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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

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This commit is contained in:
Lloyd McKenzie 2020-10-14 21:35:38 -06:00
commit 27295db891
84 changed files with 1326 additions and 643 deletions
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2
org.hl7.fhir.convertors/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

252
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/UTGVersionSorter.java Normal file
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@ -0,0 +1,252 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Provenance;
import org.hl7.fhir.r5.model.Provenance.ProvenanceAgentComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformation;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class UTGVersionSorter {
private FilesystemPackageCacheManager pcm;
public class CanonicalResourceAnalysis {
private CanonicalResource resource;
private CanonicalResource r2;
private CanonicalResource r3;
private CanonicalResource r4;
private String fmm;
private boolean normative;
private String recommendation;
private String filename;
public CanonicalResourceAnalysis(CanonicalResource cr, String filename) {
this.resource = cr;
this.filename = filename;
}
public String summary() {
// return "Relevant: "+resource.getUrl()+" [r2: "+r2Ver+"/"+r2Fmm+"]"+" [r3: "+r3Ver+"/"+r3Fmm+"]"+" [r4: "+r4Ver+"/"+r4Fmm+"/"+r4Normative+"] ---> "+recommendation;
return resource.getUrl()+" ---> "+recommendation+" in "+filename;
}
public void analyse(Map<String, CanonicalResource> r2l, Map<String, CanonicalResource> r3l, Map<String, CanonicalResource> r4l) {
r2 = findMatch(r2l);
r3 = findMatch(r3l);
r4 = findMatch(r4l);
fmm = r4 != null ? ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_FMM_LEVEL) : null;
normative = (r4 != null) && ToolingExtensions.readStringExtension(r4, ToolingExtensions.EXT_NORMATIVE_VERSION) != null;
if (normative) {
recommendation = "1.0.0";
} else if (Utilities.existsInList(fmm,"3", "4", "5")) {
recommendation = "0.5.0";
} else {
int i = 1;
if (r2 != null && r3 != null && !match(r2, r3, r2l, r3l)) {
i++;
}
if (r3 != null && r4 != null && !match(r3, r4, r3l, r4l)) {
i++;
}
recommendation = "0."+i+".0";
}
}
private boolean match(CanonicalResource l, CanonicalResource r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l instanceof CodeSystem && r instanceof CodeSystem) {
return matchCS((CodeSystem) l, (CodeSystem) r);
} else if (l instanceof ValueSet && r instanceof ValueSet) {
return matchVS((ValueSet) l, (ValueSet) r, ll, rl);
} else {
return false;
}
}
private boolean matchVS(ValueSet l, ValueSet r, Map<String, CanonicalResource> ll, Map<String, CanonicalResource> rl) {
if (l.getCompose().getInclude().size() == 1 && l.getCompose().getExclude().isEmpty() && l.getCompose().getIncludeFirstRep().hasSystem() && !l.getCompose().getIncludeFirstRep().hasConcept() && !l.getCompose().getIncludeFirstRep().hasFilter() &&
r.getCompose().getInclude().size() == 1 && r.getCompose().getExclude().isEmpty() && r.getCompose().getIncludeFirstRep().hasSystem() && !r.getCompose().getIncludeFirstRep().hasConcept() && !r.getCompose().getIncludeFirstRep().hasFilter()) {
CodeSystem lc = (CodeSystem) ll.get(l.getCompose().getIncludeFirstRep().getSystem());
CodeSystem rc = (CodeSystem) rl.get(l.getCompose().getIncludeFirstRep().getSystem());
if (lc != null && rc != null) {
return matchCS(lc, rc);
}
}
return false;
}
private boolean matchCS(CodeSystem l, CodeSystem r) {
return Base.compareDeep(l.getConcept(), r.getConcept(), false);
}
public CanonicalResource findMatch(Map<String, CanonicalResource> r2) {
CanonicalResource r = r2.get(resource.getUrl());
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/", "http://hl7.org/fhir/"));
}
if (r == null) {
r = r2.get(resource.getUrl().replaceAll("http://terminology.hl7.org/CodeSystem", "http://hl7.org/fhir/"));
}
return r;
}
public String getId() {
return resource.getId();
}
public String fhirType() {
return resource.fhirType();
}
}
private Date runTime = new Date();
public static void main(String[] args) throws FileNotFoundException, FHIRException, IOException, ParseException, URISyntaxException {
new UTGVersionSorter().execute("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth");
}
private void execute(String source) throws IOException {
List<CanonicalResourceAnalysis> list = new ArrayList<>();
System.out.println("Loading UTG");
loadFromSource(list, new File(source));
Map<String, CanonicalResource> r2 = loadPackageR2("hl7.fhir.r2.core");
Map<String, CanonicalResource> r3 = loadPackageR3("hl7.fhir.r3.core");
Map<String, CanonicalResource> r4 = loadPackageR4("hl7.fhir.r4.core");
System.out.println("Processing");
for (CanonicalResourceAnalysis cr : list) {
cr.analyse(r2,r3,r4);
}
Bundle b = (Bundle) new JsonParser().parse(new FileInputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"));
System.out.println("Summary");
for (CanonicalResourceAnalysis cr : list) {
System.out.println(cr.summary());
Provenance p = new Provenance();
b.addEntry().setResource(p).setFullUrl("http://terminology.hl7.org/fhir/Provenance/fhir-1.0.51-"+cr.getId());
p.setId("hx-fhir-1.0.51-"+cr.getId());
p.addTarget().setReference(cr.fhirType()+"/"+cr.getId());
p.getOccurredPeriod().setEnd(runTime, TemporalPrecisionEnum.DAY);
p.setRecorded(runTime);
p.addReason().setText("Reset Version after migration to UTG").addCoding("http://terminology.hl7.org/CodeSystem/v3-ActReason","METAMGT", null);
p.getActivity().addCoding("http://terminology.hl7.org/CodeSystem/v3-DataOperation", "UPDATE", null);
ProvenanceAgentComponent pa = p.addAgent();
pa.getType().addCoding("http://terminology.hl7.org/CodeSystem/provenance-participant-type", "author", null);
pa.getWho().setDisplay("Grahame Grieve");
pa = p.addAgent();
pa.getType().addCoding("http://terminology.hl7.org/CodeSystem/provenance-participant-type", "custodian", null);
pa.getWho().setDisplay("Vocabulary WG");
CanonicalResource res = cr.resource;
res.setVersion(cr.recommendation);
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(cr.filename), res);
}
System.out.println();
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("C:\\work\\org.hl7.fhir.igs\\UTG\\input\\sourceOfTruth\\history\\utgrel1hx-1-0-6.json"), b);
System.out.println("Done");
}
private Map<String, CanonicalResource> loadPackageR2(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR3(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(npm.load(p)), false);
res.put(r.getUrl(), r);
}
return res;
}
private Map<String, CanonicalResource> loadPackageR4(String id) throws IOException {
Map<String, CanonicalResource>res = new HashMap<>();
if (pcm == null) {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
}
System.out.println("Load "+id);
NpmPackage npm = pcm.loadPackage(id);
for (PackageResourceInformation p : npm.listIndexedResources("CodeSystem", "ValueSet")) {
CanonicalResource r = (CanonicalResource) VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(npm.load(p)));
res.put(r.getUrl(), r);
}
return res;
}
private void loadFromSource(List<CanonicalResourceAnalysis> list, File source) {
for (File f : source.listFiles()) {
if (f.isDirectory()) {
loadFromSource(list, f);
} else if (f.getName().endsWith(".xml")) {
try {
Resource r = new XmlParser().parse(new FileInputStream(f));
if (r instanceof CanonicalResource) {
CanonicalResource cr = (CanonicalResource) r;
cr.setUserData("path", f.getAbsolutePath());
if (cr.hasVersion() && cr.getVersion().startsWith("4.") && !Utilities.existsInList(cr.getId(), "v3-DataOperation", "v3-KnowledgeSubjectObservationValue")) {
list.add(new CanonicalResourceAnalysis(cr, f.getAbsolutePath()));
}
}
} catch (Exception e) {
System.out.println(f.getAbsolutePath()+" not a resource? "+e.getMessage());
}
}
}
}
}

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

59
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/model/UriType.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.dstu2.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
@ -152,6 +152,9 @@ public class UriType extends PrimitiveType<String> {
if (getValue() == null || other.getValue() == null) {
return false;
}
if (getValue().equals(other.getValue())) {
return true;
}
String normalize = normalize(getValue());
String normalize2 = normalize(other.getValue());

2
org.hl7.fhir.dstu2016may/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

59
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/model/UriType.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.dstu2016may.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
@ -153,6 +153,9 @@ public class UriType extends PrimitiveType<String> {
if (getValue() == null || other.getValue() == null) {
return false;
}
if (getValue().equals(other.getValue())) {
return true;
}
String normalize = normalize(getValue());
String normalize2 = normalize(other.getValue());

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

59
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/UriType.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.dstu3.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
@ -153,6 +153,9 @@ public class UriType extends PrimitiveType<String> {
if (getValue() == null || other.getValue() == null) {
return false;
}
if (getValue().equals(other.getValue())) {
return true;
}
String normalize = normalize(getValue());
String normalize2 = normalize(other.getValue());

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

59
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/UriType.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r4.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
@ -155,6 +155,9 @@ public class UriType extends PrimitiveType<String> {
if (getValue() == null || other.getValue() == null) {
return false;
}
if (getValue().equals(other.getValue())) {
return true;
}
String normalize = normalize(getValue());
String normalize2 = normalize(other.getValue());

