20161116 hapi fhir java beginner and advanced for dev days (1)

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HAPI-FHIR for Java Developers

James AgnewFHIR Developer DaysNovember 16, 2016


Who am I?

● Name: James Agnew● Company: Centre for Global eHealth Innovation (University Health Network)

● Background:● Software Development Manager● Project lead for HAPI for 11 years

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About this Presentation

● All code samples are available on GitHub in fully working form

https://github.com/furore-fhir/fhirstarters

● HAPI is too big a topic for 45 minutesso…● I will be around! Let’s talk!

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https://github.com/furore-fhir/fhirstarters


Show of Hands

● Who here is new to FHIR?● Who here is new to HAPI FHIR?


FHIR: A Quick Recap

● There are two key parts of FHIR to consider:● The first is a data model for healthcare Resources

and supporting Datatypes

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● The second is a RESTful API for interacting with that model

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FHIR: A Quick Recap (2)


● FHIR has had several releases● FHIR DSTU1 (Released 2014)● FHIR DSTU2 (Released 2015)● FHIR STU3 (Will be released early 2017?)

● This presentation focuses on STU3 but the concepts apply to all versions

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FHIR: A Quick Recap (3)


The HAPI Project

● HAPI started in 2001 as an HL7 v2 Library● Built to support a simple web portal, now used

in applications around the world

HL7 v2 - http://hl7api.sourceforge.net FHIR - http://hapifhir.io

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HAPI FHIR: What is it?

● Not a client or a server, but a toolkit for building either

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HAPI FHIR: Why did we build it?● Two use cases at our hospital:

● As a unified clinical data access layer● As a backend for our mobile apps

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FHIR in Java

● HAPI is now the Java Reference Implementation● Many RI features are “copied in” for each release

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Design Goals

● Use Anywhere● Apache 2.0 License for all components● Minimal dependencies

● Be Flexible● Loosely coupled, pluggable components

● Be Powerful● “Steal” all the best ideas from existing frameworks:

JAX-WS, Springframework, .NET FHIR API ☺..etc..

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ComponentsHAPI FHIR Modules


Today (Beginner)Tomorrow (Advanced)


Structures Classes:The FHIR Model



● HAPI supports multiple versions of FHIR via different “structures JARs”

hapi-fhir-structures-dstu-2.1.jar

hapi-fhir-structures-dstu2-2.1.jar

hapi-fhir-structures-dstu3-2.1.jar

FHIR Version HAPI Version

Patient Resource ModelsPatient Resource ModelsPatient Resource Models



● HAPI Defines several sets of classes which form the data model

● Resource definition classes implement IBaseResource

● Examples: Patient, CarePlan, Encounter, Practitioner, Medication

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Structures Classes: The FHIR Model (2)

● HAPI also defines a class for each data type

● Primitive classes are named [name]Type

● Primitive types include: StringType, BooleanType

● Composite types include: Address, Ratio, HumanName

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Structures Classes: The FHIR Model (3)

● JavaDocs for structures are available here: http://hapifhir.io/apidocs-dstu3/index.html

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http://hapifhir.io/apidocs-dstu3/index.html


Using the Structures:Creating a Resource

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1: public class Example01_CreateAPatient { 2: public static void main(String[] theArgs) { 3: // Create a resource instance 4: Patient pat = new Patient(); 5: 6: // Add a "name" element 7: HumanName name = pat.addName(); 8: name.addFamily("Simpson").addGiven("Homer").addGiven("J"); 9: 10: // Add an "identifier" element11: Identifier identifier = pat.addIdentifier();12: identifier.setSystem("http://acme.org/MRNs").setValue("7000135");13: 14: // Model is designed to be chained15: pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("12345");16: }17: }


1: public class Example01_CreateAPatient { 2: public static void main(String[] theArgs) { 3: // Create a resource instance 4: Patient pat = new Patient(); 5: 6: // Add a "name" element 7: HumanName name = pat.addName(); 8: name.addFamily("Simpson").addGiven("Homer").addGiven("J"); 9: 10: // Add an "identifier" element11: Identifier identifier = pat.addIdentifier();12: identifier.setSystem("http://acme.org/MRNs").setValue("7000135");13: 14: // Model is designed to be chained15: pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("12345");16: }17: }

Using the Structures:Use the Autocomplete!

