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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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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
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@ -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.convertors.conv10_50.resources10_50.Enumerations10_50;
import org.hl7.fhir.dstu2.utils.ToolingExtensions; import org.hl7.fhir.dstu2.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRException; 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.r5.model.ElementDefinition;
import org.hl7.fhir.utilities.Utilities; 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.convertors.conv14_50.resources14_50.Enumerations14_50;
import org.hl7.fhir.dstu2016may.model.ElementDefinition; import org.hl7.fhir.dstu2016may.model.ElementDefinition;
import org.hl7.fhir.exceptions.FHIRException; 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; import org.hl7.fhir.utilities.Utilities;
public class ElementDefinition14_50 { 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.formats.XmlParser;
import org.hl7.fhir.dstu2016may.model.Resource; import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.exceptions.FHIRException; 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;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent; import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r5.model.Bundle.BundleType; import org.hl7.fhir.r5.model.Bundle.BundleType;

6
org.hl7.fhir.r5/pom.xml
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@ -170,6 +170,12 @@
<version>${junit_jupiter_version}</version> <version>${junit_jupiter_version}</version>
<scope>test</scope> <scope>test</scope>
</dependency> </dependency>
<dependency>
<groupId>io.github.java-diff-utils</groupId>
<artifactId>java-diff-utils</artifactId>
<version>4.12</version>
<scope>test</scope>
</dependency>
</dependencies> </dependencies>
<build> <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.ResourceComparer.ResourceComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison; 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.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base; 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.ProfileComparer.ProfileComparison;
import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison; import org.hl7.fhir.r5.comparison.ResourceComparer.ResourceComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison; 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.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.CanonicalResource; import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement; 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.Resource;
import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.ValueSet; import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.utilities.Utilities;
public class ComparisonSession { 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.comparison.ValueSetComparer.ValueSetComparison;
import org.hl7.fhir.r5.conformance.ProfileUtilities; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.UnusedTracker; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.UnusedTracker;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser; import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser; 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRFormatError; import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.conformance.AdditionalBindingsRenderer.AdditionalBindingDetail; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider.BindingResolution;
import org.hl7.fhir.r5.model.Extension; import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.UsageContext; import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.renderers.DataRenderer; import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.r5.renderers.IMarkdownProcessor; import org.hl7.fhir.r5.renderers.IMarkdownProcessor;
import org.hl7.fhir.r5.renderers.utils.RenderingContext; 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.Utilities;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator; import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell; 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

57
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ShExGenerator.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.r5.conformance; package org.hl7.fhir.r5.conformance;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -42,6 +42,7 @@ import java.util.List;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.ImmutablePair; import org.apache.commons.lang3.tuple.ImmutablePair;
import org.apache.commons.lang3.tuple.Pair; 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.context.IWorkerContext;
import org.hl7.fhir.r5.model.Constants; import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DataType; import org.hl7.fhir.r5.model.DataType;

57
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/XmlSchemaGenerator.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.r5.conformance; package org.hl7.fhir.r5.conformance;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
import java.io.FileOutputStream; import java.io.FileOutputStream;
@ -71,6 +71,7 @@ import java.util.Queue;
import java.util.Set; import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException; 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.context.IWorkerContext;
import org.hl7.fhir.r5.model.ElementDefinition; import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.PropertyRepresentation; 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; 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;
}

13
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. 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult; import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.ObjectConverter; import org.hl7.fhir.r5.elementmodel.ObjectConverter;
@ -638,7 +640,8 @@ public class ProfileUtilities extends TranslatingUtilities {
// we actually delegate the work to a subroutine so we can re-enter it with a different cursors // 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 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();
StructureDefinitionSnapshotComponent baseSnapshot = base.getSnapshot();
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) { if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) {
String derivedType = derived.getTypeName(); String derivedType = derived.getTypeName();
@ -648,7 +651,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// debug = true; // debug = true;
// } // }
new ProfilePathProcessor(this).processPaths(base, derived, url, webUrl, diff, baseSnapshot); ProfilePathProcessor.processPaths(this, base, derived, url, webUrl, diff, baseSnapshot);
checkGroupConstraints(derived); checkGroupConstraints(derived);
if (derived.getDerivation() == TypeDerivationRule.SPECIALIZATION) { 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")) { if (dt.hasUserData("path")) {
// this is a hack, but it works for now, since we don't have deep folders // this is a hack, but it works for now, since we don't have deep folders
String url = dt.getUserString("path"); 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
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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; 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.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException; import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException; 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.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory; 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.context.TerminologyCache.CacheToken;
import org.hl7.fhir.r5.model.ActorDefinition; import org.hl7.fhir.r5.model.ActorDefinition;
import org.hl7.fhir.r5.model.BooleanType; 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;
import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode; import org.hl7.fhir.r5.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent; 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.CodeableConcept;
import org.hl7.fhir.r5.model.Coding; import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ConceptMap; 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;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent; import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus; 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.ImplementationGuide;
import org.hl7.fhir.r5.model.Library; import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure; 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.PlanDefinition;
import org.hl7.fhir.r5.model.PrimitiveType; import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Questionnaire; 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.Requirements;
import org.hl7.fhir.r5.model.Resource; import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SearchParameter; import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StringType; import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition; 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.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.StructureMap; import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities; 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.ResourceUtilities;
import org.hl7.fhir.r5.utils.ToolingExtensions; import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.validation.ValidationContextCarrier; 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.TimeTracker;
import org.hl7.fhir.utilities.ToolingClientLogger; import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.TranslationServices; 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.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nBase; import org.hl7.fhir.utilities.i18n.I18nBase;
import org.hl7.fhir.utilities.i18n.I18nConstants; 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.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationOptions; import org.hl7.fhir.utilities.validation.ValidationOptions;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

