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org.hl7.fhir.core
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Profile Utilities Refactor 2 (#1047) 

* Add test util for diff

* Start moving pathprocessor params into dedicated object

* Move diff to Params

* Move base and diff Limits to params

* Rename to newBaseCursor and newBaseLimit

* More renames

* Move url and webUrl to params

* Move profileName to params

* Add contextPathSource to params, adjust indent for processPaths calls

* Move contextPathTarget to params

* Code cleanup, unused variables + move trimDifferential to params

* Create PathSlicingParams

* Shuffle param order

* Move redirector to params

* Move sourceStructureDefinition to params

* Move derived to params

* Move debug statements to dedicated methods

* split processSimplePath

* split processPathWithSlicedBase

* Start splitting ProfilePathProcessor

* Move all params into ProfilePathProcessor

* Move all profile utility related classes to own package

Co-authored-by: dotasek <david.otasek@smilecdr.com>
This commit is contained in:
dotasek 2022-12-23 09:27:42 -05:00 committed by GitHub
parent 4028d9930b
commit b404c89aa9
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GPG Key ID: 4AEE18F83AFDEB23
43 changed files with 1594 additions and 1322 deletions
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2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv10_50/datatypes10_50/ElementDefinition10_50.java
View File

@ -15,7 +15,7 @@ import org.hl7.fhir.convertors.conv10_50.datatypes10_50.primitivetypes10_50.Stri
import org.hl7.fhir.convertors.conv10_50.resources10_50.Enumerations10_50;
import org.hl7.fhir.dstu2.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.utilities.Utilities;

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv14_50/datatypes14_50/ElementDefinition14_50.java
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@ -17,7 +17,7 @@ import org.hl7.fhir.convertors.conv14_50.datatypes14_50.primitivetypes14_50.Uri1
import org.hl7.fhir.convertors.conv14_50.resources14_50.Enumerations14_50;
import org.hl7.fhir.dstu2016may.model.ElementDefinition;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.utilities.Utilities;
public class ElementDefinition14_50 {

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/R2016MayToR5Loader.java
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@ -42,7 +42,7 @@ import org.hl7.fhir.dstu2016may.formats.JsonParser;
import org.hl7.fhir.dstu2016may.formats.XmlParser;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleType;

6
org.hl7.fhir.r5/pom.xml
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@ -170,6 +170,12 @@
<version>${junit_jupiter_version}</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>io.github.java-diff-utils</groupId>
<artifactId>java-diff-utils</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonRenderer.java
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@ -21,7 +21,7 @@ import org.hl7.fhir.r5.comparison.ResourceComparer.PlaceHolderComparison;
import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base;

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonSession.java
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@ -13,8 +13,8 @@ import org.hl7.fhir.r5.comparison.CodeSystemComparer.CodeSystemComparison;
import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
@ -22,7 +22,6 @@ import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.utilities.Utilities;
public class ComparisonSession {

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ProfileComparer.java
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@ -9,10 +9,9 @@ import java.util.List;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.comparison.ResourceComparer.MessageCounts;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.UnusedTracker;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.UnusedTracker;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/AdditionalBindingsRenderer.java
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@ -7,17 +7,15 @@ import java.util.List;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.AdditionalBindingsRenderer.AdditionalBindingDetail;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.r5.renderers.IMarkdownProcessor;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.utils.PublicationHacker;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;

1045
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfilePathProcessor.java
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File diff suppressed because it is too large Load Diff

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ShExGenerator.java
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@ -42,6 +42,7 @@ import java.util.List;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DataType;

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/XmlSchemaGenerator.java
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@ -71,6 +71,7 @@ import java.util.Queue;
import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.PropertyRepresentation;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/BaseTypeSlice.java → org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/BaseTypeSlice.java
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@ -1,4 +1,4 @@
package org.hl7.fhir.r5.conformance;
package org.hl7.fhir.r5.conformance.profile;
import org.hl7.fhir.r5.model.ElementDefinition;

22
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/PathSlicingParams.java Normal file
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@ -0,0 +1,22 @@
package org.hl7.fhir.r5.conformance.profile;
import lombok.AccessLevel;
import lombok.AllArgsConstructor;
import lombok.Getter;
import org.hl7.fhir.r5.model.ElementDefinition;
@AllArgsConstructor(access = AccessLevel.PROTECTED)
public class PathSlicingParams {
@Getter
final boolean done;
@Getter
final ElementDefinition elementDefinition;
@Getter
final String path;
public PathSlicingParams() {
done = false;
elementDefinition = null;
path = null;
}
}