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Using the Structures:Enumerated Types

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1: public class Example02_EnumeratedTypes { 2: public static void main(String[] theArgs) { 3: 4: Patient pat = new Patient(); 5: 6: pat.addName().addFamily("Simpson").addGiven("Homer").addGiven("J"); 7: pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135"); 8: 9: // Enumerated types are provided for many coded elements10: ContactPoint contact = pat.addTelecom();11: contact.setUse(ContactPointUse.HOME);12: contact.setSystem(ContactPointSystem.PHONE);13: contact.setValue("1 (416) 340-4800");14: 15: pat.setGender(AdministrativeGender.MALE);16: }17: }


Using the Structures:Primitive Fields

HumanName.family is a string in FHIR

There are two ways of interacting with this field:String HumanName.getFamily()void HumanName.setFamily(String)

StringDt HumanName.getFamilyElement();void HumanName.setFamilyElement(StringDt);


Using the Structures:Add Extensions

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1: public class Example03_AddSomeExtensions { 2: public static void main(String[] theArgs) { 3: Patient pat = new Patient(); 4: pat.addName().addFamily("Simpson").addGiven("Homer").addGiven("J"); 5: 6: // Add an extension on the resource 7: pat.addExtension() 8: .setUrl("http://hl7.org/fhir/StructureDefinition/patient-importance") 9: .setValue(new CodeableConcept().setText("Patient is a VIP"));10: 11: // Add an extension on a primitive12: pat.getBirthDateElement().setValueAsString("1955-02-22");13: pat.getBirthDateElement().addExtension()14: .setUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime")15: .setValue(new TimeType("23:30"));16: }17: }


Parsers:Serializing & Deserializing


Playing with Parsers

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● The starting point for much of the HAPI-FHIR API is the FhirContext class

● FhirContext acts as a factory for the rest of the API, including the two parsers:● XmlParser● JsonParser

● FhirContext is designed to be created once and reused (important for performance!)


Playing with Parsers:Encoding Resources

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1: public class Example04_EncodeResource { 2: public static void main(String[] theArgs) { 3: 4: // Create a Patient 5: Patient pat = new Patient(); 6: pat.addName().addFamily("Simpson").addGiven("Homer").addGiven("J"); 7: pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135"); 8: pat.addTelecom().setSystem(ContactPointSystem.PHONE).setValue("1 (416) 340-4800"); 9: pat.setGender(AdministrativeGender.MALE);10: 11: // Create a context12: FhirContext ctx = FhirContext.forDstu3();13: 14: // Create a XML parser15: IParser parser = ctx.newJsonParser();16: parser.setPrettyPrint(true);17: 18: String encode = parser.encodeResourceToString(pat);19: System.out.println(encode);20: 21: }22: }


Playing with Parsers:Encoding Resources (2)

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// Create a contextFhirContext ctx = FhirContext.forDstu3();

// Create a XML parserIParser parser = ctx.newJsonParser();parser.setPrettyPrint(true);

String encode = parser .encodeResourceToString(pat);System.out.println(encode);

1: { 2: "resourceType": "Patient", 3: "identifier": [ { 4: "system": "http://acme.org/MRNs", 5: "value": "7000135" 6: } ], 7: "name": [ { 8: "family": [ "Simpson" ], 9: "given": [ "Homer", "J" ]10: } ],11: "telecom": [ {12: "system": "phone",13: "value": "1 (416) 340-4800",14: "use": "home"15: } ],16: "gender": "male"17: }