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

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

@ -49,6 +49,7 @@ import org.apache.commons.lang3.StringUtils;
import org.fhir.ucum.UcumService;
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.context.CanonicalResourceManager.CanonicalResourceProxy;
@ -910,6 +911,9 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
txCache.cacheValidation(cacheToken, res, TerminologyCache.TRANSIENT);
return res;
} catch (Exception e) {
if (e instanceof NoTerminologyServiceException) {
return new ValidationResult(IssueSeverity.ERROR, "No Terminology Service", TerminologyServiceErrorClass.NOSERVICE);
}
}
}

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -148,6 +148,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private boolean ignoreProfileErrors;
private boolean progress;
private List<String> loadedPackages = new ArrayList<String>();
private boolean canNoTS;
public SimpleWorkerContext() throws FileNotFoundException, IOException, FHIRException {
super();
@ -299,7 +300,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
setTxCaps(txClient.getTerminologyCapabilities());
return cps.getSoftware().getVersion();
} catch (Exception e) {
throw new FHIRException(formatMessage(I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__, e.getMessage()), e);
throw new FHIRException(formatMessage(canNoTS ? I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ : I18nConstants.UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER, e.getMessage()), e);
}
}
@ -813,6 +814,15 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
public void setClock(TimeTracker tt) {
clock = tt;
}
public boolean isCanNoTS() {
return canNoTS;
}
public void setCanNoTS(boolean canNoTS) {
this.canNoTS = canNoTS;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CanonicalResource.java
View File

@ -442,7 +442,8 @@ public abstract class CanonicalResource extends DomainResource {
/**
* @param value A copyright statement relating to the canonical resource and/or its contents. Copyright statements are generally legal restrictions on the use and publishing of the canonical resource.
*/
public abstract CanonicalResource setCopyright(String value);
public abstract CanonicalResource setCopyright(String value);
protected void listChildren(List<Property> children) {
super.listChildren(children);
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeType.java
View File

@ -34,6 +34,7 @@ package org.hl7.fhir.r5.model;
import static org.apache.commons.lang3.StringUtils.defaultString;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import ca.uhn.fhir.model.api.annotation.DatatypeDef;
@ -137,4 +138,5 @@ public class CodeType extends StringType implements Comparable<CodeType>, ICodin
public boolean supportsDisplay() {
return false;
}
}

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CodeableConcept.java
View File

@ -399,7 +399,13 @@ public boolean hasCoding(String system, String code) {
}
return res;
}
public void addCoding(String system, String code, String display) {
getCoding().add(new Coding(system, code, display));
}
// end addition
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/CompartmentDefinition.java
View File

@ -2323,6 +2323,9 @@ public class CompartmentDefinition extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/GraphDefinition.java
View File

@ -3766,6 +3766,9 @@ public class GraphDefinition extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/SearchParameter.java
View File

@ -3875,6 +3875,8 @@ public class SearchParameter extends CanonicalResource {
*/
public static final ca.uhn.fhir.rest.gclient.TokenClientParam VERSION = new ca.uhn.fhir.rest.gclient.TokenClientParam(SP_VERSION);
public boolean supportsCopyright() {
return false;
}
}

63
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/UriType.java
View File

@ -1,33 +1,33 @@
package org.hl7.fhir.r5.model;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* 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
prior written permission.
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
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,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
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,
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
POSSIBILITY OF SUCH DAMAGE.
*/
@ -124,7 +124,7 @@ public class UriType extends PrimitiveType<String> {
/**
* Creates a new OidType instance which uses the given OID as the content (and prepends "urn:oid:" to the OID string
* in the value of the newly created OidType, per the FHIR specification).
*
*
* @param theOid
* The OID to use (<code>null</code> is acceptable and will result in a UriDt instance with a
* <code>null</code> value)
@ -155,6 +155,9 @@ public class UriType extends PrimitiveType<String> {
if (getValue() == null || other.getValue() == null) {
return false;
}
if (getValue().equals(other.getValue())) {
return true;
}
String normalize = normalize(getValue());
String normalize2 = normalize(other.getValue());
@ -162,7 +165,7 @@ public class UriType extends PrimitiveType<String> {
}
public String fhirType() {
return "uri";
return "uri";
}
}

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

@ -36,6 +36,9 @@ public class RendererFactory {
if ("OperationDefinition".equals(resourceName)) {
return new OperationDefinitionRenderer(context);
}
if ("SearchParameter".equals(resourceName)) {
return new SearchParameterRenderer(context);
}
if ("CompartmentDefinition".equals(resourceName)) {
return new CompartmentDefinitionRenderer(context);
}

160
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/SearchParameterRenderer.java Normal file
View File

@ -0,0 +1,160 @@
package org.hl7.fhir.r5.renderers;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.Enumeration;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.OperationDefinition.OperationDefinitionParameterComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.SearchParameter.SearchComparator;
import org.hl7.fhir.r5.model.SearchParameter.SearchModifierCode;
import org.hl7.fhir.r5.model.SearchParameter.SearchParameterComponentComponent;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.Resolver.ResourceContext;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
public class SearchParameterRenderer extends TerminologyRenderer {
public SearchParameterRenderer(RenderingContext context) {
super(context);
}
public SearchParameterRenderer(RenderingContext context, ResourceContext rcontext) {
super(context, rcontext);
}
public boolean render(XhtmlNode x, Resource dr) throws IOException, FHIRException, EOperationOutcome {
return render(x, (OperationDefinition) dr);
}
public boolean render(XhtmlNode x, SearchParameter spd) throws IOException, FHIRException, EOperationOutcome {
x.h2().addText(spd.getName());
XhtmlNode p = x.para();
p.tx("Parameter ");
p.code().tx(spd.getCode());
p.tx(":");
p.code().tx(spd.getType().toCode());
addMarkdown(x, spd.getDescription());
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Resource", spd.getBase().size()));
XhtmlNode td = tr.td();
for (CodeType t : spd.getBase()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
tr = tbl.tr();
tr.td().tx("Expression");
if (spd.hasExpression()) {
tr.td().code().tx(spd.getExpression());
} else {
tr.td().tx("(none)");
}
if (spd.hasXpathUsage()) {
tr = tbl.tr();
tr.td().tx("Usage");
tr.td().tx(spd.getXpathUsage().getDisplay());
}
if (spd.hasXpath()) {
tr = tbl.tr();
tr.td().tx("XPath");
tr.td().code().tx(spd.getXpath());
}
if (spd.hasTarget()) {
tr = tbl.tr();
tr.td().tx(Utilities.pluralize("Target Resources", spd.getTarget().size()));
td = tr.td();
for (CodeType t : spd.getTarget()) {
StructureDefinition sd = context.getWorker().fetchTypeDefinition(t.toString());
if (sd != null && sd.hasUserData("path")) {
td.sep(", ").ah(sd.getUserString("path")).tx(t.getCode());
} else {
td.sep(", ").tx(t.getCode());
}
}
}
tr = tbl.tr();
tr.td().tx("Multiples");
if (spd.getMultipleAnd() && spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) and can have repeating values (or)");
} else if (spd.getMultipleOr()) {
tr.td().tx("The parameter can repeat (and) but each repeat can only have one value");
} else if (spd.getMultipleAnd()) {
tr.td().tx("The parameter cannot repeat (and) but the single parameter can have multiple values (or)");
} else {
tr.td().tx("The parameter cannot repeat or have multiple values");
}
if (spd.hasComparator()) {
tr = tbl.tr();
tr.td().tx("Comparators");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchComparator> t : spd.getComparator()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasModifier()) {
tr = tbl.tr();
tr.td().tx("Modifiers");
td = tr.td().tx("Allowed: ");
for (Enumeration<SearchModifierCode> t : spd.getModifier()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasChain()) {
tr = tbl.tr();
tr.td().tx("Chains");
td = tr.td().tx("Allowed: ");
for (StringType t : spd.getChain()) {
td.sep(", ").tx(t.asStringValue());
}
}
if (spd.hasComponent()) {
x.para().b().tx("Components");
tbl = x.table("grid");
for (SearchParameterComponentComponent t : spd.getComponent()) {
tr = tbl.tr();
SearchParameter tsp = context.getWorker().fetchResource(SearchParameter.class, t.getDefinition());
if (tsp != null && tsp.hasUserData("path")) {
tr.td().ah(tsp.getUserString("path")).tx(tsp.present());
} else {
tr.td().tx(t.getDefinition());
}
tr.td().code().tx(t.getExpression());
}
}
return false;
}
public void describe(XhtmlNode x, OperationDefinition opd) {
x.tx(display(opd));
}
public String display(OperationDefinition opd) {
return opd.present();
}
@Override
public String display(Resource r) throws UnsupportedEncodingException, IOException {
return ((OperationDefinition) r).present();
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetCheckerSimple.java
View File

@ -37,6 +37,7 @@ import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.model.CanonicalType;
@ -515,6 +516,9 @@ public class ValueSetCheckerSimple implements ValueSetChecker {
if (res.getErrorClass() == TerminologyServiceErrorClass.UNKNOWN || res.getErrorClass() == TerminologyServiceErrorClass.CODESYSTEM_UNSUPPORTED || res.getErrorClass() == TerminologyServiceErrorClass.VALUESET_UNSUPPORTED) {
return null;
}
if (res.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) {
throw new NoTerminologyServiceException();
}
return res.isOk();
} else {
if (vsi.hasFilter()) {

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/IResourceValidator.java
View File

@ -184,6 +184,14 @@ public interface IResourceValidator {
public boolean isShowMessagesFromReferences();
public void setShowMessagesFromReferences(boolean value);
/**
* this is used internally in the publishing stack to ensure that everything is water tight, but
* this check is not necessary or appropriate at run time when the validator is hosted in HAPI
* @return
*/
public boolean isWantCheckSnapshotUnchanged();
public void setWantCheckSnapshotUnchanged(boolean wantCheckSnapshotUnchanged);
//FIXME: don't need that, gets never used?
// public String getValidationLanguage();
// public void setValidationLanguage(String value);

