caBIG™ Software Requirements and Specification Template

SOFTWARE REQUIREMENTS AND SPECIFICATION DOCUMENT

caBIG™ Proteomics LIMS

DOCUMENT CHANGE HISTORY

Version Number Date Description
1.0 June 2005 Draft
1.1 July 2005 Modified first version
2.0 January 2006 Revisited to add architecture and component chapters
2.1 February 2006 Unused notes and appendixes are deleted

April 2004
 caBIG™ Proteomics LIMS
protLIMS prototype v.1.0
Software Requirements and Specification Document
Version 2.1

[Insert approval date of document]

[Project Name] Software Requirements and Specification

Document Change Record

Version Number Date Description
1.0 June 2005 Draft
1.1 July 2005 Modified first version
2.0 January 2006 Revisited to add architecture and component chapters
2.1 February 2006 Unused notes and appendixes are deleted

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TABLE OF CONTENTS
SOFTWARE REQUIREMENTS AND SPECIFICATION DOCUMENT.....................................................................I
1. INTRODUCTION...................................................................................................................................................1
1.1 SCOPE....................................................................................................................................................... 1
1.1.1 Identification.....................................................................................................................................1
1.1.2 System Overview................................................................................................................................2
1.1.3 Document Overview..........................................................................................................................2
1.2 REFERENCE DOCUMENTS........................................................................................................................... 2
2. PROJECT DESCRIPTION....................................................................................................................................3
2.1 PROJECT PERSPECTIVE............................................................................................................................... 3
2.2 PROJECT FUNCTIONS................................................................................................................................. 4
2.3 USER CHARACTERISTICS............................................................................................................................ 4
2.4 CONSTRAINTS........................................................................................................................................... 4
2.4.1 protLIMS Statement Of Work............................................................................................................4
2.4.2 caBIG™ Compliance........................................................................................................................4
2.4.3 Additional constraints, programming language and tools being employed....................................4
2.5 QUALIFICATION PROVISIONS...................................................................................................................... 5
2.6 ASSUMPTIONS AND DEPENDENCIES............................................................................................................ 5
3. REQUIREMENTS..................................................................................................................................................6
3.1 SECURITY................................................................................................................................................. 6
3.2 INTERFACES.............................................................................................................................................. 6
3.2.1 User Interface....................................................................................................................................6
3.2.2 Application Programming Interface (API).......................................................................................6
3.3 BUSINESS TIER.......................................................................................................................................... 6
3.3.1 Business Façade................................................................................................................................6
3.3.2 Business Logic...................................................................................................................................6
3.3.3 Logic Utilities....................................................................................................................................7
3.4 FILE STORAGE........................................................................................................................................... 7
3.5 RELATIONAL DATABASE............................................................................................................................. 7
4. SYSTEM ARCHITECTURE.................................................................................................................................8
4.1 SYSTEM ARCHITECTURE OVERVIEW........................................................................................................... 8
4.2 ARCHITECTURAL DESIGN.......................................................................................................................... 8
5. COMPONENTS....................................................................................................................................................10
5.1 WEB MODULE......................................................................................................................................... 10
5.2 COMMON MODULE................................................................................................................................. 13
5.3 BUSINESS FACADE MODULE.................................................................................................................... 13
5.4 FILE ACCESS COMPONENT........................................................................................................................ 15
5.5 DATA ACCESS MODULE........................................................................................................................... 15
5.6 EJB MODULE.......................................................................................................................................... 16
5.7 SECURITY MODULE................................................................................................................................. 18
5.8 DATABASE MODULE................................................................................................................................ 18
5.9 LOGIC UTILITIES MODULE....................................................................................................................... 18
6. SIGN OFF..............................................................................................................................................................19
6.1 APPROVAL............................................................................................................................................... 19
Appendix A – Acronym List.........................................................................................................................................20

