Opasnet base structure

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This page is about the structure of Opasnet Base. For a general description, see Opasnet base.

Scope

Opasnet base is a storage and retrieval system for results of variable and data from studies. What is the structure of Opasnet base such that it enables the following functionalities?

  1. Storage of results of variables with uncertainties when necessary, and as multidimensional arrays when necessary.R↻
  2. Automatic retrieval of results when called from Opasnet wiki or other platforms or modelling systems.
  3. Description and handling of the dimensions that a variable may take.
  4. It is possible to protect some results and data from reading by unauthorised persons.
  5. If is possible to build user interfaces for easily entering observations into the Base.


Definition

Data

Software

Because Opasnet base will contain very large amounts of mostly numerical information, the state-of-the-art structure is a SQL database. Because of its flexibility, ease of use, and cost, MySQL is an optimal choice among SQL software. In addition to the database software, a variable transfer protocol is needed on top of that so that the results of variables can be retrieved and new results stored either automatically by a calculating software, or manually by the user. Fancy presenting software can be built on top of the database, but that is not the topic of this page.

Storage and retrieval of results of variables

The most important functionality is to store and retrieve the results of variables. Because variables may take very different forms (from a single value such as natural constant to an uncertain spatio-temporal concentration field over the whole Europe), the database must be very flexible. The basic solution is described in the variable page, and it is only briefly summarised here. The result is described as 

  P(R|x1,x2,...)

where P(R) is the probability distribution of the result and x1 and x2 are defining locations of a dimension where a particular P(R) applies. Typically locations are operationalised as discrete indices. A variable must have at least one dimension. Uncertainty about the true value of the variable is operationalised as a random sample from the probability distribution, in such a way that the samples are located along an index Sample, which is a list of integers 1,2,3...n, where n=number of samples.


Dependencies

Result

Opasnet base is a MySQL database located at http://base.opasnet.org.

Table structure

Formula structure

Now it has become clear that it is not enough to have samples of the result distributions. It must be possible to completely recalculate the result based on the information in the Opasnet Base. There are different approaches:

  • Calculate the result based on a formula that may refer to other variables called parents. This is a deterministic approach.
  • Calculate the result based on the marginal distribution and (conditional) rank correlations with parent variables. This is a probabilistic approach.


This approach requires new tables, namely:

  • Formula
    • id (automatic incremental integer)
    • Obj_id_v
    • Obj_id_r
    • When (what is the relationship between upload and formula/When? Is there always a new formula for a new upload? No, because the upload may change even if formula doesn't, if the parent change. Is there always a new upload for a new formula? Yes, because it is necessary to make a new upload.
    • Language (of the formula code)
    • Code (a large text or memo field for the formula)
--# : Do we need tables DIF and DIP like Uninet? --Jouni 21:50, 30 December 2009 (UTC)
  • DIP
    • DIP_node_id
    • DIP_parent_node_id
    • DIP_corr_coeff
    • DIP_parent_index
  • DIF
    • DIF_node_id
    • DIF_formula
    • DIF_varnames_in_formula


Objinfo: new structure

The structure of Objinfo should be changed. The original plan was that there is at most one row of Objinfo per Object. Now it is clear that this does not have all functionalities we need. Instead, there should be a possibility to add any number of actions per object. Therefore, even the name of the table should be changed to Act. The structure should be changed accordingly:

  • The field id is the primary field for the table. It is NOT the Obj.id any longer.
  • A new field Obj_id should be added. This is the old field id.
  • End field should be removed, it is not used.
  • Url should be changed to Comment, as it may contain also other info.
  • The length of Comment should be 250 characters (at least).
  • Begin should be replaced by When, which is the current timestamp of the row addition.
  • A new field Act_id should be added.
  • A new table Acttype for actions should be added. It would contain only fields id and Act, and the following rows:
    1. Start the object
    2. Finish the assessment
    3. Add a reference
    4. Add an URL
    5. Peer review the object definition: accept based on the discussion
    6. Peer review the object definition: reject based on the discussion
    7. Peer review the object definition: accept (personal opinion)
    8. Peer review the object definition: reject (personal opinion)
    9. Clairvoyant test for the scope: pass
    10. Clairvoyant test for the scope: fail
    11. Save a run of the object.

Merging Res and Resinfo -tables

These tables should be merged. Discussion is here D↷.

All tables: Overview

  • We need Ressec (Result secure) and Resinfosec (Result info secure) tables for secure information. All other tables are openly readable except these two. They have the same structure as Res and Resinfo tables, respectively.