43
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ResourceTests.java Normal file
View File

@ -0,0 +1,43 @@
package org.hl7.fhir.r5.test;
import static org.junit.jupiter.api.Assertions.*;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.CompartmentDefinition;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ExampleScenario;
import org.hl7.fhir.r5.model.GraphDefinition;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.MessageDefinition;
import org.hl7.fhir.r5.model.NamingSystem;
import org.hl7.fhir.r5.model.OperationDefinition;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.model.TerminologyCapabilities;
import org.hl7.fhir.r5.model.ValueSet;
import org.junit.jupiter.api.Test;
class ResourceTests {
@Test
void testSupportsCopyright() {
assertTrue(new CodeSystem().supportsCopyright());
assertTrue(new ValueSet().supportsCopyright());
assertTrue(new ConceptMap().supportsCopyright());
assertTrue(new TerminologyCapabilities().supportsCopyright());
assertTrue(new CapabilityStatement().supportsCopyright());
assertTrue(new StructureDefinition().supportsCopyright());
assertTrue(new ImplementationGuide().supportsCopyright());
assertTrue(new MessageDefinition().supportsCopyright());
assertTrue(new StructureMap().supportsCopyright());
assertTrue(new ExampleScenario().supportsCopyright());
assertFalse(new SearchParameter().supportsCopyright());
assertFalse(new NamingSystem().supportsCopyright());
assertFalse(new OperationDefinition().supportsCopyright());
assertFalse(new CompartmentDefinition().supportsCopyright());
assertFalse(new GraphDefinition().supportsCopyright());
}
}

2
org.hl7.fhir.report/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

8
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.utilities.i18n;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
public class I18nConstants {
@ -343,6 +345,9 @@ public class I18nConstants {
public static final String SD_MUST_HAVE_DERIVATION = "SD_MUST_HAVE_DERIVATION";
public static final String SD_NESTED_MUST_SUPPORT_DIFF = "SD_NESTED_MUST_SUPPORT_DIFF";
public static final String SD_NESTED_MUST_SUPPORT_SNAPSHOT = "SD_NESTED_MUST_SUPPORT_SNAPSHOT";
public static final String SD_ED_TYPE_PROFILE_UNKNOWN = "SD_ED_TYPE_PROFILE_UNKNOWN";
public static final String SD_ED_TYPE_PROFILE_NOTYPE = "SD_ED_TYPE_PROFILE_NOTYPE";
public static final String SD_ED_TYPE_PROFILE_WRONG = "SD_ED_TYPE_PROFILE_WRONG";
public static final String SEARCHPARAMETER_BASE_WRONG = "SEARCHPARAMETER_BASE_WRONG";
public static final String SEARCHPARAMETER_EXP_WRONG = "SEARCHPARAMETER_EXP_WRONG";
public static final String SEARCHPARAMETER_NOTFOUND = "SEARCHPARAMETER_NOTFOUND";
@ -410,6 +415,8 @@ public class I18nConstants {
public static final String TERMINOLOGY_TX_SYSTEM_VALUESET2 = "Terminology_TX_System_ValueSet2";
public static final String TERMINOLOGY_TX_VALUESET_NOTFOUND = "Terminology_TX_ValueSet_NotFound";
public static final String TERMINOLOGY_TX_VALUESET_NOTFOUND2 = "Terminology_TX_ValueSet_NotFound2";
public static final String TERMINOLOGY_TX_NOSVC_BOUND_REQ = "TERMINOLOGY_TX_NOSVC_BOUND_REQ";
public static final String TERMINOLOGY_TX_NOSVC_BOUND_EXT = "TERMINOLOGY_TX_NOSVC_BOUND_EXT";
public static final String TEXT_SHOULD_NOT_BE_PRESENT = "Text_should_not_be_present";
public static final String THE_BASE_SNAPSHOT_MARKS_A_SLICING_AS_CLOSED_BUT_THE_DIFFERENTIAL_TRIES_TO_EXTEND_IT_IN__AT__ = "The_base_snapshot_marks_a_slicing_as_closed_but_the_differential_tries_to_extend_it_in__at__";
public static final String THIS_BASE_PROPERTY_MUST_BE_AN_ARRAY_NOT_A_ = "This_base_property_must_be_an_Array_not_a_";
@ -478,6 +485,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_URL_RESOLVE = "Type_Specific_Checks_DT_URL_Resolve";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_STRAT = "Type_Specific_Checks_DT_UUID_Strat";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_VAID = "Type_Specific_Checks_DT_UUID_Vaid";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER = "Unable_to_connect_to_terminology_server";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ = "Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__";
public static final String UNABLE_TO_FIND_BASE_DEFINITION_FOR_LOGICAL_MODEL__FROM_ = "Unable_to_find_base_definition_for_logical_model__from_";
public static final String UNABLE_TO_FIND_BASE__FOR_ = "Unable_to_find_base__for_";

5
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
View File

@ -35,6 +35,7 @@ import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@ -1095,6 +1096,10 @@ public class NpmPackage {
public boolean isNotForPublication() {
return JSONUtil.bool(npm, "notForPublication");
}
public InputStream load(PackageResourceInformation p) throws FileNotFoundException {
return new FileInputStream(p.filename);
}
}

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlNode.java
View File

@ -92,7 +92,7 @@ public class XhtmlNode implements IBaseXhtml {
private boolean notPretty;
private boolean inPara;
private boolean inLink;
private boolean seperated;
public XhtmlNode() {
super();
@ -842,6 +842,17 @@ public class XhtmlNode implements IBaseXhtml {
}
public XhtmlNode sep(String separator) {
// if there's already text, add the separator
if (seperated) {
return this;
}
seperated = true;
return tx(separator);
}

10
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -418,7 +418,7 @@ Parser_Type__not_supported = Parser Type {0} not supported
Version_mismatch_The_context_has_version__loaded_and_the_new_content_being_loaded_is_version_ = Version mismatch. The context has version {0} loaded, and the new content being loaded is version {1}
Error_reading__from_package__ = Error reading {0} from package {1}#{2}: {3}
Error_parsing_ = Error parsing {0}:{1}
Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' tun run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__ = Unable to connect to terminology server. Use parameter ''-tx n/a'' to run without using terminology services to validate LOINC, SNOMED, ICD-X etc. Error = {0}
Display_Name_for__should_be_one_of__instead_of_ = Display Name for {0}#{1} should be one of ''{2}'' instead of ''{3}''
Unknown_Code__in_ = Unknown Code {0} in {1}
UNKNOWN_CODE__IN_FRAGMENT = Unknown Code {0} in {1} - note that the code system is labelled as a fragment, so the code may be valid in some other fragment
@ -611,4 +611,10 @@ UNSUPPORTED_IDENTIFIER_PATTERN_PROPERTY_NOT_SUPPORTED_FOR_DISCRIMINATOR_FOR_SLIC
UNSUPPORTED_IDENTIFIER_PATTERN_NO_PROPERTY_NOT_SUPPORTED_FOR_DISCRIMINATOR_FOR_SLICE = Unsupported: no properties with values found on type {2} for pattern for discriminator({0}) for slice {1}
SD_NESTED_MUST_SUPPORT_DIFF = The element {0} has types/profiles/targets that are marked as must support, but the element itself is not marked as must-support. The inner must-supports will be ignored unless the element inherits must-support = true
SD_NESTED_MUST_SUPPORT_SNAPSHOT = The element {0} has types/profiles/targets that are marked as must support, but the element itself is not marked as must-support
Unable_to_connect_to_terminology_server = Unable to connect to terminology server. Error = {0}
SD_ED_TYPE_PROFILE_UNKNOWN = Unable to resolve profile {0}
SD_ED_TYPE_PROFILE_NOTYPE = Found profile {0}, but unable to determine the type it applies it
SD_ED_TYPE_PROFILE_WRONG = Profile {0} is for type {1}, but this element has type {2}
TERMINOLOGY_TX_NOSVC_BOUND_REQ = Could not confirm that the codes provided are from the required value set {0} because there is no terminology service
TERMINOLOGY_TX_NOSVC_BOUND_EXT = Could not confirm that the codes provided are from the extensible value set {0} because there is no terminology service

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/BaseValidator.java
View File

@ -2,11 +2,7 @@ package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
/*
@ -85,7 +81,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
public class BaseValidator {

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/NativeHostServices.java
View File

@ -34,7 +34,11 @@ package org.hl7.fhir.validation;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
/**

102
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -1,7 +1,46 @@
package org.hl7.fhir.validation;
import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.*;
import org.hl7.fhir.convertors.VersionConvertorAdvisor50;
import org.hl7.fhir.convertors.VersionConvertor_10_30;
import org.hl7.fhir.convertors.VersionConvertor_10_40;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_30;
import org.hl7.fhir.convertors.VersionConvertor_14_40;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R2016MayToR5Loader;
import org.hl7.fhir.convertors.loaders.R2ToR5Loader;
@ -23,50 +62,57 @@ import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideGlobalComponent;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureMap;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.terminologies.ConceptMapEngine;
import org.hl7.fhir.r5.utils.*;
import org.hl7.fhir.r5.utils.IResourceValidator.*;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.IResourceValidator.BestPracticeWarningLevel;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.r5.utils.IResourceValidator.CheckDisplayOption;
import org.hl7.fhir.r5.utils.IResourceValidator.IValidatorResourceFetcher;
import org.hl7.fhir.r5.utils.IResourceValidator.IdStatus;
import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
import org.hl7.fhir.r5.utils.OperationOutcomeUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities;
import org.hl7.fhir.r5.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.PackageClient;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.TimeTracker;
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.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.validation.BaseValidator.ValidationControl;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.xml.sax.SAXException;
import java.io.*;
import java.net.HttpURLConnection;
import java.net.URISyntaxException;
import java.net.URL;
import java.net.URLConnection;
import java.util.*;
import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -354,6 +400,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
public ValidationEngine() throws IOException {
pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromNothing();
initContext(null);
}
public String setTerminologyServer(String src, String log, FhirPublication version) throws FHIRException, URISyntaxException {
@ -436,6 +483,11 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion(), new PackageVersion(src));
grabNatives(source, "http://hl7.org/fhir");
}
initContext(tt);
}
public void initContext(TimeTracker tt) throws IOException, FileNotFoundException {
context.setCanNoTS(true);
context.setCacheId(UUID.randomUUID().toString());
context.setAllowLoadingDuplicates(true); // because of Forge
context.setExpansionProfile(makeExpProfile());