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1. INTRODUCTION
This Software Requirements and Specification Document (SRSD) captures the complete software
requirements for the proteomics LIMS (protLIMS) and describes the design decisions,
architectural design and the detailed design needed to implement the software. It provides the
acquirer visibility into the design and provides information needed for software support.
The purpose of protLIMS is to allow the recording of all experimental samples, processes,
procedures, analyses, and results of proteomics studies to a searchable relational database.
Recording of such data, and associated metadata, will provide improved record keeping, record
retrieval, and report generation and review.
protLIMS is a LIMS system dedicated to studies in the realm of proteomics. The initial goal (goal
of this version) is to develop the system to the point in the analytical workflow where sample are
prepared for mass spectroscopy. This entails recording of biological sample data, sample
preparation, protein separation/resolution (if any is performed), and isolated protein sample
preparation (if separation was performed and further preparation is performed). Goals of the
protLIMS development are:
1. Allow the recording of all necessary, and desired, data and metadata pertaining to
proteomic analyses.
2. Allow interoperability with parallel LIMS and/or analytical systems.
3. Remain caBIG™ compliant.
4. Though not required, design with future web services is in mind.
The system is being developed in collaboration with the Fox Chase Cancer Center (FCCC)
Proteomics Facility and the caBIG™ adopters: H. Lee Moffitt Cancer Center & Research
Institute.

1.1 SCOPE
The Fox Chase Proteomics Laboratory Information Management System (protLIMS) is being
developed as part of the Cancer Bioinformatics Grid (caBIG™) initiative sponsored by the
National Cancer Institute and facilitated by Booz Allen Hamilton. The system is being developed
in collaboration with the Fox Chase Cancer Center Proteomics Facility and the caBIG™ adopters:
H. Lee Moffitt Cancer Center & Research Institute.
The goal of this project is to develop a stand-alone LIMS system dedicated to studies in the realm
of proteomics. The goal of the current version is to capture the data and metadata to the point in
the analytical workflow where sample are prepared for mass spectroscopy.

1.1.1 Identification
This is the initial version of the Fox Chase Proteomics Laboratory Information Management
System (protLIMS).

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1.1.2 System Overview

This is the initial version of the Fox version of the Fox Chase Proteomics Laboratory Information
Management System (protLIMS). Choices on which data to store and some use cases were
initially taken from the caLIMS project. The caLIMS data model, however, did not satisfy the full
needs of the proteomics laboratories. As a result data models devoted to proteomics, PeDRO and
its successor, HUPO’s Proteomics Standards Initiative/General Proteomics Standards (PSI/GSP),
are being leveraged. In addition, an effort is being made to coordinate with other caBIG™
proteomics efforts (e.g., Rproteomics) and to harmonize the object model with related object
models (e.g., MicroArray and Gene Expression [MAGE]) to improve and simplify protLIMS
interoperability with other systems.

1.1.3 Document Overview

This SRSD captures the complete software requirements for initial development of the Fox Chase
Proteomics Laboratory Information Management System (protLIMS), as part of NCI’s caBIG™
initiative
There are no additional or specific security or privacy considerations associated with this
document. The document and associated software system is being developed transparently and as
open source. Questions, comments and requests may be submitted to the Fox Chase Cancer
Center Bioinformatics Facility.
The remaining SRSD sections are organized as follows:
The remaining SRSD sections are organized as follows:

 Section 2. Project Description: Describes the general factors that affect the protLIMS.

 Section 3. Requirements: Describes all the software requirements to a level of detail

sufficient to enable designers to design a system to satisfy those requirements.

 Section 4. System architecture: Describes architectural aspects of the system as a whole.

 Section 5. Components: Describes functional and architectural aspects of the system

components.

 Appendix A. Acronym List: Defines the abbreviations used on the project.

1.2 REFERENCE DOCUMENTS

For additional project, and requirement specific information, refer to the following documents:

 Use-case requirements document is available at the caBIG™ cvs server:

http://cabigcvs.nci.nih.gov/viewcvs/viewcvs.cgi/proteomicslims/caBIG_Use_Case_protLIMS_
2005_03_08.doc

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Other documentation is also available at the Fox Chase Cancer Center Bioinformatics Facility
website:
http://bioinformatics.fccc.edu/software/caBIG/protLIMS/protlims.shtml

