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Update hapi fhir version 5.5.3 #318

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merged 3 commits into from
Dec 7, 2021
Merged

Update hapi fhir version 5.5.3 #318

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c647780
update hapi fhir version 5.5.3
mdnazmulkarim Nov 24, 2021
e9f487a
dummy push
mdnazmulkarim Dec 3, 2021
fc04311
Merge branch 'master' into update-hapi-fhir-version
mdnazmulkarim Dec 6, 2021
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9 changes: 4 additions & 5 deletions pom.xml
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Expand Up @@ -10,12 +10,11 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>

<cql-engine.version>1.5.1</cql-engine.version>
<cql-evaluator.version>1.2.0</cql-evaluator.version>
<cql-engine.version>1.5.3-SNAPSHOT</cql-engine.version>
<cql-evaluator.version>1.3.1-SNAPSHOT</cql-evaluator.version>
<cqframework.version>1.5.5-SNAPSHOT</cqframework.version>
<hapi.version>5.4.2</hapi.version>
<core.version>5.4.8</core.version>
<hapi.version>5.5.3</hapi.version>
<core.version>5.5.16</core.version>
</properties>

<name>cqf-tooling</name>
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9 changes: 6 additions & 3 deletions src/main/java/org/opencds/cqf/tooling/library/r4/R4LibraryProcessor.java
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Expand Up @@ -8,7 +8,8 @@

import com.google.common.base.Strings;

import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.r4.formats.FormatUtilities;
import org.hl7.fhir.r4.model.Library;
import org.hl7.fhir.r4.model.Resource;
Expand Down Expand Up @@ -70,8 +71,9 @@ else if (file.isDirectory()) {

List<String> refreshedLibraryNames = new ArrayList<String>();
List<org.hl7.fhir.r5.model.Library> refreshedLibraries = super.refreshGeneratedContent(libraries);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
for (org.hl7.fhir.r5.model.Library refreshedLibrary : refreshedLibraries) {
Library library = (Library) VersionConvertor_40_50.convertResource(refreshedLibrary);
Library library = (Library) versionConvertor_40_50.convertResource(refreshedLibrary);
String filePath = null;
Encoding fileEncoding = null;
if (fileMap.containsKey(refreshedLibrary.getId()))
Expand Down Expand Up @@ -118,7 +120,8 @@ else if (file.isDirectory()) {
private void loadLibrary(Map<String, String> fileMap, List<org.hl7.fhir.r5.model.Library> libraries, File libraryFile) {
try {
Resource resource = FormatUtilities.loadFile(libraryFile.getAbsolutePath());
org.hl7.fhir.r5.model.Library library = (org.hl7.fhir.r5.model.Library) VersionConvertor_40_50.convertResource(resource);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
org.hl7.fhir.r5.model.Library library = (org.hl7.fhir.r5.model.Library) versionConvertor_40_50.convertResource(resource);
fileMap.put(library.getId(), libraryFile.getAbsolutePath());
libraries.add(library);
} catch (Exception ex) {
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9 changes: 6 additions & 3 deletions src/main/java/org/opencds/cqf/tooling/library/stu3/STU3LibraryProcessor.java
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Expand Up @@ -9,7 +9,8 @@

import com.google.common.base.Strings;

import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_50;
import org.hl7.fhir.convertors.conv30_50.VersionConvertor_30_50;
import org.hl7.fhir.dstu3.model.Library;
import org.hl7.fhir.dstu3.model.RelatedArtifact;
import org.hl7.fhir.dstu3.model.Resource;
Expand Down Expand Up @@ -50,10 +51,11 @@ protected List<String> refreshLibraries(String libraryPath, String libraryOutput

List<String> refreshedLibraryNames = new ArrayList<String>();
List<org.hl7.fhir.r5.model.Library> refreshedLibraries = super.refreshGeneratedContent(libraries);
VersionConvertor_30_50 versionConvertor_30_50 = new VersionConvertor_30_50(new BaseAdvisor_30_50());
for (org.hl7.fhir.r5.model.Library refreshedLibrary : refreshedLibraries) {
String filePath = fileMap.get(refreshedLibrary.getId());
if(null != filePath) {
org.hl7.fhir.dstu3.model.Library library = (org.hl7.fhir.dstu3.model.Library) VersionConvertor_30_50.convertResource(refreshedLibrary);
org.hl7.fhir.dstu3.model.Library library = (org.hl7.fhir.dstu3.model.Library) versionConvertor_30_50.convertResource(refreshedLibrary);

cleanseRelatedArtifactReferences(library);

