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I need help #29

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merged 5 commits into from
Jun 8, 2021
Merged

I need help #29

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e9f2a8f
wip
markiantorno May 23, 2021
bcf05c1
I need help to proceed.
markiantorno Jun 6, 2021
a2c1e38
update to 5.4.4
grahamegrieve Jun 6, 2021
c8279c1
adding Jose's changes
markiantorno Jun 8, 2021
c10000d
Merge branch 'i_need_help' of https://github.com/HL7/kindling into i_…
markiantorno Jun 8, 2021
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43 changes: 17 additions & 26 deletions build.gradle.kts
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Expand Up @@ -37,14 +37,14 @@ repositories {

dependencies {
implementation("ca.uhn.hapi.fhir", "hapi-fhir-base", "4.0.0")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.utilities", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu2", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu2016may", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu3", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.r4", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.r5", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.convertors", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.validation", "5.3.9")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.utilities", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu2", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu2016may", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.dstu3", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.r4", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.r5", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.convertors", "5.4.4-SNAPSHOT")
implementation("ca.uhn.hapi.fhir", "org.hl7.fhir.validation", "5.4.4-SNAPSHOT")
implementation("ch.qos.logback", "logback-classic", "1.2.3")
implementation("com.google.code.gson", "gson", "2.8.5")
implementation("commons-codec", "commons-codec", "1.9")
Expand Down Expand Up @@ -106,24 +106,15 @@ dependencies {
implementation("com.google.guava", "guava", "23.6-jre")
implementation("org.json", "json", "20171018")
implementation("com.damnhandy", "handy-uri-templates", "2.1.6")
implementation("es.weso", "schema_2.12", "0.0.60")
implementation("es.weso", "shacl_2.12", "0.0.60")
implementation("es.weso", "shex_2.12", "0.0.60")
implementation("es.weso", "manifest_2.12", "0.0.60")
implementation("es.weso", "srdfjena_2.12", "0.0.60")
implementation("es.weso", "srdf_2.12", "0.0.60")
implementation("es.weso", "utils_2.12", "0.0.60")
implementation("es.weso", "converter_2.12", "0.0.60")
implementation("es.weso", "rbe_2.12", "0.0.60")
implementation("es.weso", "typing_2.12", "0.0.60")
implementation("es.weso", "validating_2.12", "0.0.60")
implementation("es.weso", "server_2.12", "0.0.60")
implementation("org.scalactic", "scalactic_2.12", "3.0.1")
implementation("org.scalatest", "scalatest_2.12", "3.0.1")
implementation("com.typesafe.scala-logging", "scala-logging_2.12", "3.5.0")
implementation("org.rogach", "scallop_2.12", "2.0.6")
implementation("org.typelevel", "cats-core_2.12", "0.9.0")
implementation("org.typelevel", "cats-kernel_2.12", "0.9.0")
implementation("es.weso", "schema_2.12", "0.1.98-SNAPSHOT")
implementation("es.weso", "shacl_2.12", "0.1.75")
implementation("es.weso", "shex_2.12", "0.1.91")
implementation("es.weso", "srdfjena_2.12", "0.1.101")
implementation("es.weso", "srdf_2.12", "0.1.101")
implementation("es.weso", "utils_2.12", "0.1.94")
implementation("es.weso", "rbe_2.12", "0.1.91")
implementation("es.weso", "typing_2.12", "0.1.94")
implementation("es.weso", "validating_2.12", "0.1.94")
implementation("org.antlr", "antlr4-runtime", "4.6")
implementation("io.circe", "circe-core_2.11", "0.7.0-M2")
implementation("com.atlassian.commonmark", "commonmark", "0.12.1")
Expand Down
85 changes: 30 additions & 55 deletions src/main/java/org/hl7/fhir/rdf/ShExValidator.java
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@@ -1,84 +1,59 @@
package org.hl7.fhir.rdf;
//
//import org.apache.jena.riot.RDFDataMgr;
//
//import java.nio.file.Files;
//import java.nio.file.Paths;
//import java.util.logging.Logger;