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2. PROJECT DESCRIPTION
The protLIMS records the data associated with the complete workflow of proteomic analyses,
and will provide a data pipeline from analysis step to analysis step. protLIMS is affected by the
data collected by researchers conducting proteomic analyses. These data may be from
heterogeneous sources and may be used as input to other analyses. As such, efforts are being
made to harmonize the protLIMS object model with those systems from other domains, e.g.,
microarray analysis. This will allow and simplify interoperability of systems used to analyze the
same biological materials by parallel research domain spaces.
Development of the protLIMS has begun using model drive architecture (MDA) and an iterative
development process (IDP). Each development iteration of the IDP will complete a classic
software development cascade including:

 Analysis which produces an SRS revision

 Design which produces a Software Design Document revision
 Construction which produces a new code revision
 Quality Assurance Testing both at the Unit Test and Integration System Test levels
2.1 PROJECT PERSPECTIVE
The system is being developed in collaboration with the Fox Chase Cancer Center Proteomics
Facility and the caBIG™ adopters: H. Lee Moffitt Cancer Center & Research Institute.
protLIMS is being designed to allow its function, optionally, as (1) a stand-alone proteomics
LIMS [present] or as (2) an integrated component of interoperable LIMSs [future] or (3) a
caGRID service [future].
Programming is in Java to allow platform independence for the application server (e.g., JBoss
being used in FCCC’s implementation). As a user interface, Internet web pages will be generated
by the protLIMS to allow conventional web browsers to provide a graphic user interface.
Administrative functions will also be available via the web interface.
protLIMS employs an external relational database and the server’s directory file system (or its
equivalent). The relational database provides data storage and file location information for files
stored by protLIMS. Fox Chase Cancer Center is using Oracle for this purpose but the system is
being developed to allow for alternate databases to be used. Data collected into the relational
database may be either entered directly through the web interface, or by uploading files to be
parsed by protLIMS. Parsed files may be generated by a variety of proteomics analytical tools and
are parsed by the system automatically into the database as well as being stored in the server’s
directory file system (or its equivalent). In addition, the directory file system is used by protLIMS
for the storage of other native proteomics data files, e.g., gel images, and ancillary files
(“attachments”) that the user chooses to associate with the data.

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2.2 PROJECT FUNCTIONS

This project will be focused on the creation of a caBIG™-compliant proteomics Laboratory
Information Management System (LIMS), namely: protLIMS. The initial version will track the lab
processes from biological sample registration through 2D gel electrophoresis separation of
proteins and excision of protein “spots” for analysis by mass spectroscopy. The schema and data
model support the addition of additional data types and new data types, as they emerge. The
availability of an open source proteomics LIMS will ultimately allow a distributed development
model in which additional modules can be contributed by other centers.

2.3 USER CHARACTERISTICS

Anticipated end-users of protLIMS are protein analysts in research laboratories or, more
specifically, dedicated proteomics facilities. In addition, researchers who are not performing the
analyses themselves, but have proper permissions to access the system and specific data subset(s),
may also act as end users.

2.4 CONSTRAINTS

2.4.1 protLIMS Statement Of Work

We are constrained to work within the context of our statement of work (SOW). We expect that
the system description will evolve in the course of our analysis but our core product and resource
utilization will remain framed by our SOW.

2.4.2 caBIG™ Compliance

We are constrained to comply with all caBIG™ standards on silver compatibility level. It is a
requirement that protLIMS participate as a fully functioning component of caBIG™. We seek to
adopt all caBIG™ sanctioned architectural patterns within a reasonable time after they are
established. When caBIG™ compatibility issues emerge abruptly in contrast to our development
stream we will adjust at the start of our next development iteration.
Silver level compatibility guidelines can be found at:
https://cabig.nci.nih.gov/guidelines_documentation

2.4.3 Additional constraints, programming language and tools being

employed

• Java is the programming language being used to allow platform independence.

• A Java application server is required for protLIMS implementation. FCCC’s

implementation is being developed utilizing the JBoss Application Server (www.jboss.org),
a freely available, J2EE 1.4 certified, open standards and open source, Java application
server.

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• A relational database back-end is required for protLIMS functionality. Fox Chase Cancer
Center is using Oracle for this purpose but protLIMS is being developed to allow for
alternate databases to be used. PostgreSQL (www.postgresql.org) is being used as a freely
available open source model relational database.

