodb java convert class
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| 325 | https://www.quora.com/What-are-the-ways-of-converting-a-Java-object-to-a-MongoDB-document-and-vice-versa
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| 326 | https://stackoverflow.com/questions/39320825/pojo-to-org-bson-document-and-vice-versa
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| 327 | X https://mongodb.github.io/morphia/
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| 328 | https://stackoverflow.com/questions/10170506/inserting-java-object-to-mongodb-collection-using-java
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| 329 | X https://www.google.com/search?q=morphia+example&oq=morphia+example&aqs=chrome.0.0l6.4223j0j9&sourceid=chrome&ie=UTF-8
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| 330 | https://www.baeldung.com/mongodb-morphia
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| 331 | X https://web.archive.org/web/20171117121335/http://mongodb.github.io/morphia/1.3/getting-started/
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| 332 | => https://morphia.dev/1.4/getting-started/quick-tour/
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| 333 | https://github.com/MorphiaOrg/morphia/tree/master/docs/reference
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| 334 |
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| 335 |
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| 336 | mongodb querying
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| 337 | https://docs.mongodb.com/manual/tutorial/query-embedded-documents/
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| 338 | https://docs.mongodb.com/manual/tutorial/query-arrays/
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| 339 | https://www.google.com/search?q=mongodb+find+subdocument&oq=mongodb+find+&aqs=chrome.0.69i59j69i57j0l4.7607j1j8&sourceid=chrome&ie=UTF-8
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| 340 | https://stackoverflow.com/questions/25586901/how-to-find-document-and-single-subdocument-matching-given-criterias-in-mongodb
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| 341 | https://stackoverflow.com/questions/21113543/mongodb-get-subdocument
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| 342 | https://stackoverflow.com/questions/36948856/find-subdocuments-in-mongo
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| 343 | https://docs.mongodb.com/v3.0/reference/operator/projection/positional/#proj._S_
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| 344 | https://www.google.com/search?q=mongodb+query+tutorial&oq=mongodb+query+tutorial&aqs=chrome..69i57j0l2j69i60l3.4719j0j7&sourceid=chrome&ie=UTF-8
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| 345 | https://blog.exploratory.io/an-introduction-to-mongodb-query-for-beginners-bd463319aa4c
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| 346 | https://docs.mongodb.com/manual/reference/method/db.collection.find/
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| 347 | https://docs.mongodb.com/manual/reference/method/db.collection.find/#find-projection
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[33666] | 348 |
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| 349 |
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| 350 | -------------------
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| 351 |
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| 352 | Some queries with results:
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| 353 |
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| 354 | # Num websites
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| 355 | db.getCollection('Websites').find({}).count()
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| 356 | 1446
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| 357 |
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| 358 | # Num webpages
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| 359 | db.getCollection('Webpages').find({}).count()
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| 360 | 75139
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| 361 |
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| 362 | # Find number of websites who have 1 or more pages in Maori (a positive numPagesInMRI)
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| 363 | db.getCollection('Websites').find({numPagesInMRI: { $gt: 0}}).count()
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| 364 | 361
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| 365 |
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| 366 | # Find number of webpages that are deemed to be overall in MRI (pages where isMRI=true)
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| 367 | db.getCollection('Webpages').find({isMRI:true}).count()
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| 368 | X5224
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| 369 | 5215
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| 370 |
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| 371 | # Number of pages that contain any number of MRI sentences
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| 372 | db.getCollection('Webpages').find({containsMRI: true}).count()
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| 373 | 12858
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| 374 |
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| 375 | # Number of sites with URLs containing /mi(/)
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| 376 | db.getCollection('Websites').find({urlContainsLangCodeInpath:true}).count()
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| 377 | 153
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| 378 |
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| 379 | # Number of websites that are outside NZ that contain /mi(/) in any of its sub-urls
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| 380 | db.getCollection('Websites').find({urlContainsLangCodeInpath:true, geoLocationCountryCode: {$ne : "NZ"} }).count()
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| 381 | 148
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| 382 |
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| 383 | # 5 sites with URLs containing /mi(/) that are in NZ
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| 384 | db.getCollection('Websites').find({urlContainsLangCodeInpath:true, geoLocationCountryCode: "NZ"}).count()
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| 385 | 5
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| 386 |
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| 387 | # sort websites that contain /mi(/) in path by geoLocationCountryCode
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| 388 | # https://www.quackit.com/mongodb/tutorial/mongodb_sort_query_results.cfm
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| 389 | db.getCollection('Websites').find({urlContainsLangCodeInpath:true}).sort({geoLocationCountryCode: 1})
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| 390 |
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| 391 |
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