Package ch.ahdis.matchbox.engine

Class MatchboxEngine

java.lang.Object

org.hl7.fhir.validation.ValidationEngine

ch.ahdis.matchbox.engine.MatchboxEngine

All Implemented Interfaces:

org.hl7.fhir.r5.context.IWorkerContextManager.IPackageLoadingTracker, org.hl7.fhir.r5.utils.validation.IValidationPolicyAdvisor, org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher, org.hl7.fhir.validation.cli.services.IPackageInstaller

Direct Known Subclasses:

CdaMappingEngine

public class MatchboxEngine
extends org.hl7.fhir.validation.ValidationEngine

Base Engine providing functionality on top of the ValdiationEngine

Author:

oliveregger

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	MatchboxEngine.MatchboxEngineBuilder	Builder class to instantiate a MappingEngine

Nested classes/interfaces inherited from class org.hl7.fhir.validation.ValidationEngine

org.hl7.fhir.validation.ValidationEngine.IValidationEngineLoader, org.hl7.fhir.validation.ValidationEngine.ValidationEngineBuilder

Field Summary

Fields

Modifier and Type	Field	Description
protected static final org.slf4j.Logger	log
protected final List<String>	suppressedWarnInfoPatterns

Constructor Summary

Constructors

Constructor	Description
MatchboxEngine(@NonNull org.hl7.fhir.validation.ValidationEngine other)

Method Summary

Modifier and Type	Method	Description
void	addCanonicalResource(InputStream stream)	adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url
void	addCanonicalResource(org.hl7.fhir.r4.model.Resource resource)	adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R4
void	addCanonicalResource(org.hl7.fhir.r4b.model.CanonicalResource resource)	adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R4B
void	addCanonicalResource(org.hl7.fhir.r5.model.CanonicalResource resource)	adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R5
void	addSuppressedWarnInfo(@NonNull String text)	Adds a text to the list of suppressed validation warning/information-level issues.
void	addSuppressedWarnInfoPattern(@NonNull String pattern)	Adds a Regex pattern to the list of suppressed validation warning/information-level issues.
List<org.hl7.fhir.r5.model.StructureDefinition>	asSdList(@Nullable List<String> profiles)	internal use, checks if all profiles can be resolved
protected List<Pattern>	compileSuppressedWarnInfoPatterns()	Compiles the list of suppressed validation warning/information-level issues into a list of Pattern.
org.hl7.fhir.r4.model.StructureDefinition	createSnapshot(org.hl7.fhir.r4.model.StructureDefinition sd)	creates the snapshot for the provided StructureDefinition
String	evaluateFhirPath(@NonNull String input, boolean inputJson, @NonNull String expression)
boolean	fetchesCanonicalResource(org.hl7.fhir.r5.utils.validation.IResourceValidator validator, String url)
List<org.hl7.fhir.utilities.validation.ValidationMessage>	filterValidationMessages(@NonNull List<org.hl7.fhir.utilities.validation.ValidationMessage> messages)	Copies the given list, removes messages if they are warning and match a list of ignored messages.
org.hl7.fhir.r4.model.Resource	getCanonicalResource(String canonical)	Returns a canonical resource defined by its url
org.hl7.fhir.instance.model.api.IBaseResource	getCanonicalResource(String canonical, String fhirVersion)	Returns a canonical resource defined by its url
org.hl7.fhir.instance.model.api.IBaseResource	getCanonicalResourceById(String type, @NonNull String id)	Returns a canonical resource defined by its type and uri
org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager	getPcm()	A safe getter for the PCM.
org.hl7.fhir.r4.model.StructureDefinition	getStructureDefinition(String profile)	Get the corresponding Struc
List<String>	getSuppressedWarnInfoPatterns()	Returns the list of suppressed validation warning/information-level issues.
void	loadPackage(@NonNull InputStream inputStream)	Loads an IG in the engine from its NPM package as an InputStream, its ID and version.
protected org.hl7.fhir.r4.model.OperationOutcome	messagesToOutcome(@NonNull List<org.hl7.fhir.utilities.validation.ValidationMessage> messages, @NonNull org.hl7.fhir.r5.context.SimpleWorkerContext context)	Maps a list of ValidationMessage to an R4 OperationOutcome.
org.hl7.fhir.r4.model.StructureMap	parseMap(String content)	Parses a FHIR Structure Map from the textual representation according to the FHIR Mapping Language grammar (see http://build.fhir.org/mapping-language.html#grammar)
org.hl7.fhir.r5.model.StructureMap	parseMapR5(String content)	Parses a FHIR Structure Map from the textual representation according to the FHIR Mapping Language grammar (see http://build.fhir.org/mapping-language.html#grammar) for FHIR release 5
String	transform(String input, boolean inputJson, String mapUri, boolean outputJson)	Transforms an input with the map identified by the uri to the output defined by the map
org.hl7.fhir.r5.elementmodel.Element	transform(org.hl7.fhir.r5.elementmodel.Element src, String mapUri)	Adapted transform operation from Validation Engine to use patched MatchboxStructureMapUtilities
org.hl7.fhir.r5.elementmodel.Element	transform(org.hl7.fhir.utilities.ByteProvider source, org.hl7.fhir.r5.elementmodel.Manager.FhirFormat cntType, String mapUri)	Adapted transform operation from Validation Engine to use patched MatchboxStructureMapUtilities
org.hl7.fhir.r4.model.Resource	transformToFhir(String input, boolean inputJson, String mapUri)	Transforms an input with the map identified by the uri to the output defined by the map
org.hl7.fhir.r4.model.OperationOutcome	validate(@NonNull InputStream stream, @NonNull org.hl7.fhir.r5.elementmodel.Manager.FhirFormat format, @Nullable String profileUrl)	validates a FHIR resources and provides OperationOutcome as output
org.hl7.fhir.r4.model.OperationOutcome	validate(@NonNull org.hl7.fhir.r4.model.Resource resource, @Nullable String profileUrl)	validates a FHIR resources and provides OperationOutcome as output
List<org.hl7.fhir.utilities.validation.ValidationMessage>	validate(@NonNull org.hl7.fhir.r5.elementmodel.Manager.FhirFormat format, @NonNull InputStream stream, @Nullable String profileUrl)