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/Validator.java
View File

@ -68,10 +68,12 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
import org.hl7.fhir.validation.cli.ValidatorGui;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.services.ComparisonService;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.utils.*;
import org.hl7.fhir.validation.cli.utils.Common;
import org.hl7.fhir.validation.cli.utils.Display;
import org.hl7.fhir.validation.cli.utils.Params;
/**
* A executable class that will validate one or more FHIR resources against

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/VersionUtil.java
View File

@ -1,5 +1,8 @@
package org.hl7.fhir.validation;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
@ -31,19 +34,13 @@ package org.hl7.fhir.validation;
import java.io.InputStream;
import java.text.SimpleDateFormat;
import java.time.Duration;
import java.time.Instant;
import java.time.OffsetDateTime;
import java.util.Date;
import java.util.Properties;
import org.hl7.fhir.r5.model.InstantType;
import org.hl7.fhir.utilities.Utilities;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
/**
* Used internally by HAPI to log the version of the HAPI FHIR framework
* once, when the framework is first loaded by the classloader.

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/RestEndpoints.java
View File

@ -1,12 +1,13 @@
package org.hl7.fhir.validation.cli;
import io.javalin.Javalin;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.controller.CliContextController;
import org.hl7.fhir.validation.cli.controller.ValidationController;
import org.hl7.fhir.validation.cli.controller.UIController;
import org.hl7.fhir.validation.cli.controller.ValidationController;
import org.hl7.fhir.validation.cli.model.CliContext;
import io.javalin.Javalin;
public class RestEndpoints {
public UIController myUIController;

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/ValidatorGui.java
View File

@ -1,15 +1,14 @@
package org.hl7.fhir.validation.cli;
import io.javalin.Javalin;
import java.awt.Desktop;
import java.net.URI;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.utils.Common;
import java.awt.*;
import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import io.javalin.Javalin;
public class ValidatorGui {

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/controller/CliContextController.java
View File

@ -1,12 +1,14 @@
package org.hl7.fhir.validation.cli.controller;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
import org.apache.http.HttpStatus;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.jetbrains.annotations.NotNull;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
public class CliContextController {
private final String JSON_MIME_TYPE = "application/json";

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/controller/ValidationController.java
View File

@ -1,14 +1,15 @@
package org.hl7.fhir.validation.cli.controller;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
import io.javalin.http.Handler;
import org.apache.http.HttpStatus;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
import org.hl7.fhir.validation.cli.services.ValidationService;
import com.fasterxml.jackson.databind.ObjectMapper;
import io.javalin.http.Context;
public class ValidationController {
private ValidationEngine myValidationEngine;

9
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
View File

@ -1,11 +1,16 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.validation.Validator;
import java.util.*;
import com.fasterxml.jackson.annotation.JsonProperty;
/**
* A POJO for storing the flags/values for the CLI validator.

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/FileInfo.java
View File

@ -1,7 +1,6 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.hl7.fhir.r5.elementmodel.Manager;
public class FileInfo {

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationOutcome.java
View File

@ -1,11 +1,12 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationOutcome {
@JsonProperty("fileInfo")

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationRequest.java
View File

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationRequest {
@JsonProperty("cliContext")

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/ValidationResponse.java
View File

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.cli.model;
import com.fasterxml.jackson.annotation.JsonProperty;
import java.util.ArrayList;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonProperty;
public class ValidationResponse {
@JsonProperty("outcomes")

16
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ComparisonService.java
View File

@ -1,27 +1,19 @@
package org.hl7.fhir.validation.cli.services;
import java.awt.Desktop;
import java.io.File;
import java.io.IOException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.CapabilityStatementUtilities;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CapabilityStatement;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.utils.Params;
import java.awt.*;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.UUID;
public class ComparisonService {
public static void doLeftRightComparison(String[] args, String dest, ValidationEngine validator) throws IOException, FHIRException, EOperationOutcome {

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -17,7 +17,6 @@ import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.npm.BasePackageCacheManager;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher.IPackageInstaller;
public class StandAloneValidatorFetcher implements IValidatorResourceFetcher {

28
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -1,11 +1,24 @@
package org.hl7.fhir.validation.cli.services;
import java.io.File;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.r5.context.TerminologyCache;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.TextFile;
@ -14,14 +27,11 @@ import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidationEngine.VersionSourceInformation;
import org.hl7.fhir.validation.cli.model.*;
import java.io.File;
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
import org.hl7.fhir.validation.cli.model.ValidationOutcome;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
public class ValidationService {

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
View File

@ -1,12 +1,12 @@
package org.hl7.fhir.validation.cli.utils;
import java.io.IOException;
import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import java.io.IOException;
/**
* Class for displaying output to the cli user.
*

8
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
View File

@ -1,14 +1,14 @@
package org.hl7.fhir.validation.cli.utils;
import java.io.File;
import java.util.Arrays;
import java.util.Locale;
import org.hl7.fhir.r5.utils.IResourceValidator.BundleValidationRule;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.validation.cli.model.CliContext;
import java.io.File;
import java.util.Arrays;
import java.util.Locale;
public class Params {
public static final String GUI = "-gui";

25
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/EnableWhenEvaluator.java
View File

@ -27,17 +27,26 @@ package org.hl7.fhir.validation.instance;
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.util.*;
import java.util.stream.*;
*/
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.*;
import org.hl7.fhir.r5.model.MeasureReport.MeasureReportGroupComponent;
import org.hl7.fhir.r5.model.Questionnaire.*;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.Expression;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.Factory;
import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Questionnaire.EnableWhenBehavior;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemEnableWhenComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemOperator;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;

