Case Study: SRM 2.0 - A next generation shared resource management system built on SpringSource dm Server

Case Study: SRM 2.0 - A next
generation shared resource
management system built on !

SpringSource dm Server
Matt Stine - St. Jude Children’s Research Hospital

Agenda

• Introduction to St. Jude
• Introduction to the SRM Domain
• SRM 1.x
• The Crossroads
• SRM 2.0
• Spring DM / OSGi Benefits
• Demo
• SRM 2.0 Data Bus
• Spring DM / OSGi Benefits
• Demo
• Q&A

SpringOne 2GX 2009. All rights reserved. Do not distribute without permission.

St. Jude Mission

To advance cures, and means of
prevention, for pediatric catastrophic
diseases through research and
treatment. Consistent with the vision
of our founder Danny Thomas, no
child is denied treatment based on
race, religion or a family’s ability to
pay.

3

About St. Jude

• Founded by entertainer Danny Thomas and opened in 1962
• Supported primarily by funds from volunteer contributions
raised by ALSAC, the fund-raising arm of St. Jude
• 500 new patients each year
– Must be referred by physician
– Generally 18 years old or younger
– Must have disease currently studied at St. Jude
• 4,300 “active” patients
• 58 inpatient beds
• 60,000 outpatient visits per year
• 500,000 appointments per year
• Average patient: 7-9 appointments per day
• 75 staff physicians and 3,300 employees

4

Research and Treatment

• Known for advances in treatment of childhood
leukemia
• Other catastrophic diseases researched & treated
at St. Jude:
– Genetic diseases such as sickle cell disease,
osteogenesis imperfecta
(brittle bone disease)
– Infectious diseases such as tuberculosis and HIV/
AIDS
– Childhood cancers including tumors of the bone,
brain and soft tissue

5

6

Research Landscape

• 16 Academic Departments
• 5 Academic Divisions
• Cancer Center
– First and only NCI-designated Comprehensive
Cancer Center solely focused on pediatric cancer
– 6 Programs:
• Cancer Prevention and Control
• Developmental Therapeutics for Solid Malignancies
• Hematological Malignancies
• Molecular Oncology
• Neurobiology and Brain Tumor
• Signal Transduction

7

Shared Resources

• Centralized facilities providing services and access
to specialized equipment for research activities
• Often centered around technology too expensive
for individual research programs to maintain their
own infrastructure
• Examples:
– High-throughput DNA Sequencing
– Gene Expression Array Technology
– Electron Microscopy
• St. Jude currently has 41 shared resources

8

Shared Resource Operational
Issues

9

Issues

Service
Request

9

Issues

Service Sample
Request Check In

9

Issues

Service Sample
Request Check In

Process1

...

Processn

9

Issues

Service Sample
Request Check In

Process1

...

Processn

Sample
Check
Out

9

Issues

Service Sample
Request Check In

Process1

...

Processn

Generate
Sample
Bill
Check
Out

9

Shared Resource
Management (SRM) 1.x

• Web-based application providing a single,
integrated portal for management of shared
resource facility activities.
• Currently supports 11 St. Jude facilities offering
more than 20 distinct services.
• Available under the GNU Lesser General Public
License (LGPL) v3.0 at http://stjude-
srm.sourceforge.net.

10

SRM 1.x Development
Process

• Requirements for 5 laboratories
• Extract common requirements
• Build Core Domain Model/Database Schema
• Build Core Services Platform
• Build Web Portal
• Build laboratory specific extensions to:
– DB Schema
– Domain Model
– Services Platform
• Build laboratory specific Web UI

11

SRM 1.x Development
Process

• Requirements for 5 laboratories
• Extract common requirements
• Build Core Domain Model/Database Schema
• Build Core Services Platform
• Build Web Portal
• Build laboratory specific extensions to:
– DB Schema
– Domain Model ITERATE

– Services Platform
• Build laboratory specific Web UI

11

SRM 1.x Domain Model

Order

Sample

Workflow
Workflow
Detail

Test Sample
Data Group

12


Order

Sample
Sample
Extension

Workflow
Workflow
Detail

Sample
Test Data Test Sample
Group
Extension Data Group Extension

12

SRM 1.x Technology Stack

• Java 2 Standard Edition 1.4
• Java 2 Enterprise Edition 1.3
– Enterprise JavaBeans 2.0
• CMP Entity Beans
• Stateless Session Beans
– Servlet 2.3
– JSP 1.2
• Oracle 10g
• JBoss AS 4.2