Expand Down Expand Up @@ -114,7 +116,8 @@ private void cleanseRelatedArtifactReferences(Library library) {
private void loadLibrary(Map<String, String> fileMap, List<org.hl7.fhir.r5.model.Library> libraries, File libraryFile) {
try {
Resource resource = (Resource) IOUtils.readResource(libraryFile.getAbsolutePath(), fhirContext);
org.hl7.fhir.r5.model.Library library = (org.hl7.fhir.r5.model.Library) VersionConvertor_30_50.convertResource(resource);
VersionConvertor_30_50 versionConvertor_30_50 = new VersionConvertor_30_50(new BaseAdvisor_30_50());
org.hl7.fhir.r5.model.Library library = (org.hl7.fhir.r5.model.Library) versionConvertor_30_50.convertResource(resource);
fileMap.put(library.getId(), libraryFile.getAbsolutePath());
libraries.add(library);
} catch (Exception ex) {
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9 changes: 6 additions & 3 deletions src/main/java/org/opencds/cqf/tooling/measure/r4/R4MeasureProcessor.java
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@@ -1,6 +1,7 @@
package org.opencds.cqf.tooling.measure.r4;

import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.r4.formats.FormatUtilities;
import org.opencds.cqf.tooling.common.r4.CqfmSoftwareSystemHelper;
import org.opencds.cqf.tooling.measure.MeasureProcessor;
Expand Down Expand Up @@ -59,8 +60,9 @@ else if (file.isDirectory()) {

List<String> refreshedMeasureNames = new ArrayList<String>();
List<org.hl7.fhir.r5.model.Measure> refreshedMeasures = super.refreshGeneratedContent(measures);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
for (org.hl7.fhir.r5.model.Measure refreshedMeasure : refreshedMeasures) {
org.hl7.fhir.r4.model.Measure measure = (org.hl7.fhir.r4.model.Measure) VersionConvertor_40_50.convertResource(refreshedMeasure);
org.hl7.fhir.r4.model.Measure measure = (org.hl7.fhir.r4.model.Measure) versionConvertor_40_50.convertResource(refreshedMeasure);
String filePath = null;
IOUtils.Encoding fileEncoding = null;
if (fileMap.containsKey(refreshedMeasure.getId()))
Expand Down Expand Up @@ -104,7 +106,8 @@ else if (file.isDirectory()) {
private void loadMeasure(Map<String, String> fileMap, List<org.hl7.fhir.r5.model.Measure> measures, File measureFile) {
try {
org.hl7.fhir.r4.model.Resource resource = FormatUtilities.loadFile(measureFile.getAbsolutePath());
org.hl7.fhir.r5.model.Measure measure = (org.hl7.fhir.r5.model.Measure) VersionConvertor_40_50.convertResource(resource);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
org.hl7.fhir.r5.model.Measure measure = (org.hl7.fhir.r5.model.Measure) versionConvertor_40_50.convertResource(resource);
fileMap.put(measure.getId(), measureFile.getAbsolutePath());
measures.add(measure);
} catch (Exception ex) {
Expand Down
18 changes: 12 additions & 6 deletions src/main/java/org/opencds/cqf/tooling/npm/LibraryLoader.java
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Expand Up @@ -3,9 +3,12 @@
import java.io.IOException;
import java.io.InputStream;

import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_14_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_50;
import org.hl7.fhir.convertors.conv14_50.VersionConvertor_14_50;
import org.hl7.fhir.convertors.conv30_50.VersionConvertor_30_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.JsonParser;
Expand All @@ -26,13 +29,16 @@ public Library readLibrary(InputStream stream) throws FHIRFormatError, IOExcepti
throw new FHIRException("Library is not supported in R2");
} else if (VersionUtilities.isR2BVer(version)) {
org.hl7.fhir.dstu2016may.model.Resource res = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(stream);
return (Library) VersionConvertor_14_50.convertResource(res);
VersionConvertor_14_50 versionConvertor_14_50 = new VersionConvertor_14_50(new BaseAdvisor_14_50());
return (Library) versionConvertor_14_50.convertResource(res);
} else if (VersionUtilities.isR3Ver(version)) {
org.hl7.fhir.dstu3.model.Resource res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(stream);
return (Library) VersionConvertor_30_50.convertResource(res);
VersionConvertor_30_50 versionConvertor_30_50 = new VersionConvertor_30_50(new BaseAdvisor_30_50());
return (Library) versionConvertor_30_50.convertResource(res);
} else if (VersionUtilities.isR4Ver(version)) {
org.hl7.fhir.r4.model.Resource res = new org.hl7.fhir.r4.formats.JsonParser().parse(stream);
return (Library) VersionConvertor_40_50.convertResource(res);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
return (Library) versionConvertor_40_50.convertResource(res);
} else if (VersionUtilities.isR5Ver(version)) {
return (Library) new JsonParser().parse(stream);
} else {
Expand Down
10 changes: 6 additions & 4 deletions src/main/java/org/opencds/cqf/tooling/npm/NpmPackageManager.java
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Expand Up @@ -11,7 +11,8 @@
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;