490
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
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@ -37,10 +37,8 @@ import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.Charset;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Base64;
import java.util.Calendar;
import java.util.Collection;
import java.util.HashMap;
@ -51,15 +49,10 @@ import java.util.Set;
import java.util.UUID;
import org.apache.commons.codec.binary.Base64InputStream;
import org.apache.commons.io.Charsets;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.convertors.*;
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.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
@ -86,6 +79,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeableConcept;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.ContactPoint;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.DateTimeType;
import org.hl7.fhir.r5.model.DateType;
import org.hl7.fhir.r5.model.DecimalType;
@ -114,6 +108,7 @@ import org.hl7.fhir.r5.model.PrimitiveType;
import org.hl7.fhir.r5.model.Quantity;
import org.hl7.fhir.r5.model.Range;
import org.hl7.fhir.r5.model.Ratio;
import org.hl7.fhir.r5.model.Reference;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.SampledData;
import org.hl7.fhir.r5.model.SearchParameter;
@ -127,18 +122,30 @@ import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComp
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.TimeType;
import org.hl7.fhir.r5.model.Timing;
import org.hl7.fhir.r5.model.DataType;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.r5.utils.FHIRLexer.FHIRLexerException;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.r5.utils.XVerExtensionManager;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.Utilities.DecimalStatus;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;
import org.hl7.fhir.validation.instance.type.BundleValidator;
@ -148,19 +155,13 @@ import org.hl7.fhir.validation.instance.type.QuestionnaireValidator;
import org.hl7.fhir.validation.instance.type.SearchParameterValidator;
import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.Utilities.DecimalStatus;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.VersionUtilities.VersionURLInfo;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.hl7.fhir.validation.instance.utils.*;
import org.hl7.fhir.validation.instance.utils.ChildIterator;
import org.hl7.fhir.validation.instance.utils.ElementInfo;
import org.hl7.fhir.validation.instance.utils.IndexedElement;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ResolvedReference;
import org.hl7.fhir.validation.instance.utils.ResourceValidationTracker;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
import org.w3c.dom.Document;
import com.google.gson.Gson;
@ -343,6 +344,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
private String validationLanguage;
private boolean baseOnly;
private boolean noCheckAggregation;
private boolean wantCheckSnapshotUnchanged;
private List<ImplementationGuide> igs = new ArrayList<>();
private List<String> extensionDomains = new ArrayList<String>();
@ -1004,7 +1006,13 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ValidationResult vr = checkCodeOnServer(stack, valueset, cc, true); // we're going to validate the codings directly, so only check the valueset
if (!vr.isOk()) {
bindingsOk = false;
if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) {
if (vr.getErrorClass() != null && vr.getErrorClass() == TerminologyServiceErrorClass.NOSERVICE) {
if (binding.getStrength() == BindingStrength.REQUIRED || (binding.getStrength() == BindingStrength.EXTENSIBLE && binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"))) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOSVC_BOUND_REQ, describeReference(binding.getValueSet()));
} else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
hint(errors, IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_NOSVC_BOUND_EXT, describeReference(binding.getValueSet()));
}
} else if (vr.getErrorClass() != null && vr.getErrorClass().isInfrastructure()) {
if (binding.getStrength() == BindingStrength.REQUIRED)
txWarning(errors, vr.getTxLink(), IssueType.CODEINVALID, element.line(), element.col(), path, false, I18nConstants.TERMINOLOGY_TX_CONFIRM_1, describeReference(binding.getValueSet()), vr.getErrorClass().toString());
else if (binding.getStrength() == BindingStrength.EXTENSIBLE) {
@ -3860,7 +3868,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
} else if (element.getType().equals("SearchParameter")) {
new SearchParameterValidator(context, timeTracker, fpe).validateSearchParameter(errors, element, stack);
} else if (element.getType().equals("StructureDefinition")) {
new StructureDefinitionValidator(context, timeTracker, fpe).validateStructureDefinition(errors, element, stack);
new StructureDefinitionValidator(context, timeTracker, fpe, wantCheckSnapshotUnchanged).validateStructureDefinition(errors, element, stack);
} else if (element.getType().equals("ValueSet")) {
new ValueSetValidator(context, timeTracker, this).validateValueSet(errors, element, stack);
}
@ -4128,236 +4136,252 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept, boolean checkDisplayInContext, ElementInfo ei, String extensionUrl)
throws FHIRException, DefinitionException {
List<String> profiles = new ArrayList<String>();
if (ei.definition != null) {
String type = null;
ElementDefinition typeDefn = null;
checkMustSupport(profile, ei);
checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
extensionUrl, ei.definition, false);
}
if (ei.slice != null) {
checkChildByDefinition(hostContext, errors, profile, definition, resource, element, actualType, stack, inCodeableConcept, checkDisplayInContext, ei,
extensionUrl, ei.slice, true);
}
}
if (ei.definition.getType().size() == 1 && !"*".equals(ei.definition.getType().get(0).getWorkingCode()) && !"Element".equals(ei.definition.getType().get(0).getWorkingCode())
&& !"BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode())) {
type = ei.definition.getType().get(0).getWorkingCode();
String stype = ei.getElement().fhirType();
if (ei.definition.isChoice() && !stype.equals(type)) {
if ("Extension".equals(profile.getType())) {
// error will be raised elsewhere
} else {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), false, I18nConstants.EXTENSION_PROF_TYPE, profile.getUrl(), type, stype);
}
}
//
// Excluding reference is a kludge to get around versioning issues
if (ei.definition.getType().get(0).hasProfile()) {
for (CanonicalType p : ei.definition.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (ei.definition.getType().size() == 1 && "*".equals(ei.definition.getType().get(0).getWorkingCode())) {
String prefix = tail(ei.definition.getPath());
assert prefix.endsWith("[x]");
type = ei.getName().substring(prefix.length() - 3);
if (isPrimitiveType(type))
type = Utilities.uncapitalize(type);
if (ei.definition.getType().get(0).hasProfile()) {
for (CanonicalType p : ei.definition.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (ei.definition.getType().size() > 1) {
public void checkChildByDefinition(ValidatorHostContext hostContext, List<ValidationMessage> errors, StructureDefinition profile,
ElementDefinition definition, Element resource, Element element, String actualType, NodeStack stack, boolean inCodeableConcept,
boolean checkDisplayInContext, ElementInfo ei, String extensionUrl, ElementDefinition checkDefn, boolean isSlice) {
List<String> profiles = new ArrayList<String>();
String type = null;
ElementDefinition typeDefn = null;
checkMustSupport(profile, ei);
String prefix = tail(ei.definition.getPath());
assert typesAreAllReference(ei.definition.getType()) || ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix;
if (ei.definition.hasRepresentation(PropertyRepresentation.TYPEATTR))
type = ei.getElement().getType();
else {
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : ei.definition.getType())
if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
type = t.getWorkingCode();
// Excluding reference is a kludge to get around versioning issues
if (t.hasProfile() && !type.equals("Reference"))
profiles.add(t.getProfile().get(0).getValue());
}
}
if (type == null) {
TypeRefComponent trc = ei.definition.getType().get(0);
if (trc.getWorkingCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOTYPE, ei.getName(), describeTypes(ei.definition.getType()));
}
} else if (ei.definition.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), ei.definition.getContentReference());
} else if (ei.definition.getType().size() == 1 && ("Element".equals(ei.definition.getType().get(0).getWorkingCode()) || "BackboneElement".equals(ei.definition.getType().get(0).getWorkingCode()))) {
if (ei.definition.getType().get(0).hasProfile()) {
CanonicalType pu = ei.definition.getType().get(0).getProfile().get(0);
if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT))
profiles.add(pu.getValue() + "#" + pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
else
profiles.add(pu.getValue());
if (checkDefn.getType().size() == 1 && !"*".equals(checkDefn.getType().get(0).getWorkingCode()) && !"Element".equals(checkDefn.getType().get(0).getWorkingCode())
&& !"BackboneElement".equals(checkDefn.getType().get(0).getWorkingCode())) {
type = checkDefn.getType().get(0).getWorkingCode();
String stype = ei.getElement().fhirType();
if (checkDefn.isChoice() && !stype.equals(type)) {
if ("Extension".equals(profile.getType())) {
// error will be raised elsewhere
} else {
rule(errors, IssueType.STRUCTURE, element.line(), element.col(), ei.getPath(), false, I18nConstants.EXTENSION_PROF_TYPE, profile.getUrl(), type, stype);
}
}
if (type != null) {
if (type.startsWith("@")) {
ei.definition = findElement(profile, type.substring(1));
type = null;
//
// Excluding reference is a kludge to get around versioning issues
if (checkDefn.getType().get(0).hasProfile()) {
for (CanonicalType p : checkDefn.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
NodeStack localStack = stack.push(ei.getElement(), ei.count, ei.definition, type == null ? typeDefn : resolveType(type, ei.definition.getType()));
} else if (checkDefn.getType().size() == 1 && "*".equals(checkDefn.getType().get(0).getWorkingCode())) {
String prefix = tail(checkDefn.getPath());
assert prefix.endsWith("[x]");
type = ei.getName().substring(prefix.length() - 3);
if (isPrimitiveType(type))
type = Utilities.uncapitalize(type);
if (checkDefn.getType().get(0).hasProfile()) {
for (CanonicalType p : checkDefn.getType().get(0).getProfile()) {
profiles.add(p.getValue());
}
}
} else if (checkDefn.getType().size() > 1) {
String prefix = tail(checkDefn.getPath());
assert typesAreAllReference(checkDefn.getType()) || checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR) || prefix.endsWith("[x]") : prefix;
if (checkDefn.hasRepresentation(PropertyRepresentation.TYPEATTR))
type = ei.getElement().getType();
else {
prefix = prefix.substring(0, prefix.length() - 3);
for (TypeRefComponent t : checkDefn.getType())
if ((prefix + Utilities.capitalize(t.getWorkingCode())).equals(ei.getName())) {
type = t.getWorkingCode();
// Excluding reference is a kludge to get around versioning issues
if (t.hasProfile() && !type.equals("Reference"))
profiles.add(t.getProfile().get(0).getValue());
}
}
if (type == null) {
TypeRefComponent trc = checkDefn.getType().get(0);
if (trc.getWorkingCode().equals("Reference"))
type = "Reference";
else
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOTYPE, ei.getName(), describeTypes(checkDefn.getType()));
}
} else if (checkDefn.getContentReference() != null) {
typeDefn = resolveNameReference(profile.getSnapshot(), checkDefn.getContentReference());
} else if (checkDefn.getType().size() == 1 && ("Element".equals(checkDefn.getType().get(0).getWorkingCode()) || "BackboneElement".equals(checkDefn.getType().get(0).getWorkingCode()))) {
if (checkDefn.getType().get(0).hasProfile()) {
CanonicalType pu = checkDefn.getType().get(0).getProfile().get(0);
if (pu.hasExtension(ToolingExtensions.EXT_PROFILE_ELEMENT))
profiles.add(pu.getValue() + "#" + pu.getExtensionString(ToolingExtensions.EXT_PROFILE_ELEMENT));
else
profiles.add(pu.getValue());
}
}
if (type != null) {
if (type.startsWith("@")) {
checkDefn = findElement(profile, type.substring(1));
if (isSlice) {
ei.slice = ei.definition;
} else {
ei.definition = ei.definition;
}
type = null;
}
}
NodeStack localStack = stack.push(ei.getElement(), ei.count, checkDefn, type == null ? typeDefn : resolveType(type, checkDefn.getType()));
// if (debug) {
// System.out.println(" check " + localStack.getLiteralPath()+" against "+ei.getDefinition().getId()+" in profile "+profile.getUrl());
// }
String localStackLiterapPath = localStack.getLiteralPath();
String eiPath = ei.getPath();
assert (eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath;
boolean thisIsCodeableConcept = false;
String thisExtension = null;
boolean checkDisplay = true;
String localStackLiterapPath = localStack.getLiteralPath();
String eiPath = ei.getPath();
assert (eiPath.equals(localStackLiterapPath)) : "ei.path: " + ei.getPath() + " - localStack.getLiteralPath: " + localStackLiterapPath;
boolean thisIsCodeableConcept = false;
String thisExtension = null;
boolean checkDisplay = true;
checkInvariants(hostContext, errors, profile, typeDefn != null ? typeDefn : ei.definition, resource, ei.getElement(), localStack, true);