Tables_in_opasnet_base
Table Description
Cell Cells of an object
Formula Formulas for computing variable results
Item
Loc Location information
Loccell Locations of a cell
Log
Obj Object information (all objects)
Objinfo Additional information about the objects
Objtype Types of objects
Res Result distribution (actual values)
Resinfo Additional description of the result
Resinfosec Additional description of the result
Ressec Result distribution (actual values)
Sett Memberships of items in sets
Settype Types of set-item memeberships
Wiki Wiki information
⇤3 : Res and Resinfo should be merged. Similarly, Ressec and Resinfosec should be merged. --Jouni 09:48, 31 December 2009 (UTC)
⇤4 : We may need to divide Obj into Obj and Task. Task table would contain uploads (previously Runs) and formula updates. --Jouni 09:48, 31 December 2009 (UTC)


Tables with primary content
Table Field Type Null Key Default Extra
Cell id int(12) unsigned NO PRI NULL auto_increment
Cell Obj_id_v int(10) unsigned NO MUL NULL
Cell Obj_id_r int(10) unsigned NO NULL
Cell Mean float YES NULL
Cell SD float NO NULL
Cell N int(10) NO NULL
Formula id int(10) unsigned NO PRI NULL auto_increment
Formula Obj_id_v int(10) unsigned NO MUL NULL
Formula When timestamp NO CURRENT_TIMESTAMP
Formula Language smallint(5) unsigned NO NULL
Formula Code longtext YES NULL
Loc id int(10) unsigned NO PRI NULL auto_increment
Loc Std_id int(10) unsigned NO MUL NULL
Loc Obj_id_i int(10) unsigned NO MUL NULL
Loc Location varchar(100) NO NULL
Loc Roww mediumint(8) unsigned NO NULL
Loc Description varchar(150) NO NULL
Loccell id int(10) unsigned NO PRI NULL auto_increment
Loccell Cell_id int(10) unsigned NO MUL NULL
Loccell Loc_id int(10) unsigned NO NULL
Obj id int(10) unsigned NO PRI NULL auto_increment
Obj Ident varchar(20) NO UNI NULL
Obj Name varchar(200) NO NULL
Obj Unit varchar(16) NO NULL
Obj Objtype_id tinyint(3) unsigned NO MUL NULL
Obj Page int(10) unsigned NO NULL
Obj Wiki_id tinyint(3) unsigned NO NULL
Obj Newest int(10) unsigned NO MUL NULL
Objinfo id int(10) unsigned NO PRI NULL auto_increment
Objinfo Obj_id int(10) unsigned NO MUL NULL
Objinfo Acttype_id tinyint(3) unsigned NO NULL
Objinfo Begin date NO MUL NULL
Objinfo End date NO NULL
Objinfo Who varchar(50) NO NULL
Objinfo Comments varchar(250) NO NULL
Objinfo Moment timestamp NO CURRENT_TIMESTAMP
Res id bigint(20) unsigned NO PRI NULL auto_increment
Res Cell_id int(12) unsigned NO MUL NULL
Res Obs int(10) unsigned NO NULL
Res Result float NO NULL
Resinfo id bigint(20) unsigned NO PRI NULL auto_increment
Resinfo Restext varchar(250) NO NULL
Resinfo Who varchar(50) NO NULL
Resinfo When timestamp NO CURRENT_TIMESTAMP
Resinfosec id bigint(20) unsigned NO PRI NULL auto_increment
Resinfosec Restext varchar(250) NO NULL
Resinfosec Who varchar(50) NO NULL
Resinfosec When timestamp NO CURRENT_TIMESTAMP
Ressec id bigint(20) unsigned NO PRI NULL auto_increment
Ressec Cell_id int(12) unsigned NO MUL NULL
Ressec Obs int(10) unsigned NO NULL
Ressec Result float NO NULL
⇤1: Obj.Unit should have at least 32 characters. --Jouni 19:29, 17 September 2009 (EEST)
←2: We can increase it to 64 at once. --Juha Villman 07:52, 18 September 2009 (EEST)
⇤5 : We should add Res.Formula_id. --Jouni 21:50, 30 December 2009 (UTC)


