An sql api for object oriented perl
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An SQL API for Object Oriented Perl. Tim Adye BaBar Collaboration Particle Physics Department eScience Centre informal seminar 12 th November 2004. Talk Plan. Summary of BaBar and its bookkeeping system “large-scale distributed metadata catalogue” in Gridspeak The problem

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An sql api for object oriented perl

An SQL API for Object Oriented Perl

Tim Adye

BaBar Collaboration

Particle Physics Department

eScience Centre informal seminar

12th November 2004

Tim Adye


Talk plan

Talk Plan

  • Summary of BaBar and its bookkeeping system

    • “large-scale distributed metadata catalogue” in Gridspeak

  • The problem

    • “Why not just write SQL?”

  • The BaBar SQL API

    • User view: Perl classes and command-line tool

    • Behind the scenes

    • Table schema configuration classes

    • Summary of features

  • Could this be generalised to other applications?

    • Possible improvements

    • Comparison with other DBIx packages

  • Summary and references

Tim Adye


Feedback and discussion

Feedback and Discussion

  • Would this be useful outside BaBar?

  • Would it be worth making a public release?

    • eg. on CPAN

  • Does it need any improvements?

    • New features

    • Make it compatible with some other standards

      • eg. sit on top of another abstraction like DBIx::Table

    • A better name!

  • or have I just reinvented the wheel?

    • If so, maybe I should import some classic wheel technology into BaBar, rather than try to export my own “square wheel” idea to the rest of the world

Tim Adye


The babar collaboration

The BaBar Collaboration

10 Countries 77 Institutions 593 Physicists

Tim Adye


The babar detector at slac

The BaBar Detector at SLAC

Linear Accelerator

26th May 1999: first events recorded by BaBar

2.2 km PEP-II ring

BaBar


The babar bookkeeping

The BaBar Bookkeeping

  • New bookkeeping system created in parallel with new data model

    • Switch from OO database (Objectivity) to flat files (ROOT)

  • Much simpler to manage, but no longer have the top-level Objectivity catalogue

    • Actually the catalogue didn’t really help us, so random set of bookkeeping tools had been build up

    • The main aim of the project was to create a coherent bookkeeping system to replace these ad hoc tools

  • Successfully deployed Feb 2004. In use ever since.

    • Started development in Jan 2003

    • beta test in Autumn

Tim Adye


Bookkeeping concepts

Bookkeeping Concepts

  • Currently BaBar analysis data consists of

    • 43G events (event = results from one e+e- collision)

    • in 335k files

    • total size of 186 TB

    • 156M rows in largest table

      • Expect all to grow geometrically over the next few years

  • Data grouped in an overlapping hierarchy

    • many-to-many relations between tables, eg.

      • 1.7M runs: unit of datataking

      • 219k collections: unit of access to event store

      • 335k files: each collection stored in a few physical files

      • 18k datasets: groups of data that analysis users want

    • Need to select runs, collections, etc based on attributes from any of these tables

Tim Adye


Features of the babar bookkeeping

Features of the BaBar Bookkeeping

  • Decoupled from event store

    • Job configuration written to site-independent tcl file

    • Worker nodes don’t need access to database server

  • Mirrored to other sites

    • From SLAC to 4 “Tier A”, ~15 “Tier C”, user laptops

    • Supports Oracle and MySQL (mirror OracleMySQL)

  • Remote access

    • Used for mirroring and for sites who don’t want local db

    • Connection parameter/key distribution system

      • Eg. BookkeepingCommand –-site=slac or –-site=ral transparently connects to correct Oracle server at SLAC or MySQL at RAL.

    • Allows fallback servers if there are problems

Tim Adye


Other features of the bookkeeping

Other Features of the Bookkeeping

  • Import of data to each site managed by local bookkeeping system

    • Each site knows what it has and what it wants

    • New data imported automatically in cron job

  • Task management system

    • Controls job submission, checking, resubmission

    • Currently just for “production jobs”, but soon for user analysis jobs too

    • Looking at interfacing this to LCG job submission

      • Already use LCG for UK Monte Carlo production

Tim Adye


User access

User Access

  • Users need to query database to find out what data to process

    • May also need other information

      • eg. luminosity, run numbers, file sizes

    • Mostly select by dataset, but may need to limit further

      • eg. only data available locally, taken at “peak” energy, excluding some problem datataking period

  • Cannot expect users to know which tables to use, how to join them, or even the SQL syntax

    • Even worse if the schema change

  • Cannot expect developers to code for all combinations of queries with all possible selections

    • Previous ad hoc tools (some mine!) tried to do this and it was a nightmare, even for a simpler table structure

Tim Adye


Babar sql api user view

BaBar SQL API – user view

  • Each column that users might want to query or select on is given a unique logical name – regardless of which table it lives in

  • These names are used to specify query values

    $query->addValues('collection', 'gbytes');

    and selections

    $query->addSelector('dataset', 'Dilepton-*');

    $query->addSelector('run', '10000-19999');

    • Different types of data allow for different selection syntax, eg. wildcards for names, or ranges for run numbers.