//import com.hp.hpl.jena.rdf.model.Model;

import cats.effect.IO;
import es.weso.rdf.PrefixMap;
import es.weso.rdf.RDFBuilder;
import es.weso.rdf.RDFReader;
import es.weso.rdf.jena.RDFAsJenaModel;
import es.weso.rdf.jena.RDFAsJenaModel$;
import es.weso.rdf.locations.Location;
import es.weso.rdf.nodes.IRI;
import es.weso.rdf.triples.RDFTriple;
import es.weso.schema.Result;
import es.weso.schema.Schema;
import es.weso.schema.ShExSchema$;
import org.apache.jena.rdf.model.Model;
import es.weso.rdf.nodes.RDFNode;
import scala.Option;
import scala.collection.immutable.Map;
import scala.collection.immutable.Map$;
import scala.collection.immutable.Set;
import scala.Predef$;
import cats.effect.IO;

import java.nio.file.Files;
import java.nio.file.Paths;
import static cats.effect.unsafe.implicits.*;

public class ShExValidator {

// private Logger log = Logger.getLogger(ShExValidator.class.getName());
private final Schema schema;

public ShExValidator(String schemaFile) throws Exception {
// load shex from the path
// log.info("Reading ShEx file " + schemaFile);
schema = readSchema(schemaFile);
}

public Schema readSchema(String schemaFile) throws Exception {
// Create a none, see: http://stackoverflow.com/questions/1997433/how-to-use-scala-none-from-java-code
Option<String> none = Option.apply((String) null); // Create a none
Option<String> none = Option.apply(null); // Create a none
String contents = new String(Files.readAllBytes(Paths.get(schemaFile)));
return ShExSchema$.MODULE$.fromString(contents, "SHEXC", none).get();
return ShExSchema$.MODULE$.fromString(contents, "SHEXC", none).unsafeRunSync(global());
}

public void validate(Model dataModel) {
Option<String> none = Option.apply(null); // Create a none
RDFReader rdf = new RDFAsJenaModel(dataModel);
Result result = schema.validate(rdf, "TARGETDECLS", none, none, rdf.getPrefixMap(), schema.pm());
if (result.isValid()) {
// log.info("Result is valid");
// System.out.println("Valid. Result: " + result.show());
} else {
System.out.println("Not valid");
}
Option<String> noneStr = Option.empty();
Option<IRI> noneIri = Option.empty();
Option<RDFBuilder> noneBuilder = Option.empty();
new java.util.HashMap<RDFNode, Set<Location>>();
Map<RDFNode, Set<Location>> nodesLocations = Map$.MODULE$.empty() ;
Map<RDFTriple, Set<Location>> tripleLocations = Map$.MODULE$.empty() ;
IO<Result> r = null ;
PrefixMap pm = PrefixMap.empty();
IO<PrefixMap> ioPm = IO.pure(pm);
RDFAsJenaModel rdf = RDFAsJenaModel.fromModel(dataModel, noneIri, noneIri, nodesLocations, tripleLocations).unsafeRunSync(global());
IO<Result> ioResult = schema.validate(rdf, "TARGETDECLS", "", noneStr, noneStr, pm, schema.pm(), noneBuilder);
Result result = ioResult.unsafeRunSync(global());
if (!result.isValid()) System.out.println("Not valid");
}


//
//
//
// public void validate(Model dataModel, Schema schema, PrefixMap pm) throws Exception {
// RDFReader rdf = new RDFAsJenaModel(dataModel);
// ShExMatcher matcher = new ShExMatcher(schema,rdf);
//// ShExResult result = matcher.validate();
//// if (result.isValid()) {
//// log.info("Result is valid");
//// System.out.println("Valid. Result: " + result.show(1,pm));
//// } else {
//// System.out.println("Not valid");
//// }
// }
//
// public void validate(String dataFile, String schemaFile) throws Exception {
//// log.info("Reading data file " + dataFile);
//// Model dataModel = RDFDataMgr.loadModel(dataFile);
//// log.info("Model read. Size = " + dataModel.size());
//
//
////
//// Schema schema = pair._1();
//// PrefixMap pm = pair._2();
//////
////// log.info("Schema read" + schema.show());
////
//// validate(dataModel,schema,pm);
// }
//
//
}
}
53 changes: 7 additions & 46 deletions src/main/java/org/hl7/fhir/tools/converters/DSTU2ValidationConvertor.java
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Expand Up @@ -3,19 +3,16 @@
import java.io.FileInputStream;
import java.io.FileOutputStream;

import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_10_50;
import org.hl7.fhir.dstu2.formats.IParser.OutputStyle;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CompartmentDefinition;
import org.hl7.fhir.r5.model.ValueSet;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;

public class DSTU2ValidationConvertor implements VersionConvertorAdvisor50 {
public class DSTU2ValidationConvertor extends BaseAdvisor_10_50 {

private Bundle source;
private VersionConvertor_10_50 vc;
Expand All @@ -31,9 +28,9 @@ public void convert(String bundleSource, String bundleTarget) throws Exception {
throw new Exception(e);
}
}