• Programming tools

Function Application
UML modeling tools Sybase PowerDesigner 10.0
Sparx Systems - Enterprise Architect
Compuware OptimalJ 3.3
MDA modeling tool Compuware OptimalJ 3.3
Source code generation tool Compuware OptimalJ 3.3
Java IDE JetBrains IntelliJ IDEA 4.5
JSP and HTML code editor Macromedia DreamWeaver MX 2004
Database modeling tool Sybase PowerDesigner 10.0
Database mining tool Benthic Software Golden 5.7

2.5 QUALIFICATION PROVISIONS

 Project management requires that all generated and non-generated code and interfaces
(application program interface [API] and graphical user interface [GUI]) will be tested.

 Change management requires that all generated and non-generated code and interfaces
(application program interface [API] and graphical user interface [GUI]) will be regression
tested.

 All non-generated code shall be documented in the IDE.

 Unit testing includes empty data tests, known incorrect data tests, and limit testing.
System tests will be performed on newly installed machines to demonstrate that normal operation
does not require any software that is not explicitly stated in the requirements.

2.6 ASSUMPTIONS AND DEPENDENCIES

protLIMS is a LIMS dedicated to those areas of research involved in protein isolation, separation
and identification – i.e., “proteomics.” As such, it is assumed that proteomics researchers,
analytical systems and tools are available for interaction with protLIMS.

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3. REQUIREMENTS

3.1 SECURITY
protLIMS is required to use Java Authentication and Authorization Service (jaas) implementation
to provide security aspect of the system. Authentication options include LDAP and alternative
method for non-LDAP users (database or password file)
protLIMS allows user and role based authorization. Initial protLIMS prototype version will be
designed with these authorization requirements in mind, but may actually contain user and role
based authorization only partially.

3.2 INTERFACES

3.2.1 User Interface

protLIMS is accessed by user via internet browser, thus a web user interface is required. The web
interface is created with by the Jakarta Struts Framework composed of Struts forms, JSPs, and
Struts actions.
User interface provides user access to system functionality defined by use cases (see Referenced
documents section). User interface allows user to create and review information about conducted
proteomics research. User interface also allows authorized personnel to administer protLIMS.

3.2.2 Application Programming Interface (API)

Silver level compatibility requires that a well-described API’s provide access to data in the form of
data objects that are instances of classes represented by a domain model.

3.3 BUSINESS TIER

3.3.1 Business Façade

A Business Façade is required in the protLIMS architecture to handle communication between the
presentation and web tiers and the business logic (EJB) tier. Functionally this hides or exposes
business component functionality. In addition, the Business Façade manages data transfer to and
from the business components and handles Application transactions.

3.3.2 Business Logic

Business logic implements all system functions:

 Maintenance of data (create and update) with EJB (Enterprise Java Beans)

 Read-only querying of data with DAC (Data Access Components)

 File upload/download to/from File Storage

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3.3.3 Logic Utilities

Logic utilities provide functionality for parsing of supported format data files. Initial version of
protLIMS supports:

 Nonlinear Dynamics Progenesis image analysis export file for Microsoft Excel

 Pick list in Microsoft Excel file

3.4 FILE STORAGE

protLIMS requires access to, and use of, the server’s local file system (or its equivalent) as a
dedicated named user (e.g., user_name “protLIMS;” group_name “lims”). This access is used for
the storage of data, and associated files in their native format. protLIMS control of the relevant
directory tree organization is required and organized in a project oriented structure. In this way,
if for any reason the directory tree must be accessed directly by the System Administrator, the tree
may be navigated logically.
Data and associated files stored may be of any type of electronic storage format (e.g., digital
images [e.g., jpeg or tiff], digital text [e.g., XML or pdf], or binary files). Metadata about file
location is retained in the required relational database (Section 3.6). If for some unforeseen reason
stored files are damaged or deleted by external means, protLIMS is required to fail retrieval
“gracefully” returning an appropriate error message about file unavailability.
Limitation of file size and total storage space are independent of protLIMS, being a limitation of
the computer storage operating system and storage media. Earlier operating systems had
maximum file sizes of approximately 2 gb, but this limit has been increased more recently. File size
is not a likely limitation to use. Total storage media does become a concern due to the relatively
large size of files, and number of files, the proteomics experiments generate.