Methods inherited from class org.hl7.fhir.validation.ValidationEngine

compile, connectToTSServer, connectToTSServer, convert, dropResource, evaluateFhirPath, fetch, fetchCanonicalResource, fetchRaw, generate, genResource, getBestPracticeLevel, getBinaries, getBundleValidationRules, getContext, getExtensionDomains, getFetcher, getFhirPathEngine, getHtmlInMarkdownCheck, getIgLoader, getIgs, getJurisdiction, getLanguage, getLevel, getLocale, getLocator, getMapLog, getPolicyAdvisor, getQuestionnaireMode, getValidationControl, getValidator, getVersion, handleOutput, initContext, isAllowDoubleQuotesInFHIRPath, isAllowExampleUrls, isAnyExtensionsAllowed, isAssumeValidRestReferences, isCheckIPSCodes, isCrumbTrails, isDebug, isDisplayWarnings, isDoImplicitFHIRPathStringConversion, isDoNative, isForPublication, isHintAboutNonMustSupport, isNoExtensibleBindingMessages, isNoInvariantChecks, isNoUnicodeBiDiControlChars, isSecurityChecks, isShowMessagesFromReferences, isShowTimes, isWantInvariantInMessage, loadCanonicalResource, loadPackage, loadProfile, loadResource, packageExists, packageLoaded, policyForCodedContent, policyForContained, policyForReference, prepare, resolveURL, seeResource, setAllowDoubleQuotesInFHIRPath, setAllowExampleUrls, setAnyExtensionsAllowed, setAssumeValidRestReferences, setBestPracticeLevel, setBinaries, setBundleValidationRules, setCheckIPSCodes, setContext, setCrumbTrails, setDebug, setDisplayWarnings, setDoImplicitFHIRPathStringConversion, setDoNative, setExtensionDomains, setFetcher, setFhirPathEngine, setForPublication, setHintAboutNonMustSupport, setHtmlInMarkdownCheck, setIgLoader, setIgs, setJurisdiction, setLanguage, setLevel, setLocale, setLocator, setMapLog, setNoExtensibleBindingMessages, setNoInvariantChecks, setNoUnicodeBiDiControlChars, setPcm, setPolicyAdvisor, setQuestionnaireMode, setSecurityChecks, setShowMessagesFromReferences, setShowTimes, setSnomedExtension, setTerminologyServer, setValidationControl, setVersion, setWantInvariantInMessage, snapshot, transform, transformVersion, validate, validate, validate, validate, validate, validate, validateAsFragments