Playing with Parsers:Parsing Resources

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1: public class Example05_ParseResource { 2: public static void main(String[] theArgs) { 3: String resourceBody = "{\"resourceType\":\"Patient\",\"identifier\":[{\"system\":\"http://acme.org/MRNs\",\"value\":\"7000135\"}],\"name\":[{\"family\":[\"Simpson\"],\"given\":[\"Homer\",\"J\"]}]}"; 4: 5: // Create a context 6: FhirContext ctx = FhirContext.forDstu3(); 7: 8: // Create a JSON parser 9: IParser parser = ctx.newJsonParser();10: Patient pat = parser.parseResource(Patient.class, resourceBody);11: 12: List<Identifier> identifiers = pat.getIdentifier();13: String idSystemString = identifiers.get(0).getSystem();14: String idValueString = identifiers.get(0).getValue();15: 16: System.out.println(idSystemString + " " + idValueString);17: }18: } http://acme.org/MRNs - 7000135


Clients:Moving Data Around


FHIR Clients:Recap on REST● FHIR defines basic CRUD operations that

can be performed on a FHIR compliant server (*not a complete list)

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Name HTTP URL

type create POST http://base/[type]

instance read GET http://base/[type]/[id]

instance update PUT http://base/[type]/[id]

instance delete DELETE http://base/[type]/[id]

type search GET http://base/[type]?[params]


FHIR Clients:Basic CRUD - Create

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1: public class Example06_ClientCreate { 2: public static void main(String[] theArgs) { 3: Patient pat = new Patient(); 4: pat.addName().addFamily("Simpson").addGiven("Homer").addGiven("J"); 5: pat.addIdentifier().setSystem("http://acme.org/MRNs").setValue("7000135"); 6: pat.setGender(AdministrativeGender.MALE); 7: 8: // Create a context 9: FhirContext ctx = FhirContext.forDstu3();10: 11: // Create a client12: String serverBaseUrl = "http://fhirtest.uhn.ca/baseDstu3";13: IGenericClient client = ctx.newRestfulGenericClient(serverBaseUrl);14: 15: // Use the client to store a new resource instance 16: MethodOutcome outcome = client.create().resource(pat).execute();17: 18: // Print the ID of the newly created resource19: System.out.println(outcome.getId());20: }21: } http://fhirtest.uhn.ca/base/Patient/4529/_history/1


1: public class Example07_ClientReadAndUpdate { 2: public static void main(String[] theArgs) { 3: // Create a client 4: String serverBaseUrl = "http://fhirtest.uhn.ca/baseDstu3"; 5: FhirContext ctx = FhirContext.forDstu3(); 6: IGenericClient client = ctx.newRestfulGenericClient(serverBaseUrl); 7: 8: // Use the client to read back the new instance using the ID 9: Patient patient = client.read(Patient.class, "190002");10: 11: // Print the ID of the newly created resource12: System.out.println("Found ID: " + patient.getId());13: 14: // Change the gender and send an update to the server15: patient.setGender(AdministrativeGender.FEMALE);16: MethodOutcome outcome = client.update().resource(patient).execute();17: 18: System.out.println("Now have ID: " + outcome.getId());19: }20: }

FHIR Clients:Basic CRUD - Read/Update

http://fhirtest.uhn.ca/base/Patient/190002/_history/2

http://fhirtest.uhn.ca/base/Patient/190002/_history/1


● FHIR defines a powerful search mechanism● Searches are specially crafted URLs to

express queries such as:● Find a Patient with the given Identifier● Find all Patients with given gender and

DOB● Find all lab reports for a given patient

identifier with an “abnormal” interpretation34

FHIR Clients:Searching


● Searching is powerful! Learn about it athttp://hl7.org/fhir/search.html

● For now, let’s imagine a search for a Patient named “Test” whose birthdate is before 2014

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FHIR Clients:Searching (2)