3.5 RELATIONAL DATABASE

A relational database back-end is required for protLIMS functionality. Fox Chase Cancer Center is
using Oracle for this purpose but protLIMS is being developed to allow for alternate databases to
be used. PostgreSQL (www.postgresql.org) is being used as a freely available open source model
relational database. No other database alternative is being tested in the immediate future.
Alternatives must be capable of views and hierarchical queries.
The relational database retains all data entered through the web interface and network paths to
data and associated files. It is required that no data is ever deleted from the database, itself,
though the user may use the web interface “delete” function to delete data entries from the list of
viewed data. In this way all data is retrievable for future access if necessary, e.g., for auditing
purposes.

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4. SYSTEM ARCHITECTURE

4.1 SYSTEM ARCHITECTURE OVERVIEW

The protLIMS utilizes a multi-tiered systems architecture (Figure 4.1-1). The system is being built
using model driven architecture (MDA). This separates functional roles in the system into
individual domain models. The “application model” (Platform Specific Model; PSM) is generated
from the “domain model” (Platform Independent Model; PIM) using technology patterns of J2EE.
User access is provided by an internet/web interface (Tier 1: Client Tier). The client accesses the
interface using an internet/web browser application of their choosing.
The Client Tier communicates with the systems web components composed of the web server and
(Tier 2: Web Tier) and application server (Tier 3: Business Tier). These tiers are isolated from the
user by system modules providing a business façade and business logic.
The Business Tier communicates with the Database Server (Tier 4: Data Storage Tier) for data
storage and retrieval. As specified in the present requirements and specifications document, in
addition to the relational database, collateral files are stored in a dedicated file directory structure.
 
Tier 1:  Tier 2:  Tier 3:  Tier 4: 
Client Tier  Web Tier  Business Tier  Data Storage 
      Tier 
       
 HTML   Java Server   EJB session   JDBC 
  Pages  beans   Connector 
   Struts   EJB entity  technologies 
    beans   
     Data access   
    components   

       
Web  Web  Application  Database 
Browser  Server  Server  Server & 
Directory 
Network  Network  Network 

Figure 4.1-1: System Architecture Overview

4.2 ARCHITECTURAL DESIGN

The user interface (Figure 4.1-1, see: Presentation) is generated by a Jakarta Struts framework:
Struts forms, Java Server Pages (JSPs), and Struts Actions. The Presentation Tier and Business
Logic components communicate with the Business Façade by utilization of shared components
accessible to all components of the system (Figure 4.1-1, see: Common). Methods of the session
beans of the Business Logic component (Figure 4.1-1, see: Business Logic) access Entity Beans
and Data Access Components (DAC) as appropriate for user selected functions. Data of the
database records are recorded and retrieved by methods of the Entity Beans and DAC as
necessary for user selected functions. Similarly, files stored in the protLIMS directory tree are
stored and retrieved as necessary for user selected functions.

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  Files 

Presentation  Business  Business Logic 

Facade 
Struts 
Forms  File 
Access 
Component 
Entity  DBMS 
Beans 
JSPs  Business 
 Facade 
Session  Data 
Beans  Access 
Struts  Components 
Actions 

Web 
Services* 

Common 
Update  Key  Data 
Object  Object 

Collection, List  Collection, List  Collection, List 

Security Model  Logic Utilities 

Figure 4.2-1: protLIMS Architectural Design

* Web services integration is not part of first year requirements

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5. COMPONENTS

5.1 WEB MODULE

Purpose The Web Module provides the user interface (section 3.2.1)

Function The Web Module allows user to access, update and create information via web
browser.

Subordinate The Web Module is implemented with Jakarta Struts framework. The Web
module consists of jsp pages, struts forms, actions and configuration files, and
also resource, style-sheet and java script files.
Dependencies Web interface appearance may depend on used web browser. Primary browsers
are: Internet Explorer on Windows, Safari on MacOS and Mozilla Firefox on
other operating systems. Web interface is not guaranteed to be displayed
correctly on other browsers.
Interfaces User-to-Web Module (for Input files to be parsed by the system):

­ Files exported from gel image analyzing software with data about
detected spots (DeCyder and Progenesis)

­ Pick list (exported by software and modified by researcher)

Interfaces Web Module-to-Business Façade, and vice versa:

 The Web Module accesses system logic via Business façade module.