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

log

protected static final org.slf4j.Logger log

suppressedWarnInfoPatterns

protected final List<String> suppressedWarnInfoPatterns

Constructor Details

MatchboxEngine

public MatchboxEngine(@NonNull org.hl7.fhir.validation.ValidationEngine other)
               throws org.hl7.fhir.exceptions.FHIRException,
IOException

Throws:

org.hl7.fhir.exceptions.FHIRException

IOException

Method Details

getPcm

public org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager getPcm()

A safe getter for the PCM. It has been created in the constructor, so it should be safe to access.

Overrides:

getPcm in class org.hl7.fhir.validation.ValidationEngine

transformToFhir

public org.hl7.fhir.r4.model.Resource transformToFhir(String input,
 boolean inputJson,
 String mapUri)
                                               throws org.hl7.fhir.exceptions.FHIRException,
IOException

Transforms an input with the map identified by the uri to the output defined by the map

Parameters:

input - content to be transformed

inputJson - true if input is in json (if false xml is expected)

mapUri - canonical url of StructureMap

Returns:

FHIR resource

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

transform

public String transform(String input,
 boolean inputJson,
 String mapUri,
 boolean outputJson)
                 throws org.hl7.fhir.exceptions.FHIRException,
IOException

Transforms an input with the map identified by the uri to the output defined by the map

Parameters:

input - source in UTF-8 format

inputJson - if input is in json (or xml)

mapUri - map to use for transformation

outputJson - if output is formatted as json (or xml)

Returns:

transformed input as string

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

transform

public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.utilities.ByteProvider source,
 org.hl7.fhir.r5.elementmodel.Manager.FhirFormat cntType,
 String mapUri)
                                               throws org.hl7.fhir.exceptions.FHIRException,
IOException

Adapted transform operation from Validation Engine to use patched MatchboxStructureMapUtilities

Overrides:

transform in class org.hl7.fhir.validation.ValidationEngine

Throws:

org.hl7.fhir.exceptions.FHIRException

IOException

transform

public org.hl7.fhir.r5.elementmodel.Element transform(org.hl7.fhir.r5.elementmodel.Element src,
 String mapUri)
                                               throws org.hl7.fhir.exceptions.FHIRException,
IOException

Adapted transform operation from Validation Engine to use patched MatchboxStructureMapUtilities

Parameters:

src -

mapUri -

Returns:

Throws:

org.hl7.fhir.exceptions.FHIRException

IOException

addCanonicalResource

public void addCanonicalResource(InputStream stream)
                          throws org.hl7.fhir.exceptions.FHIRException

adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url

Parameters:

stream - canonical resource to add

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

addCanonicalResource

public void addCanonicalResource(org.hl7.fhir.r4.model.Resource resource)
                          throws org.hl7.fhir.exceptions.FHIRException

adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R4

Parameters:

resource - canonical resource to add

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

addCanonicalResource

public void addCanonicalResource(org.hl7.fhir.r4b.model.CanonicalResource resource)
                          throws org.hl7.fhir.exceptions.FHIRException

adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R4B

Parameters:

resource - canonical resource to add

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

addCanonicalResource

public void addCanonicalResource(org.hl7.fhir.r5.model.CanonicalResource resource)
                          throws org.hl7.fhir.exceptions.FHIRException

adds a canonical resource to the loaded packages, please note that it will replace a resource with the same canonical url for FHIR R5

