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package org.hl7.fhir.validation;
/*
Copyright (c) 2011+, HL7, Inc.
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are permitted provided that the following conditions are met:
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import java.io.ByteArrayOutputStream;
import java.io.IOException;
import javax.annotation.Nonnull;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.exceptions.FHIRException;
/**
* This class wraps up the validation and conversion infrastructure
* so it can be hosted inside a native server
*
* workflow is pretty simple:
* - create a DelphiLibraryHost, provide with path to library and tx server to use
* (tx server is usually the host server)
* - any structure definitions, value sets, code systems changes on the server get sent to tp seeResource or dropResource
* - server wants to validate a resource, it calls validateResource and gets an operation outcome back
* - server wants to convert from R4 to something else, it calls convertResource
* - server wants to convert to R4 from something else, it calls unConvertResource
*
* threading: todo: this class should be thread safe
*
* note: this is a solution that uses lots of RAM...
*/
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.validation.constants.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.validation.constants.CheckDisplayOption;
import org.hl7.fhir.r5.utils.validation.constants.IdStatus;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonObject;
/**
* This class allows you to host the java validator in another service, and use the services it has in a wider context. The way it works is
- put the jar in your class path
- Find the class org.hl7.fhir.validation.NativeHostServices
- call init(path) where path refers to one of the definitions files from the main build (e.g. definitions.xml.zip) - required, do only once, do before anything else
- call load(path) where path refers to the igpack.zip produced by the ig publisher (do this once for each IG you care about)
- call connectToTxSvc(url) where the url is your terminology service of choice (can be http://tx.fhir.org/r4 or /r3)
now the jar is ready for action. There's 3 functions you can call (all are thread safe):
- validate - given a resource, validate it against all known rules
- convert - given a resource in a different version convert it to this version (if possible)
- unconvert - given a resource, convert it to a different version (if possible)
also, call "status" to get a json object that describes the internals of the jar (e.g. for server status)
The interface is optimised for JNI.
* @author Grahame Grieve
*
*/
public class NativeHostServices {
private class NH_10_50_Advisor extends BaseAdvisor_10_50 {
@Override
public void handleCodeSystem(@Nonnull CodeSystem tgtcs, @Nonnull ValueSet source) throws FHIRException {}
@Override
public CodeSystem getCodeSystem(@Nonnull ValueSet src) throws FHIRException {
throw new FHIRException("Code systems cannot be handled at this time"); // what to do? need thread local storage?
}
}
private ValidationEngine validator;
private IgLoader igLoader;
private int validationCount = 0;
private int resourceCount = 0;
private int convertCount = 0;
private int unConvertCount = 0;
private int exceptionCount = 0;
private String lastException = null;
private Object lock = new Object();
private final BaseAdvisor_10_50 conv_10_50_advisor = new NH_10_50_Advisor();
/**
* Create an instance of the service
*/
public NativeHostServices() {
super();
}
/**
* Initialize the service and prepare it for use
*
* @param pack - the filename of a pack from the main build - either definitions.xml.zip, definitions.json.zip, or igpack.zip
* @throws Exception
*/
public void init(String pack) throws Exception {
validator = new ValidationEngine.ValidationEngineBuilder().fromSource(pack);
validator.getContext().setAllowLoadingDuplicates(true);
igLoader = new IgLoader(validator.getPcm(), validator.getContext(), validator.getVersion(), validator.isDebug());
}
/**
* Load an IG so that the validator knows all about it.
*
* @param pack - the filename (or URL) of a validator.pack produced by the IGPublisher
*
* @throws Exception
*/
public void load(String pack) throws Exception {
igLoader.loadIg(validator.getIgs(), validator.getBinaries(), pack, false);
}
/**
* Set up the validator with a terminology service
*
* @param txServer - the URL of the terminology service (http://tx.fhir.org/r4 default)
* @throws Exception
*/
public void connectToTxSvc(String txServer, String log) throws Exception {
validator.connectToTSServer(txServer, log, FhirPublication.R5, false);
}
/**
* Set up the validator with a terminology service
*
* @param txServer - the URL of the terminology service (http://tx.fhir.org/r4 default)
* @throws Exception
*/
public void connectToTxSvc(String txServer, String log, String txCache) throws Exception {
validator.connectToTSServer(txServer, log, txCache, FhirPublication.fromCode(validator.getVersion()), false);
}
/**
* get back a JSON object with information about the process.