@Override
public boolean ignoreEntry(BundleEntryComponent src) {
public boolean ignoreEntry(@Nullable BundleEntryComponent src, @NotNull FhirPublication fhirPublication) {
return src.getResource() instanceof CompartmentDefinition || src.getResource() instanceof CodeSystem;
}

Expand All @@ -53,35 +50,6 @@ public static void main(String[] args) throws Exception {
dstu2.convert(src + "dataelements.xml", dst + "dataelements-r2.xml");
}

@Override
public Resource convertR2(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
if (resource instanceof ValueSet) {
ValueSet vs = (ValueSet) resource;
if (vs.hasCompose() && vs.getCompose().getExclude().isEmpty() && vs.getCompose().getInclude().size() == 1 && !vs.getCompose().getInclude().get(0).hasValueSet()) {
String url = vs.getCompose().getInclude().get(0).getSystem();
CodeSystem cs = findCodeSystem(url);
if (cs != null) {
org.hl7.fhir.dstu2.model.ValueSet vst = (org.hl7.fhir.dstu2.model.ValueSet) VersionConvertor_10_50.convertResource(vs);
vst.setCompose(null);
vst.setCodeSystem(vc.convertCodeSystem(cs));
return vst;
}
}
}
return null;
}

@Override
public org.hl7.fhir.dstu2016may.model.Resource convertR2016May(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
return null;
}

@Override
public org.hl7.fhir.dstu3.model.Resource convertR3(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
return null;
}


private CodeSystem findCodeSystem(String url) {
for (BundleEntryComponent b : source.getEntry()) {
if (b.getResource() instanceof CodeSystem) {
Expand All @@ -103,11 +71,4 @@ public void handleCodeSystem(CodeSystem tgtcs, ValueSet vs) {
public CodeSystem getCodeSystem(ValueSet src) {
return null;
}

@Override
public org.hl7.fhir.r4.model.Resource convertR4(org.hl7.fhir.r5.model.Resource resource) throws FHIRException {
// TODO Auto-generated method stub
return null;
}

}
4 changes: 2 additions & 2 deletions src/main/java/org/hl7/fhir/tools/converters/SpecNPMPackageGenerator.java
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Expand Up @@ -210,7 +210,7 @@ private void addConvertedIg4(NPMPackageGenerator npm, ImplementationGuide ig) th
}

private void addConvertedIg3(NPMPackageGenerator npm, ImplementationGuide ig) throws IOException, FHIRException {
org.hl7.fhir.dstu3.model.Resource res = VersionConvertor_30_50.convertResource(ig, false);
org.hl7.fhir.dstu3.model.Resource res = VersionConvertor_30_50.convertResource(ig);
npm.addFile(Category.RESOURCE, "ImplementationGuide-"+ig.getId()+".json", new org.hl7.fhir.dstu3.formats.JsonParser().composeBytes(res));
}

Expand Down Expand Up @@ -247,7 +247,7 @@ private void addConvertedIg4X(NPMPackageGenerator npm, ImplementationGuide ig) t
}

private void addConvertedIg3X(NPMPackageGenerator npm, ImplementationGuide ig) throws IOException, FHIRException {
org.hl7.fhir.dstu3.model.Resource res = VersionConvertor_30_50.convertResource(ig, false);
org.hl7.fhir.dstu3.model.Resource res = VersionConvertor_30_50.convertResource(ig);
npm.addFile(Category.RESOURCE, "ImplementationGuide-"+ig.getId()+".xml", new org.hl7.fhir.dstu3.formats.XmlParser().composeBytes(res));
}

Expand Down
17 changes: 9 additions & 8 deletions src/main/java/org/hl7/fhir/tools/publisher/ExampleInspector.java
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Expand Up @@ -62,6 +62,7 @@
import org.hl7.fhir.utilities.CSFileInputStream;
import org.hl7.fhir.utilities.Logger;
import org.hl7.fhir.utilities.Logger.LogMessageType;
import org.hl7.fhir.utilities.SIDUtilities;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
Expand Down Expand Up @@ -528,7 +529,7 @@ public void setByRdf(boolean byRdf) {