1290
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfilePathProcessor.java Normal file
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File diff suppressed because it is too large Load Diff

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfilePathProcessorState.java Normal file
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@ -0,0 +1,17 @@
package org.hl7.fhir.r5.conformance.profile;
import lombok.AccessLevel;
import lombok.AllArgsConstructor;
import org.hl7.fhir.r5.model.StructureDefinition;
@AllArgsConstructor(access = AccessLevel.PROTECTED)
public class ProfilePathProcessorState {
protected StructureDefinition.StructureDefinitionSnapshotComponent base;
protected int baseCursor;
protected int diffCursor;
protected String contextName;
protected String resultPathBase;
}

11
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java → org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
View File

@ -1,4 +1,4 @@
package org.hl7.fhir.r5.conformance;
package org.hl7.fhir.r5.conformance.profile;
/*
Copyright (c) 2011+, HL7, Inc.
@ -48,7 +48,9 @@ import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.conformance.AdditionalBindingsRenderer;
import org.hl7.fhir.r5.conformance.ElementRedirection;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.ObjectConverter;
@ -638,6 +640,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors
StructureDefinitionDifferentialComponent diff = cloneDiff(derived.getDifferential()); // we make a copy here because we're sometimes going to hack the differential while processing it. Have to migrate user data back afterwards
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getTypeName();
@ -648,7 +651,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// debug = true;
// }
new ProfilePathProcessor(this).processPaths(base, derived, url, webUrl, diff, baseSnapshot);
ProfilePathProcessor.processPaths(this, base, derived, url, webUrl, diff, baseSnapshot);
checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
@ -1297,7 +1300,7 @@ public class ProfileUtilities extends TranslatingUtilities {
}
protected String getWebUrl(StructureDefinition dt, String webUrl, String indent) {
protected String getWebUrl(StructureDefinition dt, String webUrl) {
if (dt.hasUserData("path")) {
// this is a hack, but it works for now, since we don't have deep folders
String url = dt.getUserString("path");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/TypeSlice.java → org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/TypeSlice.java
View File

@ -1,4 +1,4 @@
package org.hl7.fhir.r5.conformance;
package org.hl7.fhir.r5.conformance.profile;
import org.hl7.fhir.r5.model.ElementDefinition;

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -52,10 +52,9 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.context.IWorkerContextManager.IPackageLoadingTracker;
import org.hl7.fhir.r5.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.model.ActorDefinition;
import org.hl7.fhir.r5.model.BooleanType;
@ -66,7 +65,6 @@ import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeSystem.ConceptPropertyComponent;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap;
@ -75,7 +73,6 @@ import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.Identifier;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
@ -90,13 +87,11 @@ import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.model.PlanDefinition;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Requirements;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
@ -120,7 +115,6 @@ import org.hl7.fhir.r5.utils.PackageHackerR5;
import org.hl7.fhir.r5.utils.ResourceUtilities;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier;
import org.hl7.fhir.utilities.OIDUtils;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.TranslationServices;
@ -128,7 +122,6 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.PackageHacker;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationOptions;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
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@ -10,8 +10,8 @@ import java.util.Set;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.ElementDefinition;

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -37,11 +37,9 @@ import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
@ -52,22 +50,17 @@ import org.apache.commons.io.IOUtils;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.ParserType;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapStructureComponent;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.JurisdictionUtilities;
import org.hl7.fhir.r5.terminologies.TerminologyClient;
import org.hl7.fhir.r5.utils.validation.IResourceValidator;
@ -82,9 +75,6 @@ import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import ca.uhn.fhir.parser.DataFormatException;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -43,7 +43,7 @@ import java.util.Set;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DataType;
@ -55,7 +55,6 @@ import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.TypeConvertor;
import org.hl7.fhir.r5.model.Base.ValidationInfo;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.utilities.ElementDecoration;

7
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -39,7 +39,6 @@ import java.math.BigDecimal;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
@ -47,7 +46,7 @@ import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
@ -55,13 +54,9 @@ import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorDirect;
import org.hl7.fhir.r5.formats.JsonCreatorGson;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.StringPair;
import org.hl7.fhir.utilities.TextFile;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ObjectConverter.java
View File

@ -36,8 +36,8 @@ import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java
View File

@ -32,14 +32,12 @@ package org.hl7.fhir.r5.elementmodel;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.model.ElementDefinition;