 The Web Module uses data objects defined in the Common Module to
communicate with the Business Façade.

 The Web module uses the Security Model to provide Authentication and
Authorization.
Each web component deals with its corresponding business façade components.
For example, SampleSvcWebComponent:

­ Uses SampleSvcBusinessFacade to create the sample in the database

­ Uses SpeciesTypeBusinessFacadeComponent to populate the dropdown

menu list of available species in the user interface

­ Uses SampleProviderBusinessFacadeComponent to populate the

dropdown menu list of available providers in the user interface

­ and so on for other dependent look-ups

Other components work in a similar fashion: RawSampleSvc, GelImageSvc,

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ProjectSvc, ProcedureSvc, etc.

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Interfaces

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Processing The Web Module is implemented with Jakarta Struts framework:

Client Web Tier EJB Tier

Controller Model

Controller Action r/w Business r/w Session

Servlet create Class data Facade data
request Bean
Read r/w Create
Browser data r/w
Struts- Update data
Config.xml r/w Object
r/w data
data r/w
forward data Entity
View Bean
Form
JSP
HTML Bean Data
response read Object

get data

Elements of the Struts framework include:

 Controller Servlet—Implements the Controller part of the MVC. It

receives and forwards requests using the struts-config.xml file

 Actions Classes—Implement the Model part of the MVC. They perform

actions and return statuses

 JavaServer Pages (JSPs)—Implement the View part of the MVC. They

are filled with data from the update objects and produce an HTML output
to the client

 Struts-config.xml—Defines the action mapping

 Form Bean—A helper class that contains get and set methods for all the
attributes that can be submitted via an HTML form.

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5.2 COMMON MODULE

Purpose Describes the LIMS shared data structures for generation of, and LIMS
interaction with, the user interface (section 3.2.1).

Function The Common Module contains objects that are used to transfer information
between modules inside system and also between system itself and other
applications.
Subordinate Common module contains two separate modules:

 Core data elements – Reflect the database tables

 Browser – Reflects the database read-only views

Dependencies None
Interfaces None

5.3 BUSINESS FACADE MODULE

Purpose Control tier-to-tier (Web Unit to Business Logic Model) communication, and
therefore improves network traffic performance in the LIMS.

Function The business facade model provides access to business logic. It allows the
presentation model to use the data and access the methods provided by
Business Logic Model components.
Subordinate Business façade components: one for each ejb bean plus one BrowserSvc
Business Facade Component for all DAC components.
Dependencies None

Interfaces Business façade serves as firewall between presentation and business logic tiers:
web module  business façade  entity bean
web module  business façade  session bean
web module  business façade  File Access Component
web module  business façade  Logic utilities

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Interfaces

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5.4 FILE ACCESS COMPONENT

Purpose Provide upload and download of native file to and from directory file storage
(see section 3.4).

Function Saves uploaded file from LimsFileSvcUpdateObject into file storage

Checks if requested file is available for reading
Copies downloaded file from file storage to LimsFileSvcUpdateObject
Subordinate None

Dependencies File Storage for File Access Component is located on the servers’ local file
system.

Interfaces void uploadFile(limsFileSvcUO LimsFileSvcUpdateObject)

void downloadFile(limsFileSvcUO LimsFileSvcUpdateObject)
boolean isReadyForDownload (limsFileSvcUO LimsFileSvcUpdateObject)

5.5 DATA ACCESS MODULE

Purpose Provide read-only access to big subsets of information

Function Perform queries on database views

Subordinate Data Access Components - one for each database view

Dependencies Oracle supports hierarchical queries, PostgreSQL doesn’t. Sample-data

hierarchy DAC analyzes connection metadata to determine current DBMS, and
for Oracle hierarchical queries are performed (where applicable), for other
DBMS (including PostgreSQL) hierarchical queries are replaced by simple
queries that only retrieve one level of children/parents
Interfaces Each DAC has findByProperties() method:
findByProperties (filter <NameOfTheView>UpdateObject) returns
<NameOfTheView>UpdateObjectCollection
NameOfTheView>UpdateObjects belongs to“browser” part of common module
Sample-data hierarchy DAC also provides findAllChildren() and
findAllParents() methods to retrieve information about pedigree for particular
sample or datafile.