checkInvariants(hostContext, errors, profile, typeDefn != null ? typeDefn : checkDefn, resource, ei.getElement(), localStack, true);
ei.getElement().markValidation(profile, ei.definition);
boolean elementValidated = false;
if (type != null) {
if (isPrimitiveType(type)) {
checkPrimitive(hostContext, errors, ei.getPath(), type, ei.definition, ei.getElement(), profile, stack);
} else {
if (ei.definition.hasFixed()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getFixed(), profile.getUrl(), ei.definition.getSliceName(), null);
}
if (ei.definition.hasPattern()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), ei.definition.getPattern(), profile.getUrl(), ei.definition.getSliceName(), null, true);
}
}
if (type.equals("Identifier")) {
checkIdentifier(errors, ei.getPath(), ei.getElement(), ei.definition);
} else if (type.equals("Coding")) {
checkCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("Quantity")) {
checkQuantity(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack);
} else if (type.equals("Attachment")) {
checkAttachment(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("CodeableConcept")) {
checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack);
thisIsCodeableConcept = true;
} else if (type.equals("Reference")) {
checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, ei.definition, actualType, localStack);
// We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension
} else if (type.equals("Extension")) {
Element eurl = ei.getElement().getNamedChild("url");
if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
String url = eurl.primitiveValue();
thisExtension = url;
if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), I18nConstants.EXTENSION_EXT_URL_ABSOLUTE)) {
checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), ei.definition, profile, localStack, stack, extensionUrl);
}
}
}
} else if (type.equals("Resource") || isResource(type)) {
validateContains(hostContext, errors, ei.getPath(), ei.definition, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if
elementValidated = true;
// (str.matches(".*([.,/])work\\1$"))
} else if (Utilities.isAbsoluteUrl(type)) {
StructureDefinition defn = context.fetchTypeDefinition(type);
if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) {
List<String> txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep());
if (txtype.contains("CodeableConcept")) {
checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, ei.definition, stack, defn);
thisIsCodeableConcept = true;
} else if (txtype.contains("Coding")) {
checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, ei.definition, inCodeableConcept, checkDisplayInContext, stack, defn);
}
}
}
ei.getElement().markValidation(profile, checkDefn);
boolean elementValidated = false;
if (type != null) {
if (isPrimitiveType(type)) {
checkPrimitive(hostContext, errors, ei.getPath(), type, checkDefn, ei.getElement(), profile, stack);
} else {
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), ei.definition != null, I18nConstants.VALIDATION_VAL_CONTENT_UNKNOWN, ei.getName()))
validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, false, true, null);
}
StructureDefinition p = null;
String tail = null;
if (profiles.isEmpty()) {
if (type != null) {
p = getProfileForType(type, ei.definition.getType());
// If dealing with a primitive type, then we need to check the current child against
// the invariants (constraints) on the current element, because otherwise it only gets
// checked against the primary type's invariants: LLoyd
//if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
// checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element);
//}
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_NOTYPE, type);
if (checkDefn.hasFixed()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getFixed(), profile.getUrl(), checkDefn.getSliceName(), null);
}
} else if (profiles.size() == 1) {
String url = profiles.get(0);
if (checkDefn.hasPattern()) {
checkFixedValue(errors, ei.getPath(), ei.getElement(), checkDefn.getPattern(), profile.getUrl(), checkDefn.getSliceName(), null, true);
}
}
if (type.equals("Identifier")) {
checkIdentifier(errors, ei.getPath(), ei.getElement(), checkDefn);
} else if (type.equals("Coding")) {
checkCoding(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("Quantity")) {
checkQuantity(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack);
} else if (type.equals("Attachment")) {
checkAttachment(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack);
} else if (type.equals("CodeableConcept")) {
checkDisplay = checkCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack);
thisIsCodeableConcept = true;
} else if (type.equals("Reference")) {
checkReference(hostContext, errors, ei.getPath(), ei.getElement(), profile, checkDefn, actualType, localStack);
// We only check extensions if we're not in a complex extension or if the element we're dealing with is not defined as part of that complex extension
} else if (type.equals("Extension")) {
Element eurl = ei.getElement().getNamedChild("url");
if (rule(errors, IssueType.INVALID, ei.getPath(), eurl != null, I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
String url = eurl.primitiveValue();
thisExtension = url;
if (rule(errors, IssueType.INVALID, ei.getPath(), !Utilities.noString(url), I18nConstants.EXTENSION_EXT_URL_NOTFOUND)) {
if (rule(errors, IssueType.INVALID, ei.getPath(), (extensionUrl != null) || Utilities.isAbsoluteUrl(url), I18nConstants.EXTENSION_EXT_URL_ABSOLUTE)) {
checkExtension(hostContext, errors, ei.getPath(), resource, element, ei.getElement(), checkDefn, profile, localStack, stack, extensionUrl);
}
}
}
} else if (type.equals("Resource") || isResource(type)) {
validateContains(hostContext, errors, ei.getPath(), checkDefn, definition, resource, ei.getElement(), localStack, idStatusForEntry(element, ei)); // if
elementValidated = true;
// (str.matches(".*([.,/])work\\1$"))
} else if (Utilities.isAbsoluteUrl(type)) {
StructureDefinition defn = context.fetchTypeDefinition(type);
if (defn != null && hasMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep())) {
List<String> txtype = getMapping("http://hl7.org/fhir/terminology-pattern", defn, defn.getSnapshot().getElementFirstRep());
if (txtype.contains("CodeableConcept")) {
checkTerminologyCodeableConcept(errors, ei.getPath(), ei.getElement(), profile, checkDefn, stack, defn);
thisIsCodeableConcept = true;
} else if (txtype.contains("Coding")) {
checkTerminologyCoding(errors, ei.getPath(), ei.getElement(), profile, checkDefn, inCodeableConcept, checkDisplayInContext, stack, defn);
}
}
}
} else {
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), stack.getLiteralPath(), checkDefn != null, I18nConstants.VALIDATION_VAL_CONTENT_UNKNOWN, ei.getName()))
validateElement(hostContext, errors, profile, checkDefn, null, null, resource, ei.getElement(), type, localStack, false, true, null);
}
StructureDefinition p = null;
String tail = null;
if (profiles.isEmpty()) {
if (type != null) {
p = getProfileForType(type, checkDefn.getType());
// If dealing with a primitive type, then we need to check the current child against
// the invariants (constraints) on the current element, because otherwise it only gets
// checked against the primary type's invariants: LLoyd
//if (p.getKind() == StructureDefinitionKind.PRIMITIVETYPE) {
// checkInvariants(hostContext, errors, ei.path, profile, ei.definition, null, null, resource, ei.element);
//}
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_NOTYPE, type);
}
} else if (profiles.size() == 1) {
String url = profiles.get(0);
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, url);
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, profiles.get(0));
} else {
elementValidated = true;
HashMap<String, List<ValidationMessage>> goodProfiles = new HashMap<String, List<ValidationMessage>>();
HashMap<String, List<ValidationMessage>> badProfiles = new HashMap<String, List<ValidationMessage>>();
for (String typeProfile : profiles) {
String url = typeProfile;
tail = null;
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, url);
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, profiles.get(0));
} else {
elementValidated = true;
HashMap<String, List<ValidationMessage>> goodProfiles = new HashMap<String, List<ValidationMessage>>();
HashMap<String, List<ValidationMessage>> badProfiles = new HashMap<String, List<ValidationMessage>>();
for (String typeProfile : profiles) {
String url = typeProfile;
tail = null;
if (url.contains("#")) {
tail = url.substring(url.indexOf("#") + 1);
url = url.substring(0, url.indexOf("#"));
}
p = this.context.fetchResource(StructureDefinition.class, typeProfile);
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, typeProfile)) {
List<ValidationMessage> profileErrors = new ArrayList<ValidationMessage>();
validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
if (hasErrors(profileErrors))
badProfiles.put(typeProfile, profileErrors);
else
goodProfiles.put(typeProfile, profileErrors);
p = this.context.fetchResource(StructureDefinition.class, typeProfile);
if (rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), p != null, I18nConstants.VALIDATION_VAL_UNKNOWN_PROFILE, typeProfile)) {
List<ValidationMessage> profileErrors = new ArrayList<ValidationMessage>();
validateElement(hostContext, profileErrors, p, getElementByTail(p, tail), profile, checkDefn, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
if (hasErrors(profileErrors))
badProfiles.put(typeProfile, profileErrors);
else
goodProfiles.put(typeProfile, profileErrors);
}
}
if (goodProfiles.size() == 1) {
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size() == 0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOMATCH, StringUtils.join("; ", profiles));
for (String m : badProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : badProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
if (goodProfiles.size() == 1) {
errors.addAll(goodProfiles.values().iterator().next());
} else if (goodProfiles.size() == 0) {
rule(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_NOMATCH, StringUtils.join("; ", profiles));
for (String m : badProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : badProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
} else {
warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_MULTIPLEMATCHES, StringUtils.join("; ", goodProfiles.keySet()));
for (String m : goodProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : goodProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
} else {
warning(errors, IssueType.STRUCTURE, ei.line(), ei.col(), ei.getPath(), false, I18nConstants.VALIDATION_VAL_PROFILE_MULTIPLEMATCHES, StringUtils.join("; ", goodProfiles.keySet()));
for (String m : goodProfiles.keySet()) {
p = this.context.fetchResource(StructureDefinition.class, m);
for (ValidationMessage message : goodProfiles.get(m)) {
message.setMessage(message.getMessage() + " (validating against " + p.getUrl() + (p.hasVersion() ? "|" + p.getVersion() : "") + " [" + p.getName() + "])");
errors.add(message);
}
}
}
if (p != null) {
trackUsage(p, hostContext, element);
}
if (p != null) {
trackUsage(p, hostContext, element);
if (!elementValidated) {
if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER)
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, ei.getElement(), ei.getElement(), type, localStack.resetIds(), thisIsCodeableConcept, checkDisplay, thisExtension);
else
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, ei.definition, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
int index = profile.getSnapshot().getElement().indexOf(ei.definition);
if (index < profile.getSnapshot().getElement().size() - 1) {
String nextPath = profile.getSnapshot().getElement().get(index + 1).getPath();
if (!nextPath.equals(ei.definition.getPath()) && nextPath.startsWith(ei.definition.getPath()))
validateElement(hostContext, errors, profile, ei.definition, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
if (!elementValidated) {
if (ei.getElement().getSpecial() == SpecialElement.BUNDLE_ENTRY || ei.getElement().getSpecial() == SpecialElement.BUNDLE_OUTCOME || ei.getElement().getSpecial() == SpecialElement.PARAMETER)
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, checkDefn, ei.getElement(), ei.getElement(), type, localStack.resetIds(), thisIsCodeableConcept, checkDisplay, thisExtension);
else
validateElement(hostContext, errors, p, getElementByTail(p, tail), profile, checkDefn, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
int index = profile.getSnapshot().getElement().indexOf(checkDefn);
if (index < profile.getSnapshot().getElement().size() - 1) {
String nextPath = profile.getSnapshot().getElement().get(index + 1).getPath();
if (!nextPath.equals(checkDefn.getPath()) && nextPath.startsWith(checkDefn.getPath()))
validateElement(hostContext, errors, profile, checkDefn, null, null, resource, ei.getElement(), type, localStack, thisIsCodeableConcept, checkDisplay, thisExtension);
}
}
}
@ -5091,4 +5115,12 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
return questionnaireMode;
}
public boolean isWantCheckSnapshotUnchanged() {
return wantCheckSnapshotUnchanged;
}
public void setWantCheckSnapshotUnchanged(boolean wantCheckSnapshotUnchanged) {
this.wantCheckSnapshotUnchanged = wantCheckSnapshotUnchanged;
}
}