=

http://hl7.org/fhir/search.html

http://hl7.org/fhir/search.html


1: public class Example08_ClientSearch { 2: public static void main(String[] theArgs) { 3: FhirContext ctx = FhirContext.forDstu3(); 4: IGenericClient client = ctx.newRestfulGenericClient("http://fhirtest.uhn.ca/baseDstu3"); 5: 6: // Log requests and responses (very verbose for testing!) 7: client.registerInterceptor(new LoggingInterceptor(true)); 8: 9: // Build a search and execute it10: Bundle response = client.search()11: .forResource(Patient.class)12: .where(Patient.NAME.matches().value("Test"))13: .and(Patient.BIRTHDATE.before().day("2014-01-01"))14: .count(100)15: .returnBundle(Bundle.class)16: .execute();17: 18: // How many resources did we find?19: System.out.println("Responses: " + response.getTotal());20: 21: // Print the ID of the first one22: System.out.println(response.getEntry().get(0).getResource().getId());23: }24: }


http://fhirtest.uhn.ca/baseDstu3/Patient/82599/_history/1

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9: // Build a search and execute it10: Bundle response = client.search()11: .forResource(Patient.class)12: .where(Patient.NAME.matches().value("Test"))13: .and(Patient.BIRTHDATE.before().day("2014-01-01"))14: .count(100)15: .returnBundle(Bundle.class)16: .execute();


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Many more available options for searching!

See:http://hapifhir.io/doc_rest_client.html#SearchQuery_-_Type


FHIR Clients:Lots More● You can follow a similar pattern to do many

more operations:● Delete, Validate, History, Tags, etc…

● Client logging interceptor can be very helpful● http://hapifhir.io/hapi-fhir/doc_rest_client_interceptor.html#Lo

gging:_Log_Requests_and_Responses

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http://hapifhir.io/hapi-fhir/doc_rest_client_interceptor.html#Logging:_Log_Requests_and_Responses




FHIR Server in a boxhapi-fhir-cli


Questions?

We will cover more tomorrow at HAPI Advanced Tutorial. Any requests?


HAPI-FHIR for Java Developers -

AdvancedJames Agnew

FHIR Developer DaysNovember 17, 2016


Today’s Agenda

We will cover more tomorrow at HAPI Advanced Tutorial


Validation


Error checking vs Validation in HAPIError Checking during Parsing (learn more: hapifhir.io)

● Parser can be configured with an “Error Handler” which logs or fails on error

● Only catches structural issues

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Validation

(our focus for today)

● Applies a complete set of rules to a resource instance

● Currently far more powerful


Using Schema Validator1: public class Example12_ParserErrorHandler { 2: public static void main(String[] args) { 3: String input = "<Encounter xmlns=\"http://hl7.org/fhir\"><AAAA value=\"foo\"/></Encounter>"; 4: 5: IParser p = FhirContext.forDstu3().newXmlParser(); 6: 7: // Parse with (default) lenient error handler 8: p.setParserErrorHandler(new LenientErrorHandler()); 9: p.parseResource(input);10: 11: // Parse with strict error handler12: p.setParserErrorHandler(new StrictErrorHandler());13: p.parseResource(input);14: }15: }


Parser Error Handling1: public class Example12_ParserErrorHandler { 2: public static void main(String[] args) { 3: String input = "<Encounter xmlns=\"http://hl7.org/fhir\"><AAAA value=\"foo\"/></Encounter>"; 4: 5: IParser p = FhirContext.forDstu3().newXmlParser(); 6: 7: // Parse with (default) lenient error handler 8: p.setParserErrorHandler(new LenientErrorHandler()); 9: p.parseResource(input);10: 11: // Parse with strict error handler12: p.setParserErrorHandler(new StrictErrorHandler());13: p.parseResource(input);14: }15: }

07:53:40.536 WARN c.u.fhir.parser.LenientErrorHandler Unknown element 'AAAA' found while parsing


Parser Error Handling1: public class Example12_ParserErrorHandler { 2: public static void main(String[] args) { 3: String input = "<Encounter xmlns=\"http://hl7.org/fhir\"><AAAA value=\"foo\"/></Encounter>"; 4: 5: IParser p = FhirContext.forDstu3().newXmlParser(); 6: 7: // Parse with (default) lenient error handler 8: p.setParserErrorHandler(new LenientErrorHandler()); 9: p.parseResource(input);10: 11: // Parse with strict error handler12: p.setParserErrorHandler(new StrictErrorHandler());13: p.parseResource(input);14: }15: }