  • Can also use SQL expressions (in terms of logical names)

    $query->addValues('SUM(lumi)/1000');

    and sorting, row limits, etc

  • Each of these happens to be in

    a different table

    Tim Adye


    Sql api returning results

    SQL API – returning results

    • That’s enough to generate a valid SQL SELECT query. To return the results:-

      my $sta = $query->execute();

      while (my $row = $sta->fetch()) {

      print $row->gbytes(), $row->collection(), "\n";

      }

      • The $query object collects the user requests

      • $query->execute() returns a “statement accessor” (like a DBI statement handle).

      • $sta iterates over row objects, each of which has accessors for each query value, gbytes and collection.

  • That’s all there is to it!

    • After the usual DBI connect, and $query object instantiation (see later), these statements form a working program

  • Tim Adye


    Command line tools

    Command-Line Tools

    • Standard BaBar tools use this API to create job configuration, create datasets, calculate luminosities, etc.

      • Standard tasks, but optionally allowing additional selections

    • Also provide an “expert” tool that allows access to full API functionality from the command line

      • This has proved very popular, with many “non-experts” making their own unique queries

    Tim Adye


    Examples

    Examples

    $ BbkUser --dataset=A0-Run4-OnPeak-R14 \ --is_local=1 --file_status=0 \ dse_lumi events gbytes file

    DSE_LUMI EVENTS GBYTES FILE

    ======== ====== ====== ====================================================

    1250.3 526115 1.6 /store/PRskims/R14/14.4.0d/A0/02/A0_0239.01.root

    1250.3 526115 0.8 /store/PRskims/R14/14.4.0d/A0/02/A0_0239.02HBCA.root

    1348.4 576239 1.6 /store/PRskims/R14/14.4.0d/A0/02/A0_0240.01.root

    1348.4 576239 1.0 /store/PRskims/R14/14.4.0d/A0/02/A0_0240.02HBCA.root

    ...

    156 rows returned

    $ BbkUser –-collection-file=coll.lis \

    tot_gbytes collection

    Tim Adye


    What happens behind your back

    What happens behind your back

    • The SQL API

      • translates the logical names to table columns

      • selects the required tables and joins

        • including otherwise unused tables required for the joins

      • generates and executes a valid SQL SELECT statement

      • creates a statement accessor object

      • dynamically generates a class for the row objects with accessors for each query value

    Tim Adye


    Our example

    BbkUser --dataset=A0-Run4-OnPeak-R14 --is_local=1 --file_status=0

    dse_lumi events gbytes file

    Our Example

    • That first BbkUser command involved 5 tables

      • including one that provides the join between dataset and collection tables

        SELECT dse.lumi_sum AS "dse_lumi", dse.output_nev AS "events",

        file.bytes, dse.name AS "collection",

        file.suffix AS "file_suffix", ds.id AS "ds_id",

        dse.id AS "dse_id", dtd.id AS "dtd_id",

        dtd.link_status

        FROM bbk_dataset ds, bbk_dsentities dse, data_files dfile,

        bbk_files file, bbk_dstodse dtd

        WHERE ds.id=dtd.ds_id

        AND dtd.dse_id=dse.id

        AND dse.id=file.dse_id

        AND file.id=dfile.file_id

        AND ds.name='A0-Run4-OnPeak-R14'

        AND dse.is_local='1'

        AND dfile.status='0';

    The SQL API can even

    pretty-print it like this for you 

    (What’s shown here is somewhat abbreviated: actual command includes full database and table names in case of ambiguities)

    Tim Adye


    Table schema configuration classes

    Table schema configuration classes

    • Mapping between logical names and table columns is defined in the configuration classes.

      • One class per table

      • Can also define special properties of each column (eg. whether to allow ranges (“100-199”) for selection).

    • Possible joins between tables defined here too

      • Use logical column names for join conditions, so one table class does not need to know about column names in other classes.

    • In most cases it’s just a matter of listing logical vs. column names

      • with a little Perl syntactic sugar

    • Inheritence of config classes expresses commonalities

      • eg. common id and created, and modified columns

    Tim Adye


    Example table configuration

    Example Table Configuration

    sub table { return 'bbk_files' }

    sub tableConfig {

    return {

    alias => 'file',

    columns => [

    bytes => 'bytes‘,

    uuid => 'uuid',

    checksum => 'checksum',

    file_suffix => 'suffix',

    nfiles => 'COUNT(DISTINCT file_id)',

    gbytes => '(bytes/1073741824)',

    tot_gbytes => 'SUM(bytes)/1073741824',

    file_dse_id => { column => 'dse_id', selectorType => 'range' },

    file => { valueAction => 'addLfnValue', selectorAction => 'lfnSelector' },

    ],

    joins => [

    dse_id => 'file_dse_id',

    file_id => 'dfile_file_id',

    ],

    }}

    Tim Adye


    Putting it all together

    Putting it all together

    • Configuration classes must be registered with $query object

      my $query = new BbkSqlSelect;

      $query->addModules(new MyTableClass($dbi));

      but of course it is usually simpler to provide a $query object pre-registered with all the table configs as part of a specific API.