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/SpecialExtensions.java
View File

@ -1,12 +1,9 @@
package org.hl7.fhir.validation.instance;
import java.io.IOException;
import java.io.InputStream;
import org.hl7.fhir.convertors.VersionConvertorConstants;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.Utilities;

5
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureContext.java
View File

@ -1,19 +1,14 @@
package org.hl7.fhir.validation.instance.type;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.Attachment;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
import org.hl7.fhir.r5.model.Measure.MeasureGroupComponent;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.xml.sax.SAXException;
public class MeasureContext {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/MeasureValidator.java
View File

@ -5,7 +5,6 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.util.ArrayList;
import java.util.List;
@ -22,27 +21,23 @@ import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.Library;
import org.hl7.fhir.r5.model.Measure;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.model.Measure.MeasureGroupComponent;
import org.hl7.fhir.r5.model.Measure.MeasureGroupPopulationComponent;
import org.hl7.fhir.r5.model.Measure.MeasureGroupStratifierComponent;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.renderers.DataRenderer;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.utils.NodeStack;
import org.hl7.fhir.validation.instance.utils.ValidatorHostContext;
import org.w3c.dom.Document;
import net.sf.saxon.tree.tiny.LargeStringBuffer;
public class MeasureValidator extends BaseValidator {
public MeasureValidator(IWorkerContext context, TimeTracker timeTracker) {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/QuestionnaireValidator.java
View File

@ -23,26 +23,25 @@ import org.hl7.fhir.r5.elementmodel.ObjectConverter;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.DateType;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.Questionnaire;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemAnswerOptionComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.TimeType;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.Enumerations.FHIRVersion;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemAnswerOptionComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemComponent;
import org.hl7.fhir.r5.model.Questionnaire.QuestionnaireItemType;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.Validator.QuestionnaireMode;

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/SearchParameterValidator.java
View File

@ -5,14 +5,12 @@ import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.ExpressionNode.Kind;
import org.hl7.fhir.r5.model.ExpressionNode.Operation;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
@ -21,7 +19,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.SearchParameterValidator.FhirPathSorter;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class SearchParameterValidator extends BaseValidator {

79
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -3,18 +3,15 @@ package org.hl7.fhir.validation.instance.type;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.conformance.ProfileUtilities.ProfileKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
@ -22,14 +19,10 @@ import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ExpressionNode;
import org.hl7.fhir.r5.model.ExpressionNode.Kind;
import org.hl7.fhir.r5.model.ExpressionNode.Operation;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.SearchParameter;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.i18n.I18nConstants;
import org.hl7.fhir.utilities.validation.ValidationMessage;
@ -37,7 +30,6 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueType;
import org.hl7.fhir.utilities.validation.ValidationMessage.Source;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.type.StructureDefinitionValidator.FhirPathSorter;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class StructureDefinitionValidator extends BaseValidator {
@ -52,16 +44,18 @@ public class StructureDefinitionValidator extends BaseValidator {
}
private FHIRPathEngine fpe;
private boolean wantCheckSnapshotUnchanged;
public StructureDefinitionValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe) {
public StructureDefinitionValidator(IWorkerContext context, TimeTracker timeTracker, FHIRPathEngine fpe, boolean wantCheckSnapshotUnchanged) {
super(context);
source = Source.InstanceValidator;
this.fpe = fpe;
this.timeTracker = timeTracker;
this.wantCheckSnapshotUnchanged = wantCheckSnapshotUnchanged;
}
public void validateStructureDefinition(List<ValidationMessage> errors, Element src, NodeStack stack) {
StructureDefinition sd;
StructureDefinition sd = null;
try {
sd = loadAsSD(src);
List<ElementDefinition> snapshot = sd.getSnapshot().getElement();
@ -85,7 +79,7 @@ public class StructureDefinitionValidator extends BaseValidator {
errors.add(msg);
}
}
if (!snapshot.isEmpty()) {
if (!snapshot.isEmpty() && wantCheckSnapshotUnchanged) {
int was = snapshot.size();
int is = sd.getSnapshot().getElement().size();
rule(errors, IssueType.NOTFOUND, stack.getLiteralPath(), was == is, I18nConstants.SNAPSHOT_EXISTING_PROBLEM, was, is);
@ -99,29 +93,33 @@ public class StructureDefinitionValidator extends BaseValidator {
List<Element> differentials = src.getChildrenByName("differential");
List<Element> snapshots = src.getChildrenByName("snapshot");
for (Element differential : differentials) {
validateElementList(errors, differential, stack.push(differential, -1, null, null), false, snapshots.size() > 0);
validateElementList(errors, differential, stack.push(differential, -1, null, null), false, snapshots.size() > 0, sd);
}
for (Element snapshot : snapshots) {
validateElementList(errors, snapshot, stack.push(snapshot, -1, null, null), true, true);
validateElementList(errors, snapshot, stack.push(snapshot, -1, null, null), true, true, sd);
}
}
private void validateElementList(List<ValidationMessage> errors, Element elementList, NodeStack stack, boolean snapshot, boolean hasSnapshot) {
private void validateElementList(List<ValidationMessage> errors, Element elementList, NodeStack stack, boolean snapshot, boolean hasSnapshot, StructureDefinition sd) {
List<Element> elements = elementList.getChildrenByName("element");
int cc = 0;
for (Element element : elements) {
validateElementDefinition(errors, element, stack.push(element, cc, null, null), snapshot, hasSnapshot);
validateElementDefinition(errors, element, stack.push(element, cc, null, null), snapshot, hasSnapshot, sd);
cc++;
}
}
private void validateElementDefinition(List<ValidationMessage> errors, Element element, NodeStack stack, boolean snapshot, boolean hasSnapshot) {
private void validateElementDefinition(List<ValidationMessage> errors, Element element, NodeStack stack, boolean snapshot, boolean hasSnapshot, StructureDefinition sd) {
boolean typeMustSupport = false;
List<Element> types = element.getChildrenByName("type");
for (Element type : types) {
if (hasMustSupportExtension(type)) {
typeMustSupport = true;
}
// check the stated profile - must be a constraint on the type
if (snapshot || sd != null) {
validateElementType(errors, type, stack.push(type, -1, null, null), sd, element.getChildValue("path"));
}
}
if (typeMustSupport) {
if (snapshot) {
@ -132,6 +130,53 @@ public class StructureDefinitionValidator extends BaseValidator {
}
}
private void validateElementType(List<ValidationMessage> errors, Element type, NodeStack stack, StructureDefinition sd, String path) {
String code = type.getNamedChildValue("code");
if (code == null && path != null) {
code = getTypeCodeFromSD(sd, path);
}
if (code != null) {
List<Element> profiles = type.getChildrenByName("profile");
for (Element profile : profiles) {
validateTypeProfile(errors, profile, code, stack.push(type, -1, null, null));
}
}
}
private String getTypeCodeFromSD(StructureDefinition sd, String path) {
ElementDefinition ed = null;
for (ElementDefinition t : sd.getSnapshot().getElement()) {
if (t.hasPath() && t.getPath().equals(path)) {
if (ed == null) {
ed = t;
} else {
return null; // more than one match, we don't know which is which
}
}
}
return ed != null && ed.getType().size() == 1 ? ed.getTypeFirstRep().getCode() : null;
}
private void validateTypeProfile(List<ValidationMessage> errors, Element profile, String code, NodeStack stack) {
String p = profile.primitiveValue();
StructureDefinition sd = context.fetchResource(StructureDefinition.class, p);
if (warning(errors, IssueType.EXCEPTION, stack.getLiteralPath(), sd != null, I18nConstants.SD_ED_TYPE_PROFILE_UNKNOWN, p)) {
String t = determineBaseType(sd);
if (t == null) {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_NOTYPE, p);
} else {
rule(errors, IssueType.EXCEPTION, stack.getLiteralPath(), code.equals(t), I18nConstants.SD_ED_TYPE_PROFILE_WRONG, p, t, code);
}
}
}
private String determineBaseType(StructureDefinition sd) {
while (sd != null && !sd.hasType() && sd.getDerivation() == TypeDerivationRule.CONSTRAINT) {
sd = context.fetchResource(StructureDefinition.class, sd.getBaseDefinition());
}
return sd == null ? null : sd.getType();
}
private boolean hasMustSupportExtension(Element type) {
if ("true".equals(getExtensionValue(type, ToolingExtensions.EXT_MUST_SUPPORT))) {
return true;