* @return
*/
public String status() {
JsonObject json = new JsonObject();
json.addProperty("custom-resource-count", resourceCount);
validator.getContext().reportStatus(json);
json.addProperty("validation-count", validationCount);
json.addProperty("convert-count", convertCount);
json.addProperty("unconvert-count", unConvertCount);
json.addProperty("exception-count", exceptionCount);
synchronized (lock) {
json.addProperty("last-exception", lastException);
}
json.addProperty("mem-max", Runtime.getRuntime().maxMemory() / (1024*1024));
json.addProperty("mem-total", Runtime.getRuntime().totalMemory() / (1024*1024));
json.addProperty("mem-free", Runtime.getRuntime().freeMemory() / (1024*1024));
json.addProperty("mem-used", (Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / (1024*1024));
Gson gson = new GsonBuilder().create();
return gson.toJson(json);
}
/**
* Call when the host process encounters one of the following:
* - (for validation):
* - profile
* - extension definition
* - value set
* - code system
*
* - (for conversion):
* - structure map
* - concept map
*
* @param source
* @throws Exception
*/
public void seeResource(byte[] source, FhirFormat fmt) throws Exception {
try {
Resource r;
if (fmt == FhirFormat.JSON) {
r = new JsonParser().parse(source);
} else if (fmt == FhirFormat.JSON) {
r = new XmlParser().parse(source);
} else {
throw new Exception("Unsupported format "+fmt.name());
}
validator.seeResource(r);
resourceCount++;
} catch (Exception e) {
exceptionCount++;
synchronized (lock) {
lastException = e.getMessage();
}
throw e;
}
}
/**
* forget a resource that was previously seen (using @seeResource)
*
* @param type - the resource type
* @param id - the resource id
*
* @throws Exception
*/
public void dropResource(String type, String id) throws Exception {
try {
validator.dropResource(type, id);
resourceCount--;
} catch (Exception e) {
exceptionCount++;
synchronized (lock) {
lastException = e.getMessage();
}
throw e;
}
}
/**
* Validate a resource.
*
* Possible options:
* - id-optional : no resource id is required (default)
* - id-required : a resource id is required
* - id-prohibited : no resource id is allowed
* - any-extensions : allow extensions other than those defined by the encountered structure definitions
* - bp-ignore : ignore best practice recommendations (default)
* - bp-hint : treat best practice recommendations as a hint
* - bp-warning : treat best practice recommendations as a warning
* - bp-error : treat best practice recommendations as an error
* - display-ignore : ignore Coding.display and do not validate it (default)
* - display-check : check Coding.display - must be correct
* - display-case-space : check Coding.display but allow case and whitespace variation
* - display-case : check Coding.display but allow case variation
* - display-space : check Coding.display but allow whitespace variation
*
* @param location - a text description of the context of validation (for human consumers to help locate the problem - echoed into error messages)
* @param source - the bytes to validate
* @param cntType - the format of the content. one of XML, JSON, TURTLE
* @param options - a list of space separated options
* @return
* @throws Exception
*/
public byte[] validateResource(String location, byte[] source, String cntType, String options) throws Exception {
try {
IdStatus resourceIdRule = IdStatus.OPTIONAL;
boolean anyExtensionsAllowed = true;
BestPracticeWarningLevel bpWarnings = BestPracticeWarningLevel.Ignore;
CheckDisplayOption displayOption = CheckDisplayOption.Ignore;
for (String s : options.split(" ")) {
if ("id-optional".equalsIgnoreCase(s))
resourceIdRule = IdStatus.OPTIONAL;
else if ("id-required".equalsIgnoreCase(s))
resourceIdRule = IdStatus.REQUIRED;
else if ("id-prohibited".equalsIgnoreCase(s))
resourceIdRule = IdStatus.PROHIBITED;
else if ("any-extensions".equalsIgnoreCase(s))
anyExtensionsAllowed = true; // This is already the default
else if ("strict-extensions".equalsIgnoreCase(s))
anyExtensionsAllowed = false;
else if ("bp-ignore".equalsIgnoreCase(s))
bpWarnings = BestPracticeWarningLevel.Ignore;
else if ("bp-hint".equalsIgnoreCase(s))
bpWarnings = BestPracticeWarningLevel.Hint;
else if ("bp-warning".equalsIgnoreCase(s))
bpWarnings = BestPracticeWarningLevel.Warning;
else if ("bp-error".equalsIgnoreCase(s))
bpWarnings = BestPracticeWarningLevel.Error;
else if ("display-ignore".equalsIgnoreCase(s))
displayOption = CheckDisplayOption.Ignore;
else if ("display-check".equalsIgnoreCase(s))
displayOption = CheckDisplayOption.Check;
else if ("display-case-space".equalsIgnoreCase(s))
displayOption = CheckDisplayOption.CheckCaseAndSpace;
else if ("display-case".equalsIgnoreCase(s))
displayOption = CheckDisplayOption.CheckCase;
