using atl/emftvm for import/export of medical data

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Using ATL/EMFTVM for import/export of medical data 8-Oct-2014, Dennis Wagelaar

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Using ATL/EMFTVM for import/export of medical data. 8-Oct-2014 , Dennis Wagelaar. Import/export a common programming scenario. SuMEHR. SuMEHR. GPSMF. GPSMF. PMF. PMF. Corilus XML. Corilus XML. Corilus XML as pivot model. SuMEHR. GPSMF. Corilus XML. PMF. Corilus XML as pivot model. - PowerPoint PPT Presentation

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Page 1: Using ATL/EMFTVM for import/export of medical data

Using ATL/EMFTVM for import/export of medical data

8-Oct-2014, Dennis Wagelaar

Page 2: Using ATL/EMFTVM for import/export of medical data

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Page 3: Using ATL/EMFTVM for import/export of medical data

Page 4: Using ATL/EMFTVM for import/export of medical data

Import/exporta common programming scenario

SuMEHR

GPSMF

PMF

Corilus XML

SuMEHR

GPSMF

PMF

Corilus XML

4

Page 5: Using ATL/EMFTVM for import/export of medical data

Corilus XML as pivot model

SuMEHR

GPSMF

PMF

Corilus XML

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Page 6: Using ATL/EMFTVM for import/export of medical data

Corilus XML as pivot model

SuMEHR

GPSMF

PMF

Corilus XML

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Page 7: Using ATL/EMFTVM for import/export of medical data

Import/exportsimplified

Corilus XML

Corilus XML

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Page 8: Using ATL/EMFTVM for import/export of medical data

Why ATL?(ATL Transformation Language)

Domain-specific language for

transformationMore expressive than mapping frameworks

embedded in Java, e.g. Dozer

Less verbose for transformations than general-

purpose languages

Uses OCL standard for expressions

Uses EMF for data representation

Closely related to plain Java objects

Enriched with additional concepts, e.g. containment and associated properties

8

Page 9: Using ATL/EMFTVM for import/export of medical data

Why EMFTVM?(EMF Transformation Virtual Machine)

Enhanced for “online” use (performance)

Reuse pre-loaded transformations for multiple executions

JIT compiler translates to Java bytecode

Adaptive matching algorithm adds

performance

Improved modularity

Supports multiple rule inheritance across different modules

Supports module import across different source

languages

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Page 10: Using ATL/EMFTVM for import/export of medical data

Why EMFTVM?(EMF Transformation Virtual Machine)

10https://wiki.eclipse.org/ATL/EMFTVM

https://wiki.eclipse.org/ATL/EMFTVM

https://wiki.eclipse.org/ATL/EMFTVM

Page 11: Using ATL/EMFTVM for import/export of medical data

EMF vs. POJOs

Uses Uses

EMF Models Plain Old Java Objects

(JPA)

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Page 12: Using ATL/EMFTVM for import/export of medical data

EMF vs. POJOsThis is what we have...

(JPA)

Uses

Plain Old Java Objects

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Page 13: Using ATL/EMFTVM for import/export of medical data

From POJOs to EMFMoDisco and EMiFy

Java Model Reverse Engineer Plain Old Java Objects

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Page 14: Using ATL/EMFTVM for import/export of medical data

From POJOs to EMFMoDisco and EMiFy

Java Model

Ecore Model

EMiFy.atl

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Page 15: Using ATL/EMFTVM for import/export of medical data

From POJOs to EMFMoDisco and EMiFy

Ecore Model

Generate Model

EMF Java Objects

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Page 16: Using ATL/EMFTVM for import/export of medical data

From POJOs to EMFMoDisco and EMiFy

Java Model

Ecore Model

EMiFy.atl

Reverse Engineer

Generate Model

EMF Java Objects

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Page 17: Using ATL/EMFTVM for import/export of medical data

Using ATL

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Page 18: Using ATL/EMFTVM for import/export of medical data