Parameters:

resource - canonical resource to add

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

validate

public org.hl7.fhir.r4.model.OperationOutcome validate(@NonNull InputStream stream,
 @NonNull org.hl7.fhir.r5.elementmodel.Manager.FhirFormat format,
 @Nullable String profileUrl)
                                                throws org.hl7.fhir.exceptions.FHIRException,
IOException,
org.hl7.fhir.r5.utils.EOperationOutcome

validates a FHIR resources and provides OperationOutcome as output

Parameters:

stream - resource to validate as input stream

format - format of resource

profileUrl - profile to validate against

Returns:

result as Operation Outcome

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

org.hl7.fhir.r5.utils.EOperationOutcome - Exception OperationOutcome

validate

public org.hl7.fhir.r4.model.OperationOutcome validate(@NonNull org.hl7.fhir.r4.model.Resource resource,
 @Nullable String profileUrl)
                                                throws org.hl7.fhir.exceptions.FHIRException,
IOException,
org.hl7.fhir.r5.utils.EOperationOutcome

validates a FHIR resources and provides OperationOutcome as output

Parameters:

resource - FHIR R4 resource

profileUrl - profile to validate against

Returns:

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

org.hl7.fhir.r5.utils.EOperationOutcome

validate

public List<org.hl7.fhir.utilities.validation.ValidationMessage> validate(@NonNull org.hl7.fhir.r5.elementmodel.Manager.FhirFormat format,
 @NonNull InputStream stream,
 @Nullable String profileUrl)
                                                                   throws org.hl7.fhir.exceptions.FHIRException,
IOException,
org.hl7.fhir.r5.utils.EOperationOutcome

Throws:

org.hl7.fhir.exceptions.FHIRException

IOException

org.hl7.fhir.r5.utils.EOperationOutcome

asSdList

public List<org.hl7.fhir.r5.model.StructureDefinition> asSdList(@Nullable List<String> profiles)
                                                         throws Error

internal use, checks if all profiles can be resolved

Overrides:

asSdList in class org.hl7.fhir.validation.ValidationEngine

Parameters:

profiles - canonical url of profiles (StructureDefinition)

Returns:

StructureDefintions

Throws:

Error - if profile cannot be resolved

getStructureDefinition

public org.hl7.fhir.r4.model.StructureDefinition getStructureDefinition(String profile)

Get the corresponding Struc

Parameters:

profile -

Returns:

getCanonicalResource

public org.hl7.fhir.r4.model.Resource getCanonicalResource(String canonical)

Returns a canonical resource defined by its url

Parameters:

canonical -

Returns:

getCanonicalResource

public org.hl7.fhir.instance.model.api.IBaseResource getCanonicalResource(String canonical,
 String fhirVersion)

Returns a canonical resource defined by its url

Parameters:

canonical -

fhirVersion -

Returns:

fetchesCanonicalResource

public boolean fetchesCanonicalResource(org.hl7.fhir.r5.utils.validation.IResourceValidator validator,
 String url)

Specified by:

fetchesCanonicalResource in interface org.hl7.fhir.r5.utils.validation.IValidatorResourceFetcher

Overrides:

fetchesCanonicalResource in class org.hl7.fhir.validation.ValidationEngine

getCanonicalResourceById

public org.hl7.fhir.instance.model.api.IBaseResource getCanonicalResourceById(String type,
 @NonNull String id)

Returns a canonical resource defined by its type and uri

Parameters:

type - resource type

id - resource id

Returns:

parseMapR5

public org.hl7.fhir.r5.model.StructureMap parseMapR5(String content)
                                              throws org.hl7.fhir.exceptions.FHIRException