    Tim Adye


    Overriding and synthetic columns

    Overriding and Synthetic Columns

    • A crutial advantage of this system is that it allows us to override the default behaviour

      • Allows us to hide complexities from user

      • Make even complex schema changes transparent to users

    • A logical name can refer to

      • ordinary database column name

      • SQL expression (in terms of database columns, or other logical names)

      • Perl method to pre- or post-process selection or query value

      • “synthetic” query value or selection

        • can return calculated value or alter behaviour

    • Global post-processing

      • Can be triggered by value, selection, or table inclusion

      • Allows global filtering of returned rows

    Tim Adye


    What happens behind your back 2

    What happens behind your back 2

    • We already used some of these features without noticing!

      • Dataset names can be found in the bbk_dataset or the bbk_aliases table

        • Requires a check and translation using the alias table

      • Datasets can evolve with time, with collection being added or removed

        • Need to query dataset for any time in the past, or use tagged dataset alias (like a CVS tag)

        • Implemented by automatically including date selection in query, and post-processing returned results to remove deleted collections

      • File names are made from a collection name + a suffix

        • $query->addSelector('file') splits the file name for the query and the $row->file() accessor rejoins them

    Tim Adye


    Features

    Features

    • Supports Oracle 8 and MySQL 3.23

    • Most queries that can be expressed in both these dialects can be expressed by users via the API – without breaking the paradigm of a flat namespace

      • aggregatation and grouping

      • sorting and distinct

      • MySQL’s LIMIT emulated in Oracle

      • inner and outer joins (generates Oracle or MySQL syntax)

      • Does not support UNION or subqueries

        • Could be added, but not in MySQL 3.23

    • Convenience features

      • automatic Getopt specification

      • query results display formatting and summary table generation

      • Configuration class summary table generation

    Tim Adye


    Limitations

    Limitations

    • Assumes tables can be joined in a unique way

      • ie. the joins form an acyclic graph

      • can still select different joins with explicit switches

    • Each column must have its own unique logical name

      • This is usually a good thing

      • but if the same data is held in different columns, it would be more efficient to automatically select from tables that are already included

    Tim Adye


    A public version

    A public version

    • Current version has a few BaBar-specific pieces

      • BaBar Connection manager – can use DBI directly

      • BaBar Options manager – can use Getopt directly

      • BaBar base objects – borrow required methods

      • BaBar table formatting class – remove functionality or publish this too

        … otherwise just uses standard Perl modules

        but with different table configs could be used elsewhere

      • Already do this in BaBar – used for QA and TM databases

      • Maybe I’m making some other assumptions that are true of our database and requirements, but not more generally so. I can’t think of any.

    • Needs a better name!

      • This is really an SQL API creator

    Tim Adye


    Possible improvements

    Possible improvements

    • Tidy up code!

      • User and config APIs are OK, but in between it’s pretty ugly

      • Separate functionality that can be used on its own

        • Already true of the DBI statement accessor class

    • More SQL dialects: PostgreSQL, MS SQL?

    • New SQL syntax: subqueries, UNIONs,…

    • INSERT, UPDATE, etc

      • these don’t need joins, so hand-coding not such a problem

    • Automatic selection of different join possibilities

    • Automatic generation of default table classes from SQL schema

      • Could use “The SQL Fairy”

      • though not much work to do it by hand

    Tim Adye


    Why not use another package

    Why not use another package?

    • More than 100 DBIx and other SQL access packages in CPAN

    • Could not find any that do all (or even most) of

      • hide table structure from user

      • allow multi-table queries, taking care of joins automatically

      • do not impose their own conventions on table schema

      • allow query values and selections to be overridden

      • allow transparent post-processing of query results

      • provide accessor functions for query results

    • I believe that taken together these features provide a clear and easy to use abstraction

    Tim Adye


    References

    References

    • The BaBar Experiment

      http://hepunx.rl.ac.uk/BFROOT/

    • BaBar Bookkeeping project

      http://hepunx.rl.ac.uk/BFROOT/www/Computing/Distributed/Bookkeeping/Documentation/

    • BaBar Bookkeeping presentation and paper

      http://indico.cern.ch/contributionDisplay.py?contribId=338&sessionId=7&confId=0

      D.A. Smith et al.,BaBar Book Keeping project –a distributed meta-data catalog of the BaBar event store,Proc. Computing in High Energy and Nuclear Physics 2004 (CHEP04).

    • CPAN Database Interfaces (see particularly DBIx)

      http://cpan.uwinnipeg.ca/chapter/Database_Interfaces

    Tim Adye


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