Exception in thread "main" ca.uhn.fhir.parser.DataFormatException: DataFormatException at [[row,col {unknown-source}]: [1,40]]: Unknown element 'AAAA' found during parse

at ca.uhn.fhir.parser.XmlParser.doXmlLoop(XmlParser.java:277)


Validation in FHIR

Schema (XSD) and Schematron (SCH)

● Uses XSD+SCH files● Covers base FHIR

specification● XML validation only

(HAPI will convert)● Simpler to use

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Profile Validation

● Uses FHIR resources:● StructureDefinition● ValueSet / CodeSystem

● Native JSON/XML support

● Profile validation● Slicing validation● Terminology

validation


Validation in HAPI

● HAPI’s validator uses modules and collects the results from any that are enabled

● Create your own if you want!


Schema/Schematron Validation

Dependencies:● hapi-fhir-validation-resources-dstu3-2.1.jar● phloc-schematron-2.7.0.jar

Inputs (pick one):● Resource Java model object● Raw JSON Resource● Raw XML Resource


Using Schema Validator1: public class Example09_ValidateResource { 2: public static void main(String[] args) { 3: 4: // Create an incomplete encounter (status is required) 5: Encounter enc = new Encounter(); 6: enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345"); 7: 8: // Create a new validator 9: FhirContext ctx = FhirContext.forDstu3();10: FhirValidator validator = ctx.newValidator();11: 12: // Did we succeed?13: ValidationResult result = validator.validateWithResult(enc);14: System.out.println("Success: " + result.isSuccessful());15: 16: // What was the result17: OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();18: IParser parser = ctx.newXmlParser().setPrettyPrint(true);19: System.out.println(parser.encodeResourceToString(outcome));20: }22: }


Using Schema Validator1: public class Example09_ValidateResource { 2: public static void main(String[] args) { 3: 4: // Create an incomplete encounter (status is required) 5: Encounter enc = new Encounter(); 6: enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345"); 7: 8: // Create a new validator 9: FhirContext ctx = FhirContext.forDstu3();10: FhirValidator validator = ctx.newValidator();11: 12: // Did we succeed?13: ValidationResult result = validator.validateWithResult(enc);14: System.out.println("Success: " + result.isSuccessful());15: 16: // What was the result17: OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();18: IParser parser = ctx.newXmlParser().setPrettyPrint(true);19: System.out.println(parser.encodeResourceToString(outcome));20: }22: }

<OperationOutcome xmlns="http://hl7.org/fhir"> <issue> <severity value="error"/> <code value="processing"/> <diagnostics value="cvc-complex-type.2.4.b: The content of element 'Encounter' is not complete. One of '{"http://hl7.org/fhir":identifier, "http://hl7.org/fhir":status}' is expected."/> <location value="Line[1] Col[140]"/> </issue></OperationOutcome>

false


Using Schema Validator with String input

1: public class Example10_ValidateResourceString { 2: public static void main(String[] args) { 3: 4: String input = "<Encounter xmlns=\"http://hl7.org/fhir\"></Encounter>"; 5: 6: // Create a new validator 7: FhirContext ctx = FhirContext.forDstu3(); 8: FhirValidator validator = ctx.newValidator(); 9: 10: // Did we succeed?11: ValidationResult result = validator.validateWithResult(input);12: System.out.println("Success: " + result.isSuccessful());13: 14: // What was the result15: OperationOutcome outcome = (OperationOutcome) result.toOperationOutcome();16: IParser parser = ctx.newXmlParser().setPrettyPrint(true);17: System.out.println(parser.encodeResourceToString(outcome));18: }19: }