Using ATL

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Page 19: Using ATL/EMFTVM for import/export of medical data

Using ATLImplicit tracing

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Page 20: Using ATL/EMFTVM for import/export of medical data

Using ATLImplicit tracing

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Page 21: Using ATL/EMFTVM for import/export of medical data

Using ATLCollaboration

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.NET developer Java developer

Java developerJava developer

Common: 178 lines of ATL codeImport: 7283 lines of ATL codeExport: 4617 lines of ATL code

4906 lines of Java import/export code

Page 22: Using ATL/EMFTVM for import/export of medical data

Runtime performance

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03-10-2014 | 13:57:19,223 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.rs.ImportResource | Import partial document 50403-10-2014 | 13:57:19,307 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Start full import for ...03-10-2014 | 13:57:20,006 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Starting transformation...03-10-2014 | 13:57:21,099 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.emftvm.impl.AbstractEMFTVMTransformer | Timing data: Loading finished at 0,000036 seconds (duration: 0,000036 seconds) Matching finished at 0,285989 seconds (duration: 0,285953 seconds) Applying finished at 1,091511 seconds (duration: 0,805522 seconds) Post-applying finished at 1,091712 seconds (duration: 0,000201 seconds) Recursive stage finished at 1,091751 seconds (duration: 0,000039 seconds) Execution finished at 1,091915 seconds (duration: 0,000203 seconds)

03-10-2014 | 13:57:21,118 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 1 Patient instances03-10-2014 | 13:57:21,155 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 3 ExternalUser instances03-10-2014 | 13:57:21,156 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 1 HealthInsurance instances03-10-2014 | 13:57:21,161 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 138 Contact instances03-10-2014 | 13:57:21,282 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 33 Episode instances03-10-2014 | 13:57:21,316 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 33 HealthApproach instances03-10-2014 | 13:57:21,349 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 553 SubContact instances03-10-2014 | 13:57:21,925 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 2 ContactPerson instances03-10-2014 | 13:57:23,240 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 1 Vaccination instances03-10-2014 | 13:57:23,255 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 134 NormalMedicationEntry instances03-10-2014 | 13:57:23,649 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 4 MagistralMedicationEntry instances03-10-2014 | 13:57:23,673 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 138 FreeTextPosology instances03-10-2014 | 13:57:24,041 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 224 SOEPRule instances03-10-2014 | 13:57:24,473 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 78 Letter instances03-10-2014 | 13:57:25,416 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 30 LabResult instances03-10-2014 | 13:57:25,495 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 776 LabResultEntry instances03-10-2014 | 13:57:28,533 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 51 ParameterGroup instances03-10-2014 | 13:57:28,657 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 72 ParameterGroupEntry instances03-10-2014 | 13:57:28,992 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 3 SickLeave instances03-10-2014 | 13:57:29,023 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.services.impl.CorilusXMLImportServiceImpl | Processing 2 Note instances03-10-2014 | 13:57:33,992 | INFO | http-0.0.0.0-8080-4 | be.healthconnect.emr.server.rs.ImportResource | Finished import partial document 504 in 14.768414891

XML

load

ing

0,7 sec Tr

ansf

orm

ation

1,1 sec

Hib

erna

te st

orag

e

12,9 sec

Medium-large patient file (2277 record entries)

Page 23: Using ATL/EMFTVM for import/export of medical data

ConclusionWe tackled a complex and common programming scenario such as import/export

by breaking it up in three ways:

23

Use specialised language for translating between

domain model and pivot model

Use regular Java to handle file I/O and

database interaction

Use pivot model for import/

export => only support a single import/export

format

XML

Page 24: Using ATL/EMFTVM for import/export of medical data

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Questions?

http://www.healthconnect.be/http://www.corilus.be/http://www.careconnect.be/

Questions

?

http://www.healthconnect.be/

http://www.corilus.be/

http://www.careconnect.be/

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