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Processing Each non-null attribute in filter update objects is parsed as additional query
condition. If all attributes are null, all available entries are retrieved from
appropriate view.

5.6 EJB MODULE

Purpose Manage information

Function Store data to persistence (database) tier

Subordinate Entity components and Session components

Dependencies EJB 2.0

Interfaces Entity beans are used by business façade to retrieve information from database:
business façade  entity bean  database

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Interfaces Session beans are used by business façade to create and update groups of objects
sometimes called domain views (not to be confused with database views)
business façade  session bean  several entity beans  database

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5.7 SECURITY MODULE

Security module purpose is to provide authentication and authorization methods to the system. In
the current version of the system authentication will be provided by Java Authentication and
Authorization Service (jaas) implementation developed at Fox Chase Cancer Center.
Authorization features will be limited to “laboratory personnel – laboratory project” access
restriction (stored in database).
Java Authentication and Authorization Service is a set of APIs that enable services to authenticate
and enforce access controls upon users. Future releases of the protLIMS should fully support
user-based authorization

5.8 DATABASE MODULE

Purpose Provide data storage

Function Keep data, response to queries

Subordinate Tables and views

Dependencies Two sets of scripts and configuration files are provided (one for Oracle and one
for PostgreSQL) to handle differences between two supported DBMS.

Interfaces None
.

5.9 LOGIC UTILITIES MODULE

Purpose Provide logic utilities to web and business façade modules

Function Utilities provide classes to handle input file parsing. Currently supported
formats are xls files exported from Progenesis or created by researcher
according to upload format requirements.
Subordinate UploadParser interface, implementations for all supported formats, factory
class.
Dependencies UploadParser implementations heavily depend on input file format each
particular implementation is supposed to parse. Changes in these formats
should be reflected in UploadParser implementation changes.

Interfaces Factory class provides access to appropriate UploadParsers for web and
business façade modules. Obtained by factory UploadParser interface provides
method for parsing input file stream into information about spot analysis or gel
plug pick list.

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6. SIGN OFF

6.1 APPROVAL

Architecture Workspace Rep Print Name Date

VCDE Workspace Rep Print Name Date

Adopter Rep Print Name Date

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APPENDIX A – ACRONYM LIST

Term/
Description
Abbreviation
protLIMS Proteomics Laboratory Information Management System
API Application Programming Interface
caCORE Cancer Common Ontologic Reference Environment
caDSR Cancer Data Standards Repository
CDE Common Data Element
CSM Common Security Module
DAC Data Access Component
DBA Database Administrator
DBMS Database Management System
EVS Enterprise Vocabulary Services
FCCC Fox Chase Cancer Center
GUI Graphical User Interface
HUPO Human Proteomics Organisation
JSP Java Server Pages
LIMS Laboratory Information Management System
MAGE MicroArray and Gene Expression (MGED Society)
MGED Microarray Gene Expression Data
PDF Portable Document Format (Adobe)
PM Project Manager
PSI/GPS Proteomics Standards Initiative/General Proteomics Standards (Human Proteomics
Organisation [HUPO])
RM Requirements Manager
RTM Requirements Traceability Matrix
SCM Software Configuration Management
SDK Software Development Kit
SDLC Software Development Lifecycle
SDP Software Development Plan
SE Software Engineering
SEPG Software Engineering Process Group
SM Software Manager
SOP Standard Operating Procedure
SOW Statement of Work
SPI Software Process Improvement
SQA Software Quality Assurance
SRS Software Requirements Specification
SW Software
TBD To Be Determined
TM Test Manager
UML Unified Modeling Language
XMI XML Metadata Interchange (Object management Group [OMG])
XML Extensible Markup Language (World Wide Web Consortium [W3C])

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