See ya CLIST: Migration of SAS Applications from the IBM Mainframe to the WebJoyce C. Zandee, Parke-Davis Pharmaceutical Research, Ann Arbor, MI

Paul Lewis, Parke-Davis Pharmaceutical Research, Ann Arbor, MI

ABSTRACT

This paper discusses the conversion and consolidationof several mainframe SAS applications to UNIX usinga single Web-based front end. The Web interfaceenables end-users to generate raw data listings andstatistical summary reports from their laboratory datawith no assistance from colleagues trained in SAS orthe native operating system, as previously had beenrequired when the analysis applications resided on themainframe computer. Laboratory technicians use theWeb interface to enter study protocol information into aSAS dataset and submit a SAS job. CGI programswritten in Perl then access SAS programs and data onUNIX. The Web interface provides a mechanism forcolleagues to review the SAS output and create PDFrenditions of the resulting reports. Features of theapplication for viewing the SAS protocol dataset,editing text, and administering application security willalso be presented. An on-line demonstration of theinterface is planned.

INTRODUCTION

When Parke-Davis IT management informed thePharmaceutical Research Division in 1996 that all IBM

mainframe applications would have to move to anotherplatform before the end of 1998, initial colleaguereaction was less than favorable. The mainframe hadbeen the mainstay of computing at Parke-DavisResearch for many years and colleagues were reluctantto change. Computer specialists within the scientificdisciplines who had become proficient in their use ofISPF, JCL, and CLISTs to evaluate and report studydata were not enthusiastic about the prospect ofmastering the intricacies of submitting jobs, printingreports, and managing files on a new platform.However, mainframe computing was no longer cost-effective for our research environment. The timetablefor the move was firm as the decision had been madenot to upgrade the mainframe operating system to beY2K compliant. Colleagues who developed andmaintained SAS applications took solace in the factthat their SAS code was portable. The challenge wouldbe to develop new front ends that would allow scientificcolleagues to evaluate and interpret their data whileminimizing their need to learn a new operating system.

Management in the Pathology and ExperimentalToxicology (PET) department viewed the Division’sdirective to move off the mainframe computer as anopportunity to give scientists more direct access toanalysis of their data. If the new analysis interface wasstraightforward and easy to use, laboratory colleaguesmost closely associated with the data collection couldbe responsible for data analysis without the need toinvolve a computer-savvy middleman. To this end, a

collaborative effort between PET colleagues andScientific Information Engineering (SIE) colleagueswas initiated to develop an integrated non-mainframesolution for three SAS applications initially inproduction on the mainframe computer for theanalysis of PET study data.

BACKGROUND

Studies conducted by the PET department at Parke-Davis are used to determine the safety profile of newchemical entities (NCEs) in development. Thesestudies are conducted and evaluated in compliancewith Good Laboratory Practice regulations and aresubject to audit by the Food and Drug Administration.Data collected in toxicology studies are analyzed todetermine the risks associated with acute and chronicexposure to the NCE. The SAS Reporting System(SRS) for Clinical Pathology data (SRS-CP), the SASReporting System for Organ Weight data (SRS-OW),and what would become the SAS Reporting systemfor Body Weight and Food Consumption data(SRS-BWFC) were applications developed on themainframe to produce raw data listings and statisticalsummary tables for data collected on generaltoxicology studies. While initially conceived as asingle integrated application, the SAS code on themainframe for the three data types diverged asdifferent support groups maintained the code.Consequently, even though each of these data typeswere collected on the same study, protocolinformation including study title, compound (NCE),dose levels, and statistical test type were enteredseparately for each of the mainframe applications.Not only was this a duplication of effort, but it wasalso a potential source of discrepancies among theresulting reports for a given study. The move off themainframe would provide the opportunity to reunitethe applications in an integrated environment.

The goals of the SRS conversion project were to:

À move the existing SRS applications off themainframe

À minimize changes to SAS code to simplifyrevalidation

À provide a simple interface to be used bylaboratory staff

À use a common protocol file for all data typesÀ make the resulting analyses available as PDF

files for on-line review and electronic regulatorysubmission.

The PET/SIE collaboration accomplished these goalsin the resulting implementation of a single, integratedWeb-based user interface for the SRS trio.

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SYSTEM ARCHITECTURE UNIX was chosen as the most suitable analysisplatform when security issues were encountered withthe Windows NT platform during preliminary testing.Users could not be authenticated by the native NTsecurity subsystem because the NT server that SAS isinstalled on is in a different domain than the passwordfile. For the most part, SAS code for the analysis andreporting of study data was moved intact to simplify thenecessary revalidation on the new platform. However,minor code changes were required to input informationfrom the integrated protocol dataset, to remove JCLand add corresponding file assignment statements, andto accommodate the SAS version change from 6.08 onthe mainframe to 6.12 on UNIX. PET colleagues access an initial SRS home pagethrough the PET Department Home Page on theParke-Davis Intranet. Besides the SRS home page anda series of help screens, the web interface is composedof four primary panels that provide access to thevarious functions of the system:

À the Study Protocol panelÀ the Generate SAS Reports panelÀ the View Reports panelÀ the Data Sourcing panel

The panels are written in HTML and JavaScript andreside on an NT server. Each of these four panels hasassociated with it a CGI program on UNIX thatprocesses the user input and responds accordingly.The CGIs are written in Perl. Apache HTTP Server isinstalled on the UNIX box to handle requests from thebrowser. User access to restricted functions iscontrolled by matching the entered user ID andpassword to the entries in the Unix /etc/passwd fileusing Perl’s getpwnam function.