13

SRM 1.x Services Platform

SRM Architecture
14

SRM 1.x Issues

15

SRM 1.x Issues

• Explosive System Growth
– Per deployed service:
• 3 new tables
• 3 new entity beans (remote, local interfaces,
implementation class, modified descriptors, ...)
• 1 new stateless session bean
• 1 new business delegate
• Multiple new servlets, JSP’s

15

SRM 1.x Issues

• Explosive System Growth
– Per deployed service:
• 3 new tables
• 3 new entity beans (remote, local interfaces,
implementation class, modified descriptors, ...)
• 1 new stateless session bean
• 1 new business delegate
• Multiple new servlets, JSP’s
• Monolithic Deployment
– Tightly coupled services
– Tightly coupled layers

15

SRM 1.x Issues

16

SRM 1.x Issues

• Isolated Defects => “Distributed Suffering”

16

SRM 1.x Issues

• Implementation inconsistent across services
– Data integrity issues
– Inconsistent technology stack
– Knowledge transfer burden

16

SRM 1.x Issues

• Implementation inconsistent across services
– Data integrity issues
– Inconsistent technology stack
– Knowledge transfer burden
• Modularity Impossible
– Tried at the web layer
– Dependency versioning made things worse!

16

The Crossroads

• Information Sciences FY ‘09 – ’13 Strategic Plan
– Develop ordering and billing functionality for ~10
additional lab-based shared resources
– Develop SRM LIMS for those shared resources
requiring such infrastructure
– Develop links to other databases on campus as
required

17

The Crossroads

• SRM 1.x is at this point roughly five years old
• Core technology stack (EJB 2.0) is about eight
years old
• Architecture/development model mandates
database schema and source code changes for any
new facilities/services
• 3-6 month delivery time for new facilities/services
with 2-3 developers engaged
• Can we do better?

18

SRM 2.0 Key Goals

19

SRM 2.0 Key Goals

• Limit System Growth
– Extend primarily by configuration
– Extend secondarily by new/modified code

19

SRM 2.0 Key Goals

• True Modularity
– Across System Components
– Across Services
– Isolate risk, complexity

19

SRM 2.0 Key Goals

• True Modularity
– Across System Components
– Across Services
– Isolate risk, complexity
• Upgrade Technology Stack
– Spring
– Hibernate/iBATIS

19

SRM 2.0 Architectural
Concepts

Entity-Attribute-Value (EAV) Data Model

20

Concepts


• Discrete set of tables used for core model
extensions

20

Concepts


extensions
• Tables => rows in Entity table

20

Concepts


extensions
• Table Columns => rows in Attribute table

20

Concepts


extensions
• Table Columns => rows in Attribute table
• Table Row-Column Values => rows in Value
table(s)

20

Conventional Data Model

Source: http://jpodb.alik.ch/twiki/bin/view/Main/DataModel

21

EAV Data Model

Source: http://
jpodb.alik.ch/twiki/
bin/view/Main/
DataModel

22


Order

Sample

Worklog

Task Task Set

23


Order

Sample
EAV

Worklog

Task Task Set

23

Concepts

Plug-in Architecture

24

Concepts


• System framework supports core business features

24

Concepts


• Features are implemented via pluggable “Business
Activity Sources”

24

Concepts


• Features are implemented via pluggable “Business
Activity Sources”
• Data, layout, behavior bound via configurable
“Business Activities”

24


Fe
at
ur
e
25
SRM Kernel



Bu ur
So
si ce

Fe
ne

at
ss

ur
e
Ac SRM Kernel
tiv
25

ity



Bu ur
Bu

So
si

Fe
si

ne

at
ne

ss
ce

ur
ss

e
Ac
Ac

25
tiv SRM Kernel
tiv

ity
ity


SRM Kernel

SRM Kernel


SRM Kernel

EAV DAO

Core Dynamic EAV
Hybrid
Services Services Engine

Data
Core DAO Generic
Source
Functions
Handlers

Core Platform SRM Kernel

Dynamic Platform


SRM Kernel
Business Business
Activity Activity
Source Source

EAV DAO

Core Dynamic EAV
Hybrid
Services Services Engine

Data
Core DAO Generic
Source
Functions
Handlers

Core Platform SRM Kernel

Dynamic Platform


SRM 2.0 Technology Stack

• Java SE 6
• Spring Framework 2.5.6
• Freemarker 2.3.15
• Prototype 1.6.1
• Hibernate 3.2.6
• iBATIS 2.3.4
• SpringSource dm Server 1.0.2
• PostgresPlus Advanced Server 8.3

27

DM/OSGi Benefits

• Modularization

• Isolation

• Plugability

28

Modularization

29

Modularization

• Clear separation of responsibility

29

Modularization


• Strict enforcement of module boundaries

29

Modularization



• “Intraapplication SOA”

29

Modularization




• Enables DRY

29

Modularization




• Enables DRY
– Especially with Web Slices!