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ResourceParser.java
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@ -3,36 +3,22 @@ package org.hl7.fhir.r5.elementmodel;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.Map.Entry;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlParser;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
public class ResourceParser extends ParserBase {

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
View File

@ -50,10 +50,9 @@ import javax.xml.transform.sax.SAXSource;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement;
import org.hl7.fhir.r5.elementmodel.ParserBase.ValidationPolicy;
import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.DateTimeType;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/ElementWrappers.java
View File

@ -7,10 +7,8 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ElementDefinitionResolution;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.XmlParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
@ -21,7 +19,6 @@ import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.renderers.ResourceRenderer;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.PropertyWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.RendererWrapperImpl;

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/RenderingContext.java
View File

@ -1,28 +1,23 @@
package org.hl7.fhir.r5.renderers.utils;
import java.io.IOException;
import java.text.DateFormat;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
import java.time.format.FormatStyle;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.TimeZone;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.renderers.utils.Resolver.IReferenceResolver;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.MarkDownProcessor;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -22,8 +22,8 @@ import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLSchemaGenerator.java
View File

@ -35,7 +35,7 @@ package org.hl7.fhir.r5.utils;
// - generate inherited search parameters
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.ElementDefinition;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/QuestionnaireBuilder.java
View File

@ -14,7 +14,7 @@ import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BooleanType;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/structuremap/StructureMapUtilities.java
View File

@ -36,8 +36,8 @@ package org.hl7.fhir.r5.utils.structuremap;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;

27
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/DiffUtils.java Normal file
View File

@ -0,0 +1,27 @@
package org.hl7.fhir.r5;
import com.github.difflib.patch.AbstractDelta;
import com.github.difflib.patch.Patch;
import org.junit.jupiter.api.Test;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.util.List;
public class DiffUtils {
public static void testDiff(String expectedPath, String actualPath) throws IOException {
//build simple lists of the lines of the two testfiles
List<String> expected = Files.readAllLines(new File(expectedPath).toPath());
List<String> actual = Files.readAllLines(new File(actualPath).toPath());
//compute the patch: this is the diffutils part
Patch<String> patch = com.github.difflib.DiffUtils.diff(expected, actual);
//simple output the computed patch to console
for (AbstractDelta<String> delta : patch.getDeltas()) {
System.out.println(delta);
}
}
}

5
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/NarrativeGenerationTests.java
View File

@ -11,8 +11,8 @@ import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
@ -28,7 +28,6 @@ import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.test.NarrativeGenerationTests.TestProfileKnowledgeProvider;
import org.hl7.fhir.r5.test.utils.CompareUtilities;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TerminologyServiceOptions;

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java
View File

@ -4,7 +4,7 @@ import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionConstraintComponent;

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
View File

@ -7,7 +7,7 @@ import java.nio.file.Path;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ShExGenerator;
import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
import org.hl7.fhir.r5.model.StructureDefinition;

13
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/SnapShotGenerationTests.java
View File

@ -16,8 +16,9 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.DiffUtils;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.test.utils.TestPackageLoader;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
@ -565,7 +566,13 @@ public class SnapShotGenerationTests {
t1.setText(null);
StructureDefinition t2 = test.output.copy();
t2.setText(null);
Assertions.assertTrue(t1.equalsDeep(t2), "Output does not match expected");
boolean structureDefinitionEquality = t1.equalsDeep(t2);
if (!structureDefinitionEquality) {
System.out.println("Encountered unexpected diff in structure definition");
DiffUtils.testDiff(dst.getAbsolutePath(), actualFilePath);
}
Assertions.assertTrue(structureDefinitionEquality, "Output does not match expected");
}
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -26,7 +26,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.txClient.TerminologyClientFactory;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -61,8 +61,8 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -13,7 +13,7 @@ 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;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.Element;

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -32,7 +32,7 @@ import org.hl7.fhir.r5.comparison.ProfileComparer;
import org.hl7.fhir.r5.comparison.ProfileComparer.ProfileComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.BaseWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/SnapShotGenerationXTests.java
View File

@ -16,8 +16,8 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -8,7 +8,6 @@ import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.io.PrintStream;
import java.net.MalformedURLException;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
@ -33,10 +32,9 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
@ -72,7 +70,6 @@ import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.validation.IgLoader;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
@ -88,7 +85,6 @@ import org.junit.runners.Parameterized.Parameters;
import com.google.common.base.Charsets;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;