STUDY PROTOCOL PANEL

The Study Protocol panel is used to access a SASdataset containing protocol information for all studies inthe system. Study records in the SAS protocol datasetare uniquely identified by the combination of atwo-character location code and the study number.The user must supply the location code and the studynumber for the study of interest. User ID and passwordfields appear on the panel but are only required foradding new studies or updating existing studies in theSAS protocol dataset.

If the user submits the panel information by selectingthe option to “Add/Update Protocol Information”, theCGI runs a SAS job to determine if the enteredlocation/study number combination already exists in theprotocol dataset. If no match is found, a web page isbuilt which allows the user to enter the protocolinformation and add a record to the SAS protocoldataset. If a match is found, a SAS program builds aweb page containing all of the existing protocol

information and displays it in the browser. The usercan enter protocol information including the study title,compound, statistical methods, and group labelinginformation that apply to all data types for the study aswell as information specific to the analysis of eachdata type. If no match is found, a web page is builtwhich allows the user to enter the protocol informationand add a record to the SAS protocol dataset.

Figure 1. Study Protocol Panel

Selecting the “View Protocol Information” optioncauses the SAS program to build a web pagecontaining all of the protocol information as above.However, the pull-down boxes, input boxes, and radiobuttons are disabled. If no match is found, an errormessage is returned to the web page.

This panel also allows the user to copy existingprotocol information to a new location/studycombination, provided the location/study does notalready exist in the SAS dataset. Additional optionsallow the user to Delete or Rename records in theSAS protocol dataset.

GENERATE REPORTS PANEL

The Generate Reports panel passes information fromthe protocol dataset for the specified location/studycombination to the SAS programs used to generateraw data listings and statistical summary tables forthe data type selected by the user, with the output filesdirected to UNIX. Because the SAS jobs may take anumber of minutes to run (2-7 minutes depending onthe size of the study and network traffic), the SAS jobsends the user an e-mail message to the user uponcompletion. This allows the user to minimize thebrowser and do other work.

After the output has been reviewed for accuracy, thispanel also allows the reports for the selected data typeto be “locked down” using the UNIX chmod commandso the reports can not be inadvertently overwritten.The process of locking down the reports sends an e-mail message to a distribution list of scientificcolleagues responsible for the interpretation of thattype of study data. If a correction to the datanecessitates that the reports be regenerated, the user

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will “unlock” the reports for that data type from thispanel as well.

Figure 2. Generate Reports Panel

VIEW REPORTS PANEL

After generating the reports, the responsible laboratorycolleague reviews the SAS log file and SAS output filethrough the View Reports panel and resolves anyunexpected warning and/or error messages generatedeither by SAS or by the logic built into the SRSprogramming code. Then the colleague uses theGenerate Reports panel to “lock down” the reports.

Figure 3. View Reports Panel

Study directors use the View Reports panel to reviewthe reports on-line after specifying the data type,location, study number, and the report of interest. Rawdata listings, statistical summary tables, and otherreports specific to the selected data type may beviewed individually or concatenated as they wouldappear in the research report.

Hard-copies of any report can be generated from theView Reports panel, although study directors areencouraged to review the data on-line. Reports canalso be saved as PDF files, accessible in our documentassembly software, Documentum. The original ASCIIreport is first transformed into a postscript file then

Acrobat distiller is used to create the PDF. Based onthe information supplied in the SAS protocol dataset,the PDF file is automatically saved to the appropriatestudy folder location within Documentum.

DATA SOURCING PANEL

The Data Sourcing panel provides the user andsystem administrator an interface to view and/or editdata dictionaries, create customized analysis macros,input flat files specific to a given data type, and editthe security access file which specifies the appropriateaccess level for authorized users of the system. Auser ID and password is required to access thesecurity access file or to edit any file. The Edit/Viewfunction combines JavaScript and Perl scripting tocreate an interface with the input and output files onUNIX to permit viewing/editing of these files.

Figure 4. Data Sourcing Panel

CONCLUSION

The SRS Web interface has provided a simple, integratedmethod for laboratory colleagues and study directors to evaluateand report their study data and has furnished a mechanism foron-line review and electronic submission of these data—majorimprovements over the application predecessors on the IBMmainframe. PET management and the PET/SIE collaborationeffectively transformed the initially-resisted directive to move offthe IBM mainframe into an opportunity to reevaluate and improveupon the way we analyze our study data and provide access tothe reports.

ACKNOWLEDGMENTS

SAS is a registered trademark or trademark of SASInstitute, Inc. in the USA and other countries. IBM is aregistered trademark or trademark of InternationalBusiness Machines Corporation. indicates USAregistration.

Other brand and product names are registeredtrademarks or trademarks of their respectivecompanies.

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CONTACT INFORMATION

Joyce C. ZandeePathology & Experimental ToxicologyParke-Davis Pharmaceutical Research2800 Plymouth RoadAnn Arbor, MI 48105Phone: 734.622.4034Email: Joyce.Zandee@wl.com

Paul LewisScientific Information EngineeringParke-Davis Pharmaceutical Research2800 Plymouth RoadAnn Arbor, MI 48105Phone: 734.622.7934Email: Paul.Lewis@wl.com

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