String is also fine as input


Profile Validation

● FhirInstanceValidator module requires an instance of IValidationSupport

● Several implementations are supplied with HAPI FHIR

● You can also create your own


Profile Validation

Use built-in FHIR definitions and terminology

Load your own definitions and terminology

Chain multiple providers together


Profile Validation1: public class Example11_ValidateResourceInstanceValidator { 2: public static void main(String[] args) { 3: // Create an incomplete encounter (status is required) 4: Encounter enc = new Encounter(); 5: enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345"); 6: 7: // Create a new validator 8: FhirValidator validator = FhirContext.forDstu3().newValidator(); 9: 10: // Cache this! Supplies structure definitions11: DefaultProfileValidationSupport support = new DefaultProfileValidationSupport();12: 13: // Create the validator14: FhirInstanceValidator module = new FhirInstanceValidator(support);15: validator.registerValidatorModule(module);16: 17: // Did we succeed?18: IParser parser = FhirContext.forDstu3().newXmlParser().setPrettyPrint(true);19: System.out.println(parser.encodeResourceToString(validator.validateWithResult(enc).toOperationOutcome()));20: }21: }


Profile Validation1: public class Example11_ValidateResourceInstanceValidator { 2: public static void main(String[] args) { 3: // Create an incomplete encounter (status is required) 4: Encounter enc = new Encounter(); 5: enc.addIdentifier().setSystem("http://acme.org/encNums").setValue("12345"); 6: 7: // Create a new validator 8: FhirValidator validator = FhirContext.forDstu3().newValidator(); 9: 10: // Cache this! Supplies structure definitions11: DefaultProfileValidationSupport support = new DefaultProfileValidationSupport();12: 13: // Create the validator14: FhirInstanceValidator module = new FhirInstanceValidator(support);15: validator.registerValidatorModule(module);16: 17: // Did we succeed?18: IParser parser = FhirContext.forDstu3().newXmlParser().setPrettyPrint(true);19: System.out.println(parser.encodeResourceToString(validator.validateWithResult(enc).toOperationOutcome()));20: }21: }

13:25:41.843 INFO Loading structure definitions from classpath: /org/hl7/fhir/instance/model/dstu3/profile/profiles-resources.xml13:25:43.962 INFO Loading structure definitions from classpath: /org/hl7/fhir/instance/model/dstu3/profile/profiles-types.xml13:25:44.085 INFO Loading structure definitions from classpath: /org/hl7/fhir/instance/model/dstu3/profile/profiles-others.xml

<OperationOutcome xmlns="http://hl7.org/fhir"> <issue> <severity value="error"/> <code value="processing"/> <diagnostics value="Profile http://hl7.org/fhir/StructureDefinition/Encounter, Element 'Encounter.status': minimum required = 1, but only found 0"/> <location value="Encounter"/> </issue></OperationOutcome>

LoadingProfiles

Friendly Errors


Creating a Server


FHIR Server: Architecture

● HAPI provides a REST Server framework● Based on standard JEE/Servlet 2.5+

(Tomcat, Glassfish, Websphere, JBoss, etc)● Inspired by (but not based on) JAX-RS, RestEasy,

Spring REST, etc.

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FHIR Server: Architecture (2)● Architecture is based

on “Resource Providers” which are custom classes you write to interact with your resources

● This is a “low level” API for building servers, not an “off the shelf” solution

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FHIR Server:Defining Resource Providers

● Resource Providers implement your server logic

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1: public class Example01_StubResourceProvider implements IResourceProvider { 2: public Class<? extends IBaseResource> getResourceType() { 3: return Patient.class; 4: } 5: 6: @Read 7: public Patient read(@IdParam IdType theId) { return null; /* populate this */ }10: 11: @Create 12: void create(@ResourceParam Patient thePatient) { /* save the resource */ }15: 16: @Search17: List<Patient> search(18: @OptionalParam(name="family") StringParam theFamily,19: @OptionalParam(name="given") StringParam theGiven20: ) {21: return null; // populate this22: }23: }


● The following slides show a simple example building a FHIR server using HAPI

● Resources are stored in a HashMap (could just as easily be a database or something else!)

