Special Interest Activity Trio – A System for Integrated Management of Data, Uncertainty, and Lineage ITK478 Yan Cui.

Special Interest ActivitySpecial Interest ActivityTrio – A System for Integrated Management of Data, Uncertainty, and Lineage

ITK478Yan Cui

AgendaAgendaUnderstand Trio new database systemSystem requirements of installing Trio systemSource codes/packages for Trio systemProcedure of Trio system installationConfiguration of Trio SystemExperiment Trio DBMS Using TrioExplorer and

TrioPlus (demo)Trio API Integrated Into Other Python ScriptsTrio API and Translator (Python)Trio Query Language (TriQL) Structure (demo)Advantage and Disadvantage of using Trio

DBMSDocumenting Trio system report/bugs

Understand Trio new database Understand Trio new database systemsystemBasic concept of new Trio DBMS

◦ Trio is a new kind of database system (DBMS), which was developed by Stanford University Lab at Dec, 2006.

◦ An extended relational model called Uncertainty Lineage Database (ULDB) , and also supports Trio’s query language Called TriQL [1].

◦ Handles structured data, uncertainty of data, and data lineage together in a fully integrated manner.

Trio System architecture (components)Uncertainty-Lineage Database (ULDB)TriQL: The Trio Query Language

Trio System architectureTrio System architecture

Four primary components of Trio DBMS◦ command-line client (TrioPlus)◦ TrioExplorer◦ Trio API and translator (Python)◦ standard relational DBMS (PostgreSQL)

Uncertainty-Lineage of Database◦ Encoded data table◦ Lineage table◦ Trio metadata◦ Trio Stored Procedures

Uncertainty-Lineage Database Uncertainty-Lineage Database (ULDB)(ULDB)Alternatives‘?’ (Maybe) AnnotationsNumerical ConfidencesLineageSample: Drives (person, color, car) and Saw

(witness, color, car) uncertainty tables with/no with confidence.

Uncertainty-Lineage Database Uncertainty-Lineage Database (ULDB)(ULDB)Alternatives

◦ Definition: Alternatives are presenting uncertainty about the contents of a tuple [2]

◦ ‘||’ annotation◦ Drives(person, color, car) and Saw (witness, color,

car) uncertainty tables◦ ‘Select * from Drives”

Uncertainty-Lineage Database Uncertainty-Lineage Database (ULDB)(ULDB)‘?’ (Maybe) Annotations

◦ Definition: ‘?’ annotation present the existence of a tuple on the x-tuple, also called maybe x-tuple [2]

◦ Drives(person, color, car) and Saw (witness, color, car) uncertainty tables

◦ ‘select * from Drives’

Uncertainty-Lineage Database Uncertainty-Lineage Database (ULDB)(ULDB)Numerical Confidences

◦ Definition: Numerical confidence also was considered as probability [2].

◦ Drives(person, color, car) and Saw (witness, color, car) uncertainty tables with confidence

◦ ‘select * from Drives’

Uncertainty-Lineage Database Uncertainty-Lineage Database (ULDB)(ULDB)Lineage

◦ Definition: “recorded at the granularity of tuple alternatives: Lineage connects as x-tuple alternative to other x-tuple alternative.” in [2]

◦ Drives(person, color, car) and Saw (witness, color, car) uncertainty tables with confidence

◦ ‘select person from Drives’

TriQL: The Trio Query LanguageTriQL: The Trio Query Language

Two major parts of TriQL◦ built-in functions and predicates for querying

confidence values and lineage◦ regular SQL syntax

System requirements of System requirements of installationinstallationOperating systems - as Linux, Mac OS X, and

Win-32 (XP, Vista, and 32-bit Server)

PostgreSQL database (version 8.2.5, 8.1.10, 8.0.14, and 7.4.18) - Linux and Win32

Python API - windows, Linux/Unix, Mac OS X, OS/2, and Amiga

Source codes/packages for Trio Source codes/packages for Trio systemsystemListing source codes Python 2.4 can be downloaded from http://www.python.org/ . Easy_install can be downloaded from

http://peak.telecommunity.com/DevCenter/EasyInstall and the file called ez_setup.py.

Readline 1.7.win32 can be downloaded from http://www.python.org/ .

ctypes-1.0.2.win32-py2.4 can be download from http://www.python.org/ .

PostgreSQL 8.1 can be downloaded from http://www.postgresql.org/

Graphviz 2.14 is the only version compatible with Trio API. It is available in http://infolab.stanford.edu/trio/code/graphviz-2.14.1.exe .