Tables with additional information
Table Field Type Null Key Default Extra
Item id int(10) unsigned NO PRI NULL auto_increment
Item Sett_id int(10) unsigned NO MUL NULL
Item Obj_id int(10) unsigned NO NULL
Item Fail tinyint(1) unsigned NO MUL NULL
Log id int(10) NO PRI NULL auto_increment
Log ip varchar(15) NO NULL
Log wiki_uid varchar(30) YES NULL
Log wiki_page varchar(30) YES NULL
Log time timestamp NO 0000-00-00 00:00:00
Log query varchar(256) NO NULL
Sett id int(10) unsigned NO PRI NULL auto_increment
Sett Obj_id int(10) unsigned NO MUL NULL
Sett Settype_id tinyint(3) unsigned NO NULL



Tables with lists
Table Field Type Null Key Default Extra
Objtype id tinyint(3) NO PRI NULL
Objtype Objtype varchar(30) NO NULL
Settype id tinyint(3) unsigned NO PRI NULL auto_increment
Settype Settype varchar(30) NO NULL
Wiki id tinyint(3) NO PRI NULL
Wiki Url varchar(255) NO NULL
Wiki Wname varchar(20) NO NULL

See also

Some useful syntax

<sql-query display=1> SELECT Obj.id, Obj.Ident, Obj.Name, Obj.Typ_id, Sty_id, Itemm.Ident as Iident, Itemm.Name as Iname FROM Obj LEFT JOIN Sett ON Obj.id = Sett.Obj_id LEFT JOIN Item ON Sett.id = Item.Sett_id LEFT JOIN Obj AS Itemm ON Item.Obj_id = Itemm.id </sql-query>


NOTE! The queries below work in the new database "opasnet_base", not "resultdb" as the old versions.

{{#sql-query: SELECT Var.Ident, Var.Name, Var.Unit, Run.Ident, Begin, Who, Run.Name as Method FROM Obj as Var, Obj as Run, Cell, Objinfo WHERE Var.Ident = "Op_en1913" AND Var.id = Cell.Obj_id_v AND Run.id = Cell.Obj_id_r AND Run.id = Objinfo.id GROUP BY Var.id, Run.id |Runs}}

{{#sql-query: SELECT Var.Ident, Var.Name, Cell.id, N, Begin, Mean, Var.Unit FROM Obj as Var, Obj as Run, Cell, Objinfo WHERE Var.Ident = "Op_en1913" AND Var.id = Cell.Obj_id_v AND Run.id = Cell.Obj_id_r AND Run.id = Objinfo.id GROUP BY Cell.id ORDER BY Run.id DESC, Var.Ident |Means and samplesizes (N)}}

{{#sql-query: SELECT Var.Ident, Cell.id, Cell.Obj_id_r as Run, Obs, Result, Var.Unit FROM Obj as Var, Cell, Res WHERE Var.Ident = "Op_en1913" AND Var.id = Cell.Obj_id_v AND Cell.id = Res.Cell_id ORDER BY Cell.Obj_id_r, Var.Ident, Cell.id |Full sample}}


List all dimensions that have indices, and the indices concatenated:

<sql-query display="1"> SELECT Dim.Ident, Dim.Name, Dim.Unit, Group_concat(Ind.Ident ORDER BY Ind.Name SEPARATOR ', ') as Indices FROM Obj AS Dim, Obj as Ind, Sett, Item WHERE Dim.id = Sett.Obj_id AND Sett.Settype_id=1 AND Sett.id = Item.Sett_id AND Item.Obj_id = Ind.id GROUP BY Dim.Name ORDER BY Dim.id </sql-query>


List all indices, and their locations concatenated:

<sql-query display="1"> SELECT Ident, Name, Unit, GROUP_CONCAT(Location ORDER BY Roww SEPARATOR ', ') AS Locations FROM Obj AS Ind, Loc WHERE Ind.id = Loc.Obj_id_i GROUP BY Name ORDER BY Name </sql-query>


List all variables and their runs, and also list all indices (concatenated) used for each variable for each run.

<sql-query display="1"> SELECT Var_id, Run_id, Ident, Name, GROUP_CONCAT(Indic SEPARATOR ', ') AS Indices, N, Method FROM 

  (SELECT Var.id as Var_id, Run.id as Run_id, Var.Ident AS Ident, Var.Name as Name, Ind.Ident AS Indic, N, Run.Name AS Method
  FROM Obj AS Var, Obj AS Run, Obj AS Ind, Loccell, Loc, Cell
  WHERE Var.id = Cell.Obj_id_v
  AND Run.id = Cell.Obj_id_r
  AND Cell.id = Loccell.Cell_id
  AND Loc.id = Loccell.Loc_id
  AND Ind.id = Loc.Obj_id_i
  GROUP BY Var_id, Run_id, Ind.Ident ) AS Temp1

GROUP BY Var_id, Run_id </sql-query>

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