● These samples can be downloaded and executed on your laptop very easily

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FHIR Server:A Simple Example


FHIR Server:A simple resource provider

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1: public class Example02_PatientResourceProvider implements IResourceProvider { 2: 3: private Map<String, Patient> myPatients = new HashMap<String, Patient>(); 4: 5: /** Constructor */ 6: public Example02_PatientResourceProvider() { 7: Patient pat1 = new Patient(); 8: pat1.setId("1"); 9: pat1.addIdentifier().setSystem("http://acme.com/MRNs").setValue("7000135");10: pat1.addName().addFamily("Simpson").addGiven("Homer").addGiven("J");11: myPatients.put("1", pat1);12: }13: 14: /** Simple implementation of the "read" method */15: @Read(version=false)16: public Patient read(@IdParam IdType theId) {17: Patient retVal = myPatients.get(theId.getIdPart());18: if (retVal == null) {19: throw new ResourceNotFoundException(theId);20: }21: return retVal;22: }23: 24: @Override25: public Class<? extends IBaseResource> getResourceType() {26: return Patient.class;27: }28: 29: 30: }


FHIR Server:A simple server

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1: @WebServlet("/*") 2: public class Example03_SimpleRestfulServer extends RestfulServer { 3: 4: @Override 5: protected void initialize() throws ServletException { 6: // Create a context for the appropriate version 7: setFhirContext(FhirContext.forDstu3()); 8: 9: // Register resource providers10: registerProvider(new Example02_PatientResourceProvider());11: }12: }

● The servlet is very simple: it creates an instance of each resource provider and declares the servlet path


● Console 1: Start Server

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FHIR Server:Trying the server out

james$ mvn jetty:run[INFO] Scanning for projects...2014-11-21 12:27:37.622:WARN:oejsh.RequestLogHandler:main: !RequestLog2014-11-21 12:27:37.669:INFO:oejs.ServerConnector:main: Started ServerConnect[INFO] Started Jetty Server

● Console 2: Try it out!james$ curl “http://localhost:8080/Patient/1"<Patient xmlns="http://hl7.org/fhir"><identifier><system value="http://acme.com/MRNs"/><value value="7000135"/></identifier><name><family value="Simpson"/><given value="Homer"/><given value="J"/></name></Patient>


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FHIR Server:Trying the server out (2)


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1: public class Example04_PatientResourceProviderWithCreate implements IResourceProvider { 2: // ---- not all methods shown ---- 3: @Create 4: public MethodOutcome create(@ResourceParam Patient thePatient) { 5: // Give the resource the next sequential ID 6: int id = myNextId++; 7: thePatient.setId(new IdType(id)); 8: 9: // Store the resource in memory10: myPatients.put(Integer.toString(id), thePatient);11: 12: // Inform the server of the ID for the newly stored resource13: return new MethodOutcome().setId(thePatient.getIdElement());14: }15: 16: @Search17: public List<Patient> search() {18: List<Patient> retVal = new ArrayList<Patient>();19: retVal.addAll(myPatients.values());20: return retVal;21: }22: }

FHIR Server:Adding Create and Search


● The following command executes a ‘create’

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curl -H "Content-Type: application/xml+fhir" \ -X POST \ -d '<Patient xmlns="http://hl7.org/fhir"><name><family value="Fireman"/><given value="John"/></name></Patient>' \ "http://localhost:8080/Patient"

FHIR Server:Testing out Create

curl "http://localhost:8080/Patient?_pretty=true"

[ … snip … ]<Bundle xmlns="http://hl7.org/fhir"> <type value="searchset"/> <total value="3"/>

● Now perform a search


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FHIR Server:Adding Search Params

https://github.com/jamesagnew/hapi-fhir/tree/master/hapi-fhir-tutorial/simple-server

1: @Search 2: public List<Patient> search(@RequiredParam(name = Patient.SP_FAMILY) StringParam theParam) { 3: List<Patient> retVal = new ArrayList<Patient>(); 4: 5: // Loop through the patients looking for matches 6: for (Patient next : myPatients.values()) { 7: String familyName = next.getNameFirstRep().getFamilyAsSingleString().toLowerCase(); 8: if (familyName.contains(theParam.getValue().toLowerCase()) == false) { 9: continue;10: }11: retVal.add(next);12: }13: 14: return retVal;15: }

“family”




FHIR Server:Much more is available● Combining multiple parameters● Parameters for sorting, limiting, paging, etc.