PyGreSQL can be downloaded from http://www.pygresql.org/ . Pylons 0.9.5 can be downloaded from http://pylonshq.com/ . PLY 2.2 can be downloaded from http://www.dabeaz.com/ply/

. PyParsing can be downloaded from

http://pyparsing.wikispaces.com/ . PyDot can be downloaded from

http://code.google.com/p/pydot/downloads/list . Trio API 1.0 can be downloaded from

http://infolab.stanford.edu/~theobald/sources/TRIO.zip .

Procedure of Trio system Procedure of Trio system installationinstallationPython

◦ Python 2.4 windows version (python-2.4.4.msi).◦ Install Python in C:/Python directory◦ Set path=c:/Python24; in environment variables

Readline◦ Readline-1.7.win32-py2.4.exe and install into Python

directoryCtypes

◦ Ctypes-1.0.2.win32-py2.4.exe and install into Python directory

PostgreSQL◦ PostgreSQL 8.1 windows version (postgresql-8.1.msi )◦ Install PostgreSQL 8.1 and set path C:\Program Files\

PostgreSQL\8.1\bin; after completed the installation.Graphviz

◦ Graphviz 2.14 version, install to your workstation and set path C:\PROGRA~1\ATT\Graphviz\bin; in environment variables after completed the installation

Procedure of Trio system Procedure of Trio system installation (cont)installation (cont)Easy_install - Download ez_setup.py in C:/ directoryPyGreSQL – In command line, cd\ to c: directory, and

run python ez_setup.py PyGreSQL to install components.

Pylons – In command line, cd\ to c: directory, and run python ez_setup.py Pylons==0.9.5 to install Pylons. Set path c:\python24\Scripts in environment variables.

PLY – In command line, cd\ to c: directory, and run python ez_setup.py Ply==2.2 or easy_install Ply==2.2.

PyParsing – In command line, cd\ to c: directory, and run python ez_setup.py PyParsing.

PyDot – download the source from website. Access to folder in command line, and then install manually by running ‘python setup.py install’.

Trio API◦ Download source code in any directory◦ Copy Trio-1.0\spi\triospi_win32.dll to PostgreSQL’s lib

directory and renamed as triospi.dll

Procedure of Trio system Procedure of Trio system installation (cont)installation (cont)

PostgreSQL installation

Configuration of Trio SystemConfiguration of Trio System

Windows superuser authentication to access PostgreSQL

TrioExplorerTrioPlus

Configuration of Trio SystemConfiguration of Trio SystemWindows superuser authentication for

PostgreSQL◦ Open pgadmin III for PostgreSQL◦ Create new login role

Role name ‘myname’ (as same as windows login account)

Set password (Password can be any) and check all role privileges and click ok.

◦ Create new database Database name ‘myname’ (as same as username) Owner is ‘myname’ and click ok

◦ Initialize Trio schema information In Trio-1.0\setup, open setup.py with notepad to

comment out the last three codes and put the following. os.system("psql %s %s < setup.sql" % (pgdbname,

username))os.system("psql %s %s < setup_triospi.sql" %

(pgdbname, username)) os.system("psql %s %s < trio_get_conf.sql" %

(pgdbname, username)) Save the file, and at the command line, cd \Trio-1.0\

setup, and run ‘python setup.py myname myname’

Configuration of Trio System Configuration of Trio System (cont)(cont)pgadmin III for PostgreSQL 8.1

Configuration of Trio System Configuration of Trio System (cont)(cont)TrioExplorer

◦ Make sure PostgreSQL is working.◦ Running TrioExplore – Ensure path ‘c:\python24\

Scripts;’ in environment variables. And double click ‘start_te_server.bat’ under Trio-1.0\explorer.

◦ At the command line, you are now prompted for an admin user login to PostgreSQL, which should have been created along with your PostgreSQL installation and which will be used by TrioExplorer to create new user roles and database instances.

◦ TrioExplorer should now be reachable from your browser using http://localhost:8080/. For new users can now press ‘Create a new user’ and create their own Trio login and database instances, which are then managed by the PostgreSQL server.

Configuration of Trio System Configuration of Trio System (cont)(cont)TrioPlus

◦ Create new PostgreSQL user role and database instance Run ‘createuser demo’ Run ‘createdb demo’, the name must be the same as

username

◦ Initialize Trio schema information for new user by access as same as windows superuser authentication to access PostgreSQL. Use TrioExplorer will be easily just press ‘Create new role’ in Web.