Parses a FHIR Structure Map from the textual representation according to the FHIR Mapping Language grammar (see http://build.fhir.org/mapping-language.html#grammar) for FHIR release 5

Parameters:

content - FHIR Mapping Language text

Returns:

parsed StructureMap resource

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

parseMap

public org.hl7.fhir.r4.model.StructureMap parseMap(String content)
                                            throws org.hl7.fhir.exceptions.FHIRException

Parses a FHIR Structure Map from the textual representation according to the FHIR Mapping Language grammar (see http://build.fhir.org/mapping-language.html#grammar)

Parameters:

content - FHIR Mapping Language text

Returns:

parsed StructureMap resource

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

createSnapshot

public org.hl7.fhir.r4.model.StructureDefinition createSnapshot(org.hl7.fhir.r4.model.StructureDefinition sd)
                                                         throws org.hl7.fhir.exceptions.FHIRException,
IOException

creates the snapshot for the provided StructureDefinition

Parameters:

sd - StructureDefinition with differential

Returns:

StructureDefinition with snapshot (differential applied to base definition)

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

evaluateFhirPath

public String evaluateFhirPath(@NonNull String input,
 boolean inputJson,
 @NonNull String expression)
                        throws org.hl7.fhir.exceptions.FHIRException,
IOException

Parameters:

input - input to run fhirpath expression against

inputJson - if input format is json or xml

expression - fhirPath expression

Returns:

result

Throws:

org.hl7.fhir.exceptions.FHIRException - FHIR Exception

IOException - IO Exception

loadPackage

public void loadPackage(@NonNull InputStream inputStream)
                 throws IOException

Loads an IG in the engine from its NPM package as an InputStream, its ID and version. The InputStream will be closed by NpmPackage.readStream(java.io.InputStream, java.lang.String, boolean).

The package dependencies shall be added manually, no recursive loading will be performed.

Parameters:

inputStream - The NPM package input stream. It will be closed.

Throws:

IOException

filterValidationMessages

public List<org.hl7.fhir.utilities.validation.ValidationMessage> filterValidationMessages(@NonNull List<org.hl7.fhir.utilities.validation.ValidationMessage> messages)

Copies the given list, removes messages if they are warning and match a list of ignored messages.

Parameters:

messages - The original list of validation messages.

Returns:

A copy of the message list, without issues that have to be filtered.

addSuppressedWarnInfo

public void addSuppressedWarnInfo(@NonNull String text)

Adds a text to the list of suppressed validation warning/information-level issues.

Implementation note: The text is Regex-escaped before being added to the list.

Parameters:

text - The text to add.

addSuppressedWarnInfoPattern

public void addSuppressedWarnInfoPattern(@NonNull String pattern)

Adds a Regex pattern to the list of suppressed validation warning/information-level issues.

Parameters:

pattern - The Regex pattern to add.

getSuppressedWarnInfoPatterns

public List<String> getSuppressedWarnInfoPatterns()

Returns the list of suppressed validation warning/information-level issues.

compileSuppressedWarnInfoPatterns

protected List<Pattern> compileSuppressedWarnInfoPatterns()

Compiles the list of suppressed validation warning/information-level issues into a list of Pattern.

messagesToOutcome

protected org.hl7.fhir.r4.model.OperationOutcome messagesToOutcome(@NonNull List<org.hl7.fhir.utilities.validation.ValidationMessage> messages,
 @NonNull org.hl7.fhir.r5.context.SimpleWorkerContext context)
                                                            throws IOException,
org.hl7.fhir.exceptions.FHIRException,
org.hl7.fhir.r5.utils.EOperationOutcome

Maps a list of ValidationMessage to an R4 OperationOutcome.

Throws:

IOException

org.hl7.fhir.exceptions.FHIRException

org.hl7.fhir.r5.utils.EOperationOutcome