Transcript WDKModel2

The GUS Web Development Kit
(WDK)
Starting with the WDK
Model
Overview
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WDK Goals
What is the “model”
User’s perspective
Implementation
Overall WDK Goals
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Ease the development of Query and Record based
web sites
(What about data input sites like StudyAnnotator?)
Site authors use declarative specifications
Substantial reuse across projects
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Model
View
Use industry standard technologies
History
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A re-design of the WDK-Classic (Crabtree)
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Incorporating ideas of CBIL’s CSP (Schug,
Fischer, Crabtree)
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Used for PlasmoDB, EPConDB, AllGenes
“CBIL Style Police”
An abstraction of Parameter acquisition
dialogues
Incorporating ideas from PageMaker (Schug)
Model-View-Controller (MVC) Design
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The Model describes the data
The View displays it
The controller
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Directs program flow based on the user’s action
Updates the model accordingly
The View knows about the Model
But, not vice versa
MVC - Courtesy of Google Images
Why is MVC important?
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By defining the Model separately we:
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Understand it better
Don’t pollute it with View implementations
Don’t commit to any particular view
By defining the View separately we:
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Can write multiple views
Have multiple views operate in one application
Don’t pollute the view with Model logic
The WDK Model – what’s in it?
(so far)
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Queries
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Results
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Parameters
Tables
Records
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Primary Key
Fields
Tables
AllGenes Query
AllGenes Result
AllGenes Record
The Flow of a Query
Dialogue
GeneName:
Species:
GoFunction:
TABLE
w/
MAIN
RESULT
Main
Query
params
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Page of Details
Page
Query
rows
4344 Blah blah blah
343344 blah blah blah
373422 blah blah blah
Record
DT.373422
Mouse
Brca1
Pageable Query
(Encapsulates two queries)
Dialogue
GeneName:
Species:
GoFunction:
params
rows
TABLE
w/
MAIN
RESULT
Main
Query
12344
23324
4344
343344
373422
4444
44444
35555
09734
23477
424
342477
9823
2783247
Page of Details
Page
Query
4344 Blah blah blah
343344 blah blah blah
373422 blah blah blah
Record
DT.373422
Mouse
Brca1
How was this specified in WDKClassic?
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See sample file… classic.config
The New WDK Uses JSP for the
View
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JSP looks like HTML but, embeds calls to
JavaBean objects.
The reverse of how we used to make
dynamic web pages:
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Instead of the Java/Perl formatting the HTML, the
HTML calls the Java
See file… simpleQueryDemo1.jsp
A WDK Query Model in XML
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<wdkModel>
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<simpleQuerySet>
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<simpleQuery>
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<param>
<pageableQuerySet>
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<pageableQuery mainQuery=q1 pageQuery=q2>
Take a look at the real XML
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See file… sampleQuerySet.xml
Test the Model - without the view!
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Three commands to test a model that you
are creating
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wdkXml – parses and checks the XML
wdkQuery – runs a Query
wdkRecord – retrieves a Record
wdkXml
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Parses and checks the Model XML file
Prints out the model
See file… wdkXml_output.txt
wdkQuery
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Tests a query found in a ModelXML file
Can run a SimpleQuery or a PageableQuery
See file… wdkQuery_output.txt
Records - What are They?
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They tell about an entity
Parameterized by a primary key (eg DT.xxxx)
Have:
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Fields
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A column from a Query
A block of text
Tables
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A result from a query
AllGenes Record Again
Fields
Tables
A WDK Record Model in XML
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<wdkModel>
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<simpleQuerySet>
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<simpleQuery>
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<param>
<wdkModel>
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<simpleQuerySet>
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<simpleQuery>
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<param>
– <column>
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<recordSet>
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<record>
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<tableQuery reference>
– <fieldQuery reference>
– <textField>
Take a Look at the Real XML
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See file… sampleRecordSet.xml
wdkRecord
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Tests a Record found in an XML file
See file… wdkRecord_output.txt
ConfigFile (XML)
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A little XML file configures the model
Specifies site-specific stuff
(the Model XML is not site specific)
See file… sampleModelConfig.xml
Upcoming (major) Features
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DTD/XMLSchema for Model XML?
Import model files into each othe
ParamSets
Boolean Queries
Query History
Flat file queries
Process queries
Allow multiple PageQueries in PageableQueries
Define special data types to handle eg URLs
Nested results (eg Gene-Centrism)
Lots of param types (hierarchy, …)
Implementation
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Uses Java Interfaces to abstract away SQL
details
Clear definition of what is public (ie, visible to
view)
UML
Third Party Resources
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From Jakarta:
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Command Line Interpreter
XML Digester
Connection Pool
Logging
Digester
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A very convenient way to transform XML into
JavaBeans Objects
See file… ModelXmlParser.java
Command Line Interpreter (CLI)
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A Java equivalent to Getopt in Perl
Parses command line args
Produces nice Usage
See file… wdkQuery_usage.txt
Quick Look at Accessing the Model
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public ResultSet getResult(String querySetName, String queryName,
Hashtable paramHash,
boolean useCache) throws Exception,
QueryParamsException {
SimpleQuerySet simpleQuerySet
= wdkModel.getSimpleQuerySet(querySetName);
SimpleQueryI query = simpleQuerySet.getQuery(queryName);
SimpleQueryInstanceI instance = query.makeInstance();
instance.setIsCacheable(useCache);
instance.setValues(paramHash);
return instance.getResult();
}
The QueryInstance Table
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Previously known as “the cache”
Captures details of a QueryInstance:
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Query name
Parameter values
Link to table holding result
Used for caching and/or pageable queries
wdkCache
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Program to create, reset and drop a cache
JavaDoc
Take a tour of the Java API
See files… wdkjdoc/index.html