◦ Connect to new Trio database using the command line clients by running ‘python trioplus.py –u demo –d demo –p’

Trio API Integrated Into Other Trio API Integrated Into Other Python ScriptsPython ScriptsTrioCnx

◦ TrioCnx(pgdb) –PyGreSQL connection pgdb

◦ cursor() – return a new TrioCursor object for the current connection.

◦ commint() – commits the current transaction.

◦ rollback() – performs a rollback for the current transaction.

◦ close() – closes the Trio connection

TrioCursor◦ execute(triql) - Executes a TriQL statement triql for this

cursor object.

◦ fetchone() - Fetches a single XTuple object from the current cursor position.

◦ fetchall() - Fetches and returns a list of all XTuple objects beginning from the current cursor position.

Trio API Integrated Into Other Trio API Integrated Into Other Python Scripts (cont)Python Scripts (cont)XTuple

◦ len() - Returns the number of Alternative objects contained in this XTuple object.

◦ getAlternative(idx) - Returns the Alternative object at the designated index idx.

◦ getConfidence() - Returns the confidence value (if any) of this XTuple object as the sum of its Alternative objects' confidence values.

◦ getQuestionMark() - Returns whether this XTuple object has a question mark or not.

Alternative getLineage() – returns a list of immediate lineage

information traceLineage() – performs a transitive lineage traversal for

this alternative back to the base data getConfidence() - Returns the confidence value of this

alternative. computeConfidence() - Computes the confidence value

Trio API And Translator Trio API And Translator (Python)(Python)

TriQL built-in functions TriQL keywordsAggregate(), Alternative(), As(), Avg(), BinaryExpression(), Brackets(), Cascade(), ColumnList(), Column(), Command(), ComputeConfidences(), Conf(), ConfUniform(), ConfScaled(), Count(), CreateIndex(), CreateTableAs(), CreateTable(), CreateTempTableAs(), CreateTempTable(), DataType(), Dot(), DropIndex(), DropTableList(), DropTable(), Eavg(), Ecount(), EcountStar(), Emax(), Emin(), Empty(), Esum(), FromClause(), GroupAlts(), GroupbyClause(), GroupByKey(), HavingClause(), HorizontalSelect(), IdentifierList(), InsertList(), Insert(), InsertSpec(), Lineage(), Literal(), Lsum(), Max(), Maybe(), Maybe(), Min(), OrderBy(), Question(), SelectClause(), Select(), SelectOptions(), SetOperator(), Star(), Sum(), UnaryExpression(), UncertainSet(), UniformTable(), ViewTable(), WhereClause(), WithConfidences()

'all', 'and', 'any', 'as', 'avg', 'by', 'cascade', ‘compute', 'conf', 'confidences', 'count', 'create', 'distinct', 'drop', 'eavg', 'ecount', 'emax', 'emin', 'esum', 'except', 'exists', ‘flatten', 'float', ‘float4', 'float8', 'from', 'group', 'groupalts', 'having','in', 'index', 'insert', 'int', 'int4', 'int8', 'intersect', 'into', 'is', 'like', 'lineage', #'lavg', #'lcount', #'lmax', #'lmin', #'lsum', 'max', 'maybe', 'min', 'noconf', 'nolineage', 'nomaybe', 'not', 'null', 'on', 'or', 'order', 'scaled', 'scaledbyexp', 'select', 'sum', 'table', 'temporary', 'trio', 'trio_aid', 'trio_xid', 'uncertain', 'uniform', 'union', 'merged', 'values', 'varchar', 'view', 'where', 'with'

DemoDemo

TrioExplorer and TrioPlusTrio Query Language (TriQL) Structure

◦ Drop index/table◦ Create Trio table/index◦ TriQL language◦ TriQL manual:

http://infolab.stanford.edu/~widom/triql.html ◦ Sample: TriQL Script

Current Supported for TriQLCurrent Supported for TriQLSupported DDL and Insert Commands Supported Subset of TriQL Query Language Create Table Create Trio Table Create Index Drop Table - Including “Cascade” option to drop

derived tables• Drop Index• Insert Into T Values <data>

o With or without alternatives, confidence values, and ?

o T must be a base table• Insert Into T <TriQL query>

o T must be a base table

Select-Project-Join queries• Create Table T as <query> Select Distinct• Union, Intersect, or Except of two subqueries (duplicate-

eliminating)• Union All of two subqueries• Merged, Flatten, and GroupAlts Horizontal subqueries in Where clause

o Including shortcuts and aggregation/group-by/having• Horizontal subqueries in Select clause

o Including shortcuts and aggregation but not group-by/having

Conf() function with any number of tables or Conf(*) o except for Conf(*) in the SELECT clause in conjunction

with DISTINCT or MERGED Maybe() predicate “Uniform <table-name>” in From clause• “as conf” for query-defined result confidence values

o Including “Uniform as conf” and “Scaled as conf”• “Compute Confidences” at end of query• Lineage() predicate

o Not in horizontal subquerieso “=⇒” abbreviation allowed

• NoLineage, NoConf, and NoMaybe

Table of TriQL contentsTable of TriQL contentsULDBs Uncertainty attributes, maybe annotations and

confidence valuesSQL over ULDBs Selection, projection, join, subqueries, duplicate-

elimination, grouping and aggregation, aggregate variants, set operators, order by