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

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -37,11 +37,9 @@ import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Locale; import java.util.Locale;
import java.util.Map; import java.util.Map;
import java.util.Set;
import java.util.zip.ZipEntry; import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream; 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory; import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.formats.IParser; import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser; 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.formats.XmlParser;
import org.hl7.fhir.r5.model.*; import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle.BundleEntryComponent; 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.StructureDefinitionKind;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule; import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.StructureMap.StructureMapModelMode; import org.hl7.fhir.r5.model.StructureMap.StructureMapModelMode;
import org.hl7.fhir.r5.model.StructureMap.StructureMapStructureComponent; 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.JurisdictionUtilities;
import org.hl7.fhir.r5.terminologies.TerminologyClient; import org.hl7.fhir.r5.terminologies.TerminologyClient;
import org.hl7.fhir.r5.utils.validation.IResourceValidator; 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.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation; 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; import ca.uhn.fhir.parser.DataFormatException;

59
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Element.java
View File

@ -2,34 +2,34 @@ package org.hl7.fhir.r5.elementmodel;
import java.io.PrintStream; import java.io.PrintStream;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
import java.util.ArrayList; import java.util.ArrayList;
@ -43,7 +43,7 @@ import java.util.Set;
import org.apache.commons.lang3.Validate; import org.apache.commons.lang3.Validate;
import org.hl7.fhir.exceptions.FHIRException; 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.ContextUtilities;
import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DataType; 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;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind; import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.TypeConvertor; 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.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome; import org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.utilities.ElementDecoration; import org.hl7.fhir.utilities.ElementDecoration;

63
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.elementmodel; package org.hl7.fhir.r5.elementmodel;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
@ -39,7 +39,6 @@ import java.math.BigDecimal;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.HashSet; import java.util.HashSet;
import java.util.IdentityHashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import java.util.Map.Entry; import java.util.Map.Entry;
@ -47,7 +46,7 @@ import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement; 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.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical; import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorDirect; 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.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine; 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.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.StringPair; import org.hl7.fhir.utilities.StringPair;
import org.hl7.fhir.utilities.TextFile; import org.hl7.fhir.utilities.TextFile;

60
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ObjectConverter.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.elementmodel; package org.hl7.fhir.r5.elementmodel;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
@ -36,8 +36,8 @@ import java.util.ArrayList;
import java.util.List; import java.util.List;
import org.hl7.fhir.exceptions.FHIRException; 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.ProfileUtilities.SourcedChildDefinitions; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement; import org.hl7.fhir.r5.elementmodel.ParserBase.NamedElement;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;

62
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java
View File

@ -1,45 +1,43 @@
package org.hl7.fhir.r5.elementmodel; package org.hl7.fhir.r5.elementmodel;
/* /*
Copyright (c) 2011+, HL7, Inc. Copyright (c) 2011+, HL7, Inc.
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; 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.ProfileUtilities.SourcedChildDefinitions; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.FormatUtilities; import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.model.ElementDefinition; import org.hl7.fhir.r5.model.ElementDefinition;

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ResourceParser.java
View File

@ -3,36 +3,22 @@ package org.hl7.fhir.r5.elementmodel;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.io.OutputStream; import java.io.OutputStream;
import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Set;
import java.util.Map.Entry;
import org.apache.commons.lang3.NotImplementedException; import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement; 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.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Resource; import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition; import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.Utilities; import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants; 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.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 { 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element.SpecialElement; 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.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.DateTimeType; import org.hl7.fhir.r5.model.DateTimeType;