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HAPI FHIR JPA

We will cover more tomorrow at HAPI Advanced Tutorial


HAPI FHIR JPA:Introduction

● HAPI JPA Server is a complete FHIR Server implementation based on Hibernate & Hibernate Search

● This is the module that powers http://fhirtest.uhn.ca


HAPI FHIR JPA:Components

Implementation of most operations, search types, terminology svc, etc.

Database of your choosing

The same server from the previous section

Generated ResourceProviders for all resource types


HAPI FHIR JPA:Features

● Supports most of the basic FHIR HTTP specification (create, search, conditionals, etc)

● Supports many advanced features too (subscriptions, patch, etc)

● Includes full validator and terminology server


HAPI FHIR JPA:Databases

● HAPI examples typically use Apache Derby database● Derby is very convenient but not scalable

● HAPI is known to work with MySQL, Postgres, Oracle, SQL Server


HAPI FHIR JPA:Lucene

● HAPI uses Apache Lucene to provide two features:● Fulltext searching within resources (_text

and _content parameters)● Terminology Services

● Lucene stores its files on the filesystem● Lucene can be safely disabled


Create your own JPA Server


Trying out HAPI FHIR JPA

There is a complete sample project available here:

https://github.com/furore-fhir/fhirstarters/tree/master/java/hapi-fhirstarters-jpaserver-example






Taking the Example for a Spin...


An Even Easier Way to Try HAPI FHIR JPA

HAPI-FHIR-CLI Bundles this


Get Help!

● See our website for documentation:http://hapifhir.io

● We also have a Google Group / Mailing Listhttps://groups.google.com/d/forum/hapi-fhir

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http://hapifhir.io

http://hapifhir.io

https://groups.google.com/d/forum/hapi-fhir

https://groups.google.com/d/forum/hapi-fhir


Get Involved!

● HAPI is a large worldwide community of developers

● Today most are working on HL7 v2, but this is changing fast

● We are very grateful to the many people who have contributed so far, maybe you could be next?

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Thank You!

● [email protected]● jamesagnew214 on Skype

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mailto:[email protected]

mailto:[email protected]


Some bonus slides follow… :)


Extensions: The Easy Way● Every element has a collection of

“undeclared” extensions

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public class Example10_Extensions {

public static void main(String[] args) {Patient pat = new Patient();pat.addName().addFamily("Simpson").addGiven("Homer");

String url = "http://acme.org#eyeColour";boolean isModifier = false;pat.addUndeclaredExtension(isModifier, url).setValue(new CodeDt(“blue"));

IParser p = new FhirContext().newXmlParser().setPrettyPrint(true);String encoded = p.encodeResourceToString(pat);

System.out.println(encoded);}

}

<Patient xmlns="http://hl7.org/fhir"> <extension url="http://acme.org#eyeColour"> <valueCode value="blue"/> </extension> <name> <family value="Simpson"/> <given value="Homer"/> </name></Patient>


● HAPI also provides a set of annotations for creating statically typed extensions

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@ResourceDef(name="Patient")public class Example11_ExtendedPatient extends Patient {

@Child(name = "eyeColour")@Extension(url="http://acme.org/#extpt", definedLocally = false, isModifier = false)private CodeDt myEyeColour;

public CodeDt getEyeColour() {if (myEyeColour == null) {

myEyeColour = new CodeDt();}return myEyeColour;

}

public void setEyeColour(CodeDt theEyeColour) {myEyeColour = theEyeColour;

}

}

Extensions: The “Hard” Way

20161116 hapi fhir java beginner and advanced for dev days (1)

Healthcare