Flatten and GroupAlts Flatten is used to turn tuples with alternative values into regular tuples, while GroupAlts is used to create or restructure alternative values

Horizontal subqeries: The [ ] construct [ ] in the where clause, [ ] with joins, Syntactic shortcuts in [ ], [ ] in the select clause, [ ] with Self-Joins

Built-in Functions Conf() and Maybe() Multi-table conf()

Result confidences Result confidence evaluation, uniform and scaled result confidences, On-Demand confidence computation

Built-in Predicate Lineage() The Lineage() predicate lets queries filter joined tuples based on whether they are related via lineage

Options Nolineage, Noconf, and NoMaybe Indicate lineage, confidence values, and/or?'s should be omitted from query results

Data modification Insert statement, delete statement, update statement

Advantage and DisadvantageAdvantage and Disadvantage

Advantage◦ Open source and free support for any non-benefit

users to experience new Trio DBMS◦ Advanced components in relational DBMS◦ Computing confidences◦ Efficient, Convenient, safe, Multi-User storage of

and access to, Massive, Persistent

Disadvantage◦ Time cost for query◦ Dependency◦ On development stage

Advantage and DisadvantageAdvantage and DisadvantageDisadvantage

◦ Time cost for query

Using ‘SELECT attr-list FROM X1, X2, ..., Xn WHERE predicate’ as a query example in [6] for a comparison between relational database and ULDB.

Over standard relational database: For each tuple in cross-product of X1, X2, ..., Xn

Evaluate the predicate If true, project attr-list to create result tuple

Over ULDB: For each tuple in cross-product of X1, X2, ..., Xn

Create “super tuple” T from all combinations of alternatives

Evaluate predicate on each alternative in T ; keep only the true ones

Project attr-list on each alternative to create result tuple

Details: ‘?’, lineage, confidences

Documenting Trio system Documenting Trio system report/bugsreport/bugs The install instruction in website

http://dbpubs.stanford.edu:8011/doku.php/trio:installation , indicated unclearly the version of Graphviz for Trio system. In Graphviz website http://www.graphviz.org/ only has version 2.16 but not compatable except version 2.14. Graphviz version 2.14 is available for download in http://infolab.stanford.edu/trio/code/graphviz-2.14.1.exe .

The windows authentication supperuser needs to be created first in the PostgreSQL in order to connect to database. After established the connection, TrioExplorer and TrioPlus can use the supperuser’s login and password as windows authentiction to access to database system. However, it doesn’t mention at all in the installation procedure on how to create this typle of new user. The only way to solve it is to use PostgreSQL->pgadmin III manually.

After created the supperuser, I have to modify some codes in setup.py in Trio-1.0->setup directory in order to run ‘python setup.py –u myname –d myname –p’.

TriQL query statements in http://infolab.stanford.edu/~widom/triql.html#options, there are many samples queries not working properly as desired.

ReferencesReferences M. Mutsuzaki, M. Theobald, A. de Keijzer, J. Widom, P.

Agrawal, O. Benjelloun, A. Das Sarma, R. Murthy, and T. Sugihara. Trio-One: Layering Uncertainty and Lineage on a Conventional DBMS. Proceedings of the Third Biennial Conference on Innovative Data Systems Research (CIDR '07), Pacific Grove, California, January 2007. Demonstration description.

O. Benjelloun, A. Das Sarma, C. Hayworth, and J. Widom. An Introduction to ULDBs and the Trio System. IEEE Data Engineering Bulletin, Special Issue on Probabilistic Databases, 29(1):5-16, March 2006.

Trio: A System for integrated Management of Data, Uncertainty, and Lineage. Retrieved on November, 18, 2007 from http://infolab.stanford.edu/trio/ .

PostgreSQL. Retrieved on November, 20, 2007 from http://www.postgresql.org/.

Python. Retrieved on November, 15, 2007 from http://www.python.org/.

Trio: A System for Data, Uncertainty, and Lineage. given by Jennifer at various venues, 2006-07. Ppt.

Questions?Questions?