Opasnet Base

This page is a knowledge crystal of subtype method. The page identifier is Op_en5474
Moderator:Jouni (see all)
Citation of this page: Juha Villman, Einari Happonen, Jouni T. Tuomisto: Opasnet Base. Opasnet 2012. [1]. Accessed 23 Nov 2024.
Upload data {{#opasnet_base_link:Op_en5474}}

This page is about the Opasnet Base database. The previous version is described on page Opasnet Base (2008-2011).

Question

How to improve the existing Opasnet Base? Following issues of Opasnet Base 1 must be resolved:

• Opasnet Base 1 structure makes filtering by location very slow on big data
• Opasnet Base 1 structure is perhaps unnecessarily complex = queries are hard to adapt and read
• MySQL is not ideal for storing huge amounts of data, or at least this is how we assume?
• MySQL tables have fixed column types = difficult to store data objects with varying types of indices into one data table
• Multiple languages (localization) not supported

Answer

MySQL is good on relations but weak on dynamic big data. Let's keep the basic "scaffold" in MySQL and store the big data (locations and results) into noSQL-base. After few days of research the best candidate for noSQL-base seems to be MongoDB. Combining relational MySQL and non-relational MongoDB will be the foundation for the new Opasnet Base 2.

Table structure in the database

All tables

acts Uploads, updates, and other actions Field Type Null Extra Key id int(10) unsigned NO auto_increment PRI obj_id int(10) unsigned NO series_id int(10) unsigned NO unit varchar(64) YES type ENUM('replace','append') NO who varchar(255) NO when timestamp NO comments varchar(255) YES lang char(3) NO ISO 639-2, default:'eng' ----1: . I guess this should have field obj_id to identify which object we are updating. In the previous version, act - obj was many-to-many relationship, but it can as well be many-to-one which makes life easier; it is not important to know that two variables were uploaded in the same model run. Also series_id and unit could be in this table. --Jouni 22:56, 22 February 2012 (EET) (type: truth; paradigms: science: comment) ←--2: . I have now altered the table structure to implement Jouni's idea. --Einari 12:31, 19 March 2012 (EET) (type: truth; paradigms: science: defence)
objs Object information (all objects) Field Type Null Extra Key id int(10) unsigned NO auto_increment PRI ident varchar(64) NO UNI name varchar(255) NO subset varchar(255) NO UNI(with ident) type ENUM('variable','study','method','assessment','class','nugget','encyclopedia') NO page int(10) unsigned NO wiki_id tinyint(3) unsigned NO	inds Indices Field Type Null Extra Key id int(10) unsigned NO auto_increment PRI series_id int(10) unsigned NO UNI(with ident) ident varchar(64) NO UNI(with series_id) type ENUM('entity','number','time') NO name varchar(255) NO unit varchar(64) YES page int(10) unsigned NO wiki_id tinyint(3) unsigned NO order_index int(10) unsigned NO hidden boolean NO false
wikis Wiki information Field Type Null Extra Key id tinyint(3) NO PRI url varchar(255) NO wname varchar(255) NO

MongoDB

Tables to store all locations and results

db.<objs.ident>(.<objs.subset>).dat

Column names:
sid(series.id), aid (act.id), <inds.ident>, <inds.ident>, ..., <inds.ident>, res (result)

Data:
<acts.series_id>, <acts.id>, <locs.id | data>, <locs.id | data>, ..., <locs.id | data>,

Index:
db.<objs.ident>(.<objs.subset>).dat.ensureIndex({_sid:1, _aid:1});

----#: . I guess this is about loc.id's, not about ind.id's. Loc.id's are either identifiers explained below or values of continuous indices. --Jouni 22:56, 22 February 2012 (EET) (type: truth; paradigms: science: comment)
⇤--#: . It was actually about ind.id, but the line described column names, not the data itself. To avoid future misleads I added data describing line as well. Object data can consist of location identifiers or e.g. real numbers, depending of the type of the column index. --Einari 13:33, 19 March 2012 (EET) (type: truth; paradigms: science: attack)

Tables to store real location values for entity type indices

db.<objs.ident>(.<objs.subset>).locs

Column names:
iid (index id), lid (location id), val

Index:
ensureIndex(array("iid" => 1, "lid" => 1));

←--#: . If the index is entity type, inds.id is the identifier of the index (whose details are in MySQL) and value is the name of the location. If the index is continuous, it does not need rows in this table, as everything necessary is described in the tables inds and db.<object.ident>.dat. --Jouni 22:56, 22 February 2012 (EET) (type: truth; paradigms: science: defence)

----#: . What is key? --Jouni 22:56, 22 February 2012 (EET) (type: truth; paradigms: science: comment)
←--#: . Key was something that I cannot really confirm. I altered the table description so that index id and location id together make the key (indexed in that order). This means that location values must always be accessed through index id. I believe that this is the fastest way in practice. --Einari 14:35, 19 March 2012 (EET) (type: truth; paradigms: science: defence)

----Toinen asia OB2:een liittyen: Indekseille pitäisi pystyä antamaan yksiköt, koska ne eivät ole itsestäänselviä (Erkki huomasi tämän). Onko tämän toteutus suunniteltu? Seka kannassa pitää olla paikka, ja lisäksi esim. t2b:ssa olisi syytä olla parametri yksiköiden antamista varten (tai pitäisikö nykyistä unit-parametrin käyttöä laajentaa?).: . --Jouni 16:25, 1 January 2013 (EET) {{{3}}} (type: truth; paradigms: science: comment)

JSON interface

The interface is based on a PHP script that outputs JSON, so data can be transferred using ordinary HTTP requests. One could even read through most of the meta-data in a web browser with a plugin that displays json better:

• firefox addon - https://addons.mozilla.org/en-US/firefox/addon/jsonview/
• list of objects http://cl1.opasnet.org/opasnet_base_2/index.php
• most recent upload of an object - http://cl1.opasnet.org/opasnet_base_2/index.php?ident=op_en5599&act=0
• data (key is unique to every download instance and is generated when the above link is opened) - http://cl1.opasnet.org/opasnet_base_2/index.php?key=8dYqLbtppz4HM7sYaAyj4t6S49jQNRWJ

Rationale

• Opasnet Base structure
• Opasnet Base
• Opasnet structure
• Open assessment

See also

Other databases with (ot without) R connectivity

• API Guide for http://www.avoindata.fi
• statfi R package for Statistics Finland [2]
• eurostat R package for Eurostat data [3]
• fmi R package for Finnish Meteorological Institute [4]
• rOpenGov project for useful data and computing for decisions
• sorvi R package for some basic functionalities such as social security number functions