import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r4.formats.FormatUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
Expand Down Expand Up @@ -48,12 +49,13 @@ public static NpmPackageManager fromPath(String igPath, String version) throws I
if (igPath == null || igPath.equals("")) {
throw new IllegalArgumentException("igPath is required");
}

return new NpmPackageManager((ImplementationGuide) VersionConvertor_40_50.convertResource(FormatUtilities.loadFile(igPath)), version);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
return new NpmPackageManager((ImplementationGuide) versionConvertor_40_50.convertResource(FormatUtilities.loadFile(igPath)), version);
}

public static NpmPackageManager fromStream(InputStream is, String version) throws IOException {
return new NpmPackageManager((ImplementationGuide) VersionConvertor_40_50.convertResource(FormatUtilities.loadFile(is)), version);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
return new NpmPackageManager((ImplementationGuide) versionConvertor_40_50.convertResource(FormatUtilities.loadFile(is)), version);
}

public NpmPackageManager(ImplementationGuide sourceIg, String version) throws IOException {
Expand Down
18 changes: 12 additions & 6 deletions src/main/java/org/opencds/cqf/tooling/processor/BaseProcessor.java
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Expand Up @@ -7,11 +7,13 @@
import org.fhir.ucum.UcumEssenceService;
import org.fhir.ucum.UcumException;
import org.fhir.ucum.UcumService;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_30_50;
import org.hl7.fhir.convertors.advisors.impl.BaseAdvisor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.conv30_50.VersionConvertor_30_50;
import org.hl7.fhir.convertors.conv40_50.VersionConvertor_40_50;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
Expand Down Expand Up @@ -173,13 +175,15 @@ private ImplementationGuide loadSourceIG(String igPath) throws Exception {
sourceIg = (ImplementationGuide) org.hl7.fhir.r5.formats.FormatUtilities.loadFile(igPath);
} catch (Exception e) {
try {
sourceIg = (ImplementationGuide) VersionConvertor_40_50.convertResource(org.hl7.fhir.r4.formats.FormatUtilities.loadFile(igPath));
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
sourceIg = (ImplementationGuide) versionConvertor_40_50.convertResource(org.hl7.fhir.r4.formats.FormatUtilities.loadFile(igPath));
} catch (Exception ex) {
byte[] src = TextFile.fileToBytes(igPath);
Manager.FhirFormat fmt = org.hl7.fhir.r5.formats.FormatUtilities.determineFormat(src);

org.hl7.fhir.dstu3.formats.ParserBase parser = org.hl7.fhir.dstu3.formats.FormatUtilities.makeParser(fmt.toString());
sourceIg = (ImplementationGuide) VersionConvertor_30_50.convertResource(parser.parse(src));
VersionConvertor_30_50 versionConvertor_30_50 = new VersionConvertor_30_50(new BaseAdvisor_30_50());
sourceIg = (ImplementationGuide) versionConvertor_30_50.convertResource(parser.parse(src));
}
}
} catch (Exception e) {
Expand All @@ -195,10 +199,12 @@ private ImplementationGuide loadSourceIG(String igPath, String specifiedFhirVers
byte[] src = TextFile.fileToBytes(igPath);
Manager.FhirFormat fmt = org.hl7.fhir.r5.formats.FormatUtilities.determineFormat(src);
org.hl7.fhir.dstu3.formats.ParserBase parser = org.hl7.fhir.dstu3.formats.FormatUtilities.makeParser(fmt.toString());
sourceIg = (ImplementationGuide) VersionConvertor_30_50.convertResource(parser.parse(src));
VersionConvertor_30_50 versionConvertor_30_50 = new VersionConvertor_30_50(new BaseAdvisor_30_50());
sourceIg = (ImplementationGuide) versionConvertor_30_50.convertResource(parser.parse(src));
} else if (VersionUtilities.isR4Ver(specifiedFhirVersion)) {
org.hl7.fhir.r4.model.Resource res = org.hl7.fhir.r4.formats.FormatUtilities.loadFile(igPath);
sourceIg = (ImplementationGuide) VersionConvertor_40_50.convertResource(res);
VersionConvertor_40_50 versionConvertor_40_50 = new VersionConvertor_40_50(new BaseAdvisor_40_50());
sourceIg = (ImplementationGuide) versionConvertor_40_50.convertResource(res);
} else if (VersionUtilities.isR5Ver(specifiedFhirVersion)) {
sourceIg = (ImplementationGuide) org.hl7.fhir.r5.formats.FormatUtilities.loadFile(igPath);
} else {
Expand Down