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/ElementWrappers.java
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@ -7,10 +7,8 @@ import java.util.ArrayList;
import java.util.List; import java.util.List;
import org.apache.commons.io.output.ByteArrayOutputStream; import org.apache.commons.io.output.ByteArrayOutputStream;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.Element;
import org.hl7.fhir.r5.elementmodel.XmlParser; import org.hl7.fhir.r5.elementmodel.XmlParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; 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.Narrative.NarrativeStatus;
import org.hl7.fhir.r5.model.StringType; import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition; 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.BaseWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.PropertyWrapper; import org.hl7.fhir.r5.renderers.utils.BaseWrappers.PropertyWrapper;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.RendererWrapperImpl; 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; package org.hl7.fhir.r5.renderers.utils;
import java.io.IOException; import java.io.IOException;
import java.text.DateFormat;
import java.time.ZoneId; import java.time.ZoneId;
import java.time.format.DateTimeFormatter; import java.time.format.DateTimeFormatter;
import java.time.format.FormatStyle;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Locale; import java.util.Locale;
import java.util.Map; import java.util.Map;
import java.util.TimeZone;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element; import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.DomainResource; 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.IReferenceResolver;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext; import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.utilities.FhirPublication; import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.MarkDownProcessor; import org.hl7.fhir.utilities.MarkDownProcessor;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
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@ -22,8 +22,8 @@ import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException; 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.conformance.ProfileUtilities.SourcedChildDefinitions; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.ContextUtilities; import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult; import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/GraphQLSchemaGenerator.java
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@ -35,7 +35,7 @@ package org.hl7.fhir.r5.utils;
// - generate inherited search parameters // - generate inherited search parameters
import org.hl7.fhir.exceptions.FHIRException; 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.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.ElementDefinition; import org.hl7.fhir.r5.model.ElementDefinition;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/QuestionnaireBuilder.java
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@ -14,7 +14,7 @@ import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.context.IWorkerContext;
import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.BooleanType; 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.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.ContextUtilities; import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult; 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.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.FHIRException; import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; 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.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Manager; import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat; 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.GenerationRules;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser; import org.hl7.fhir.r5.renderers.utils.RenderingContext.ITypeParser;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode; 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.CompareUtilities;
import org.hl7.fhir.r5.test.utils.TestingUtilities; import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TerminologyServiceOptions; 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 java.util.List;
import org.hl7.fhir.exceptions.FHIRException; 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.Base;
import org.hl7.fhir.r5.model.ElementDefinition; import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionConstraintComponent; import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionConstraintComponent;

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ShexGeneratorTests.java
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@ -7,7 +7,7 @@ import java.nio.file.Path;
import org.fhir.ucum.UcumException; import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException; 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;
import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy; import org.hl7.fhir.r5.conformance.ShExGenerator.HTMLLinkPolicy;
import org.hl7.fhir.r5.model.StructureDefinition; 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.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException; import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.r5.conformance.ProfileUtilities; import org.hl7.fhir.r5.DiffUtils;
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.test.utils.TestPackageLoader; import org.hl7.fhir.r5.test.utils.TestPackageLoader;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser; import org.hl7.fhir.r5.formats.JsonParser;
@ -565,7 +566,13 @@ public class SnapShotGenerationTests {
t1.setText(null); t1.setText(null);
StructureDefinition t2 = test.output.copy(); StructureDefinition t2 = test.output.copy();
t2.setText(null); 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.convertors.txClient.TerminologyClientFactory;
import org.hl7.fhir.exceptions.DefinitionException; import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException; 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.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager; 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.FHIRException;
import org.hl7.fhir.exceptions.PathEngineException; import org.hl7.fhir.exceptions.PathEngineException;
import org.hl7.fhir.exceptions.TerminologyServiceException; 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.conformance.ProfileUtilities.SourcedChildDefinitions; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.SourcedChildDefinitions;
import org.hl7.fhir.r5.context.ContextUtilities; import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult; 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_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50; import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.exceptions.FHIRException; 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;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult; import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.Element; 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.ProfileComparer.ProfileComparison;
import org.hl7.fhir.r5.comparison.ValueSetComparer; import org.hl7.fhir.r5.comparison.ValueSetComparer;
import org.hl7.fhir.r5.comparison.ValueSetComparer.ValueSetComparison; 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.BaseWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext; import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; 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.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException; 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.conformance.ProfileUtilities.ProfileKnowledgeProvider; import org.hl7.fhir.r5.conformance.profile.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.formats.IParser.OutputStyle; import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.XmlParser; import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base; import org.hl7.fhir.r5.model.Base;

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
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@ -8,7 +8,6 @@ import java.io.File;
import java.io.FileNotFoundException; import java.io.FileNotFoundException;
import java.io.IOException; import java.io.IOException;
import java.io.InputStream; import java.io.InputStream;
import java.io.PrintStream;
import java.net.MalformedURLException; import java.net.MalformedURLException;
import java.nio.charset.StandardCharsets; import java.nio.charset.StandardCharsets;
import java.util.ArrayList; 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.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError; import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.exceptions.PathEngineException; 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.ContextUtilities;
import org.hl7.fhir.r5.context.IWorkerContext; 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.Element;
import org.hl7.fhir.r5.elementmodel.Manager; import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat; 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.json.JsonUtilities;
import org.hl7.fhir.utilities.npm.NpmPackage; import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.validation.ValidationMessage; 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.IgLoader;
import org.hl7.fhir.validation.ValidationEngine; import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck; 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.common.base.Charsets;
import com.google.gson.GsonBuilder; import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement; import com.google.gson.JsonElement;
import com.google.gson.JsonObject; import com.google.gson.JsonObject;