else if ("display-space".equalsIgnoreCase(s))
displayOption = CheckDisplayOption.CheckSpace;
else if (!Utilities.noString(s))
throw new Exception("Unknown option "+s);
}
OperationOutcome oo = validator.validate(location, source, FhirFormat.valueOf(cntType), null, resourceIdRule, anyExtensionsAllowed, bpWarnings, displayOption);
ByteArrayOutputStream bs = new ByteArrayOutputStream();
new XmlParser().compose(bs, oo);
validationCount++;
return bs.toByteArray();
} catch (Exception e) {
exceptionCount++;
synchronized (lock) {
lastException = e.getMessage();
}
throw e;
}
}
/**
* Convert a resource to R4 from the specified version
*
* @param r - the source of the resource to convert from
* @param fmt - the format of the content. one of XML, JSON, TURTLE
* @param version - the version of the content. one of r2, r3
* @return - the converted resource (or an exception if can't be converted)
* @throws FHIRException
* @throws IOException
*/
public byte[] convertResource(byte[] r, String fmt, String version) throws FHIRException, IOException {
try {
if (VersionUtilities.isR3Ver(version)) {
org.hl7.fhir.dstu3.formats.ParserBase p3 = org.hl7.fhir.dstu3.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.dstu3.model.Resource res3 = p3.parse(r);
Resource res4 = VersionConvertorFactory_30_50.convertResource(res3);
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
convertCount++;
return p4.composeBytes(res4);
} else if (VersionUtilities.isR2Ver(version)) {
org.hl7.fhir.dstu2.formats.ParserBase p2 = org.hl7.fhir.dstu2.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.dstu2.model.Resource res2 = p2.parse(r);
Resource res4 = VersionConvertorFactory_10_50.convertResource(res2, conv_10_50_advisor);
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
convertCount++;
return p4.composeBytes(res4);
} else if (VersionUtilities.isR2BVer(version)) {
org.hl7.fhir.dstu2016may.formats.ParserBase p2 = org.hl7.fhir.dstu2016may.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.dstu2016may.model.Resource res2 = p2.parse(r);
Resource res4 = VersionConvertorFactory_14_50.convertResource(res2);
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
convertCount++;
return p4.composeBytes(res4);
} else if (VersionUtilities.isR4Ver(version)) {
org.hl7.fhir.r4.formats.ParserBase p2 = org.hl7.fhir.r4.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.r4.model.Resource res2 = p2.parse(r);
Resource res4 = VersionConvertorFactory_40_50.convertResource(res2);
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
convertCount++;
return p4.composeBytes(res4);
} else
throw new FHIRException("Unsupported version "+version);
} catch (Exception e) {
exceptionCount++;
synchronized (lock) {
lastException = e.getMessage();
}
throw e;
}
}
/**
* Convert a resource from R4 to the specified version
*
* @param r - the source of the resource to convert from
* @param fmt - the format of the content. one of XML, JSON, TURTLE
* @param version - the version to convert to. one of r2, r3
* @return - the converted resource (or an exception if can't be converted)
* @throws FHIRException
* @throws IOException
*/
public byte[] unConvertResource(byte[] r, String fmt, String version) throws FHIRException, IOException {
try {
if ("3.0".equals(version) || "3.0.1".equals(version) || "r3".equals(version)) {
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
org.hl7.fhir.dstu3.model.Resource res3 = VersionConvertorFactory_30_50.convertResource(res4);
org.hl7.fhir.dstu3.formats.ParserBase p3 = org.hl7.fhir.dstu3.formats.FormatUtilities.makeParser(fmt);
unConvertCount++;
return p3.composeBytes(res3);
} else if ("1.0".equals(version) || "1.0.2".equals(version) || "r2".equals(version)) {
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
org.hl7.fhir.dstu2.model.Resource res2 = VersionConvertorFactory_10_50.convertResource(res4, conv_10_50_advisor);
org.hl7.fhir.dstu2.formats.ParserBase p2 = org.hl7.fhir.dstu2.formats.FormatUtilities.makeParser(fmt);
unConvertCount++;
return p2.composeBytes(res2);
} else if ("1.4".equals(version) || "1.4.0".equals(version)) {
org.hl7.fhir.r5.formats.ParserBase p4 = org.hl7.fhir.r5.formats.FormatUtilities.makeParser(fmt);
org.hl7.fhir.r5.model.Resource res4 = p4.parse(r);
org.hl7.fhir.dstu2016may.model.Resource res2 = VersionConvertorFactory_14_50.convertResource(res4);
org.hl7.fhir.dstu2016may.formats.ParserBase p2 = org.hl7.fhir.dstu2016may.formats.FormatUtilities.makeParser(fmt);
unConvertCount++;
return p2.composeBytes(res2);
} else
throw new FHIRException("Unsupported version "+version);
} catch (Exception e) {
exceptionCount++;
synchronized (lock) {
lastException = e.getMessage();
}
throw e;
}
}
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