29

Isolation

30

Isolation

• Architectural Risk

30

Isolation


• Change

30

Isolation


• Change

• Technology

30

Isolation


• Change

• Technology

• Dependencies

30

Isolation


• Change

• Technology

• Dependencies

• Developer Responsibility

30

Plugability

31

Plugability

• Services

31

Plugability

• Services

• Lifecycle

31

SRM 2.0 Demo


Issues

• Data Management/Retrieval

• Reporting
– Usage Statistics
– Turnaround Time
– Service Request History

33

Data Management (SRM 1.x)

SRM Pickup Location

SRM App Server Clustered Mass Storage

Research Archives

34


SRM Pickup Location

2004 Largest File Size:
< 10 MB

SRM App Server Clustered Mass Storage

Research Archives

34


SRM Pickup Location

2004 Largest File Size:
< 10 MB

SRM App Server 2009 Largest File Size: Clustered Mass Storage
Approaching 100 GB!!!

Research Archives

34

Data Management

• Need a event-based, distributed solution

• Need to provide Data as a Service (DaaS)
– Downstream Analytics Platforms

35

Reporting

• EAV Schema
– Data/relationships too abstract for report writers
– Performance bottleneck
• Data Mart
– Must be near real-time
– Proper data partitioning
• DaaS
– Participate in other data warehouses

36

SRM Data Bus

SRM

37

SRM Data Bus

Data Bus
SRM Broker

37

SRM Data Bus

Data Bus
Worker

Data Bus
SRM Broker

37

SRM Data Bus

Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker

37

SRM Data Bus

Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

37

SRM Data Bus
External
Warehouse
Processor
Pipeline
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

37

SRM Data Bus
External
Warehouse
Processor
Pipeline External Warehouse
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

37

SRM Data Bus
External
Warehouse
Processor
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

Data Bus
Worker

37

SRM Data Bus
External
Warehouse
Processor
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

Lab Y Data
Archival
Pipeline

Data Bus
Worker

37

SRM Data Bus
External
Warehouse
Processor
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

Lab Y Data
Archival
Pipeline
Research Archive
Data Bus
Worker

37

SRM Data Bus
External
Warehouse
Processor
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

Lab Y Data
Archival
Pipeline
Research Archive
Data Bus
Worker

Lab X Data
Archival
Pipeline

37

SRM Data Bus
External
Warehouse
Processor
Data Bus
Worker

Data Mart
Processor
Pipeline

Data Bus
SRM Broker
SRM Data Mart

Lab Y Data
Archival
Pipeline
Research Archive
Data Bus
Worker

Lab X Data
Analytics
Archival
Platform
Pipeline

37

SRM Data Bus Technology
Stack

• Java SE 6
• Spring Framework 2.5.6
• Spring Integration 1.0.3
• Apache ActiveMQ 5.2
• SpringSource dm Server 1.0.2
• PostgresPlus Advanced Server 8.3

38

DM/OSGi Benefits

• Modularization

• Isolation

• Plugability

39

SRM Data Bus
Demo


Acknowledgements

• SRM 2 Team • QA
– Rama Gundapaneni – Asmita Vaidya
– Simon Hagstroem • Business Analysts
– Roshan Shrestha – Ashish Pagare
– Bhagavathy Krishna – Sundeep Shakya
– Kiran Putcha • OPS
– JP Davaleswarapu – Scott Malone
– Dinesh Devasagayam – Bill Pappas
• Management
• SRM Data Bus Team
– Charles Hurmiz
– Swetha Mandava
– Clayton Naeve
– Raghuver Kontham
• SpringSource
– Wei Cai
– Keith Donald
– Yingliang Du
– Oleg Zhurakousky
– Mark Fisher

41

Feedback

• Please send me your feedback about the
presentation/presenter:

matt.stine@stjude.org
Twitter: mstine

42

Q&A


Case Study: SRM 2.0 - A next generation shared resource management system built on SpringSource dm Server

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