@Override
public Element fetch(Object appContext, String url) throws IOException, FHIRException {
public Element fetch(IResourceValidator validator, Object appContext, String url) throws IOException, FHIRException {
String[] parts = url.split("\\/");
if (parts.length == 2 && definitions.hasResource(parts[0])) {
ResourceDefn r = definitions.getResourceByName(parts[0]);
Expand Down Expand Up @@ -580,7 +581,7 @@ public Element fetch(Object appContext, String url) throws IOException, FHIRExce


@Override
public ReferenceValidationPolicy validationPolicy(Object appContext, String path, String url) {
public ReferenceValidationPolicy validationPolicy(IResourceValidator validator, Object appContext, String path, String url) {
String[] parts = url.split("\\/");
if (VALIDATE_CONFORMANCE_REFERENCES) {
if (Utilities.existsInList(url, "ValueSet/LOINCDepressionAnswersList", "ValueSet/LOINCDifficultyAnswersList", "CodeSystem/npi-taxonomy", "ValueSet/1.2.3.4.5", "StructureDefinition/daf-patient", "ValueSet/zika-affected-area"))
Expand All @@ -595,7 +596,7 @@ public ReferenceValidationPolicy validationPolicy(Object appContext, String path


@Override
public boolean resolveURL(Object appContext, String path, String url, String type) throws IOException, FHIRException {
public boolean resolveURL(IResourceValidator validator, Object appContext, String path, String url, String type) throws IOException, FHIRException {
if (path.endsWith(".fullUrl"))
return true;
if (url.startsWith("http://hl7.org/fhir")) {
Expand All @@ -605,13 +606,13 @@ public boolean resolveURL(Object appContext, String path, String url, String typ
if (parts.length >= 5 && definitions.hasResource(parts[4])) {
if ("DataElement".equals(parts[4]))
return true;
Element res = fetch(appContext, url.substring(20));
Element res = fetch(validator, appContext, url.substring(20));
return true; // disable this test. Try again for R4. res != null || Utilities.existsInList(parts[4], "NamingSystem", "CapabilityStatement", "CompartmentDefinition", "ConceptMap");
} else if (context.fetchCodeSystem(url) != null)
return true;
else if (definitions.getMapTypes().containsKey(url))
return true;
else if (url.startsWith("http://hl7.org/fhir/sid") || Utilities.existsInList(url, "http://hl7.org/fhir/ConsentPolicy/opt-in", "http://hl7.org/fhir/ConsentPolicy/opt-out", "http://hl7.org/fhir/api",
else if (SIDUtilities.isKnownSID(url) || Utilities.existsInList(url, "http://hl7.org/fhir/ConsentPolicy/opt-in", "http://hl7.org/fhir/ConsentPolicy/opt-out", "http://hl7.org/fhir/api",
"http://hl7.org/fhir/terminology-server", "http://hl7.org/fhir/knowledge-repository", "http://hl7.org/fhir/measure-processor"))
return true;
else
Expand All @@ -629,21 +630,21 @@ public IValidatorResourceFetcher setLocale(Locale locale) {


@Override
public byte[] fetchRaw(String source) throws MalformedURLException, IOException {
public byte[] fetchRaw(IResourceValidator validator, String source) throws MalformedURLException, IOException {
URL url = new URL(source);
URLConnection c = url.openConnection();
return TextFile.streamToBytes(c.getInputStream());
}


@Override
public CanonicalResource fetchCanonicalResource(String url) {
public CanonicalResource fetchCanonicalResource(IResourceValidator validator, String url) {
return null;
}


@Override
public boolean fetchesCanonicalResource(String url) {
public boolean fetchesCanonicalResource(IResourceValidator validator, String url) {
return false;
}

Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/hl7/fhir/tools/publisher/PageProcessor.java
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Expand Up @@ -69,9 +69,9 @@ WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWIS
import org.apache.commons.lang3.NotImplementedException;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.convertors.SpecDifferenceEvaluator;
import org.hl7.fhir.convertors.TypeLinkProvider;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.convertors.SpecDifferenceEvaluator.TypeLinkProvider;
import org.hl7.fhir.convertors.txClient.TerminologyClientR5;
import org.hl7.fhir.definitions.Config;
import org.hl7.fhir.definitions.generators.specification.BaseGenerator;
Expand Down