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

@ -3,14 +3,13 @@ package org.hl7.fhir.validation.instance.type;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.CodingValidationRequest;
import org.hl7.fhir.r5.context.IWorkerContext.ValidationResult;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.CodeSystem;
import org.hl7.fhir.r5.model.Coding;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.terminologies.ValueSetExpander.TerminologyServiceErrorClass;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
@ -22,7 +21,6 @@ import org.hl7.fhir.utilities.validation.ValidationOptions;
import org.hl7.fhir.validation.BaseValidator;
import org.hl7.fhir.validation.TimeTracker;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.validation.instance.type.ValueSetValidator.VSCodingValidationRequest;
import org.hl7.fhir.validation.instance.utils.NodeStack;
public class ValueSetValidator extends BaseValidator {

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ChildIterator.java
View File

@ -1,8 +1,8 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.validation.instance.InstanceValidator;
public class ChildIterator {
private final InstanceValidator instanceValidator;

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

@ -1,11 +1,11 @@
package org.hl7.fhir.validation.instance.utils;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.List;
public class ElementInfo {
public List<ValidationMessage> sliceInfo;

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

@ -1,10 +1,10 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Element;
public class EntrySummary {
Element entry;

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/NodeStack.java
View File

@ -2,10 +2,8 @@ package org.hl7.fhir.validation.instance.utils;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.elementmodel.Element;

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ResolvedReference.java
View File

@ -2,7 +2,6 @@ package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.validation.instance.InstanceValidator;
public class ResolvedReference {

6
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ResourceValidationTracker.java
View File

@ -1,13 +1,13 @@
package org.hl7.fhir.validation.instance.utils;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
/**
* The validator keeps one of these classes for each resource it validates (e.g. when chasing references)
* <p>

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/utils/ValidatorHostContext.java
View File

@ -1,15 +1,13 @@
package org.hl7.fhir.validation.instance.utils;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Stack;
public class ValidatorHostContext {
private Object appContext;

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

@ -10,8 +10,8 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.npm.CachingPackageClient;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.npm.ToolsVersion;
import org.hl7.fhir.utilities.npm.PackageClient.PackageInfo;
import org.hl7.fhir.utilities.npm.ToolsVersion;
public class PackageValidator {

33
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/comparison/tests/ComparisonTests.java
View File

@ -1,15 +1,25 @@
package org.hl7.fhir.comparison.tests;
import com.google.common.base.Charsets;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Stream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
import org.hl7.fhir.convertors.VersionConvertor_14_50;
import org.hl7.fhir.convertors.VersionConvertor_30_50;
import org.hl7.fhir.convertors.VersionConvertor_40_50;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -49,18 +59,9 @@ import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.stream.Stream;
import com.google.common.base.Charsets;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
public class ComparisonTests {

38
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -1,6 +1,21 @@
package org.hl7.fhir.conversion.tests;
import com.google.gson.*;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.convertors.loaders.R3ToR4Loader;
import org.hl7.fhir.exceptions.DefinitionException;
@ -11,8 +26,16 @@ import org.hl7.fhir.r4.context.SimpleWorkerContext;
import org.hl7.fhir.r4.elementmodel.Element;
import org.hl7.fhir.r4.elementmodel.Manager;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.Base;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.MetadataResource;
import org.hl7.fhir.r4.model.PractitionerRole;
import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher;
@ -32,12 +55,11 @@ import org.junit.jupiter.params.provider.Arguments;
import org.junit.jupiter.params.provider.MethodSource;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.*;
import java.util.*;
import java.util.stream.Stream;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
import com.google.gson.JsonPrimitive;
@Disabled
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {

21
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/SnapShotGenerationXTests.java
View File

@ -1,5 +1,14 @@
package org.hl7.fhir.conversion.tests;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.parsers.ParserConfigurationException;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.exceptions.DefinitionException;
@ -18,12 +27,12 @@ import org.hl7.fhir.r5.model.Resource;
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.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.renderers.RendererFactory;
import org.hl7.fhir.r5.renderers.utils.RenderingContext;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.model.TypeDetails;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.r5.utils.FHIRPathEngine.IEvaluationContext;
import org.hl7.fhir.r5.utils.IResourceValidator;
@ -38,14 +47,6 @@ import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
public class SnapShotGenerationXTests {
public enum TestFetchMode {

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

@ -46,14 +46,14 @@ import javax.xml.parsers.DocumentBuilderFactory;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import org.fhir.ucum.UcumEssenceService;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.convertors.loaders.R2016MayToR5Loader;
import org.hl7.fhir.convertors.loaders.R2ToR5Loader;
import org.hl7.fhir.convertors.loaders.R3ToR5Loader;
import org.hl7.fhir.convertors.loaders.R4ToR5Loader;
import org.hl7.fhir.convertors.loaders.BaseLoaderR5.NullLoaderKnowledgeProvider;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContext.IContextResourceLoader;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.TextFile;

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

@ -6,7 +6,6 @@ import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Stream;
@ -24,7 +23,6 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.instance.InstanceValidatorFactory;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.params.ParameterizedTest;

7
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/BaseRestTest.java
View File

@ -1,14 +1,15 @@
package org.hl7.fhir.validation.cli;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException;
import org.apache.http.HttpResponse;
import org.apache.http.util.EntityUtils;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import java.io.IOException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
public abstract class BaseRestTest {

18
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/ValidatorGuiTest.java
View File

@ -1,17 +1,8 @@
package org.hl7.fhir.validation.cli;
import io.github.bonigarcia.wdm.WebDriverManager;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.validation.ValidationEngine;
import java.io.IOException;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.model.ValidationResponse;
import org.hl7.fhir.validation.cli.services.ValidationService;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
@ -19,10 +10,7 @@ import org.openqa.selenium.WebDriver;
import org.openqa.selenium.chrome.ChromeDriver;
import org.openqa.selenium.chrome.ChromeOptions;
import java.io.IOException;
import java.io.InputStream;
import java.net.URISyntaxException;
import java.util.Arrays;
import io.github.bonigarcia.wdm.WebDriverManager;
class ValidatorGuiTest {

4
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/controller/HttpGetContextTest.java
View File

@ -1,5 +1,7 @@
package org.hl7.fhir.validation.cli.controller;
import java.io.IOException;
import org.apache.http.HttpResponse;
import org.apache.http.HttpStatus;
import org.apache.http.client.methods.HttpGet;
@ -13,8 +15,6 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
import java.io.IOException;
class HttpGetContextTest extends BaseRestTest {
private final String GET_CONTEXT_URL = "http://localhost:" + ValidatorGui.getPort() + "/context";

6
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/controller/HttpPutContextTest.java
View File

@ -1,12 +1,12 @@
package org.hl7.fhir.validation.cli.controller;
import io.javalin.http.Context;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import io.javalin.http.Context;
class HttpPutContextTest {

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

@ -1,5 +1,8 @@
package org.hl7.fhir.validation.tests;
import java.io.FileNotFoundException;
import java.io.IOException;
import org.everit.json.schema.Schema;
import org.everit.json.schema.ValidationException;
import org.everit.json.schema.loader.SchemaLoader;
@ -9,9 +12,6 @@ import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.io.FileNotFoundException;
import java.io.IOException;
public class JsonSchemaTests {

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

@ -8,8 +8,6 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.validation.ValidationEngine;
import org.junit.Test;
import net.sf.saxon.expr.instruct.Message;
public class LoadIgTests {
@Test

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

@ -3,8 +3,8 @@ package org.hl7.fhir.validation.tests;
import java.io.File;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.validation.Validator;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.validation.Validator;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;

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

@ -1,5 +1,8 @@
package org.hl7.fhir.validation.tests;
import java.util.ArrayList;
import java.util.List;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.OperationOutcome;
@ -11,9 +14,6 @@ import org.hl7.fhir.validation.tests.utilities.TestUtilities;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.List;
public class ValidationEngineTests {
private static final String DEF_TX = "http://tx.fhir.org";

51
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -1,10 +1,19 @@
package org.hl7.fhir.validation.tests;
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;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.NotImplementedException;
import org.hl7.fhir.convertors.VersionConvertor_10_50;
@ -43,11 +52,11 @@ import org.hl7.fhir.r5.utils.IResourceValidator.ReferenceValidationPolicy;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtilities;
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.ValidationEngine;
import org.hl7.fhir.validation.instance.InstanceValidator;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Test;
@ -55,19 +64,11 @@ import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.junit.runners.Parameterized.Parameters;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
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;
@RunWith(Parameterized.class)
public class ValidationTests implements IEvaluationContext, IValidatorResourceFetcher {
@ -100,7 +101,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
private String version;
private String name;
private static final String DEF_TX = "http://tx.fhir.org";
private static final String DEF_TX = "http://tx.fhir.org";
// private static final String DEF_TX = "http://local.fhir.org:960";
private static Map<String, ValidationEngine> ve = new HashMap<>();
private static ValidationEngine vCurr;
@ -154,8 +155,8 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
return;
String testCaseContent = TestingUtilities.loadTestResource("validator", name);
InstanceValidator val = vCurr.getValidator();
val.setWantCheckSnapshotUnchanged(true);
val.getContext().setClientRetryCount(4);
val.setDebug(false);
if (content.has("allowed-extension-domain"))
@ -170,7 +171,13 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
val.setFetcher(this);
if (content.has("packages")) {
for (JsonElement e : content.getAsJsonArray("packages")) {
vCurr.loadIg(e.getAsString(), true);
String n = e.getAsString();
InputStream cnt = n.endsWith(".tgz") ? TestingUtilities.loadTestResourceStream("validator", n) : null;
if (cnt != null) {
vCurr.loadPackage(NpmPackage.fromPackage(cnt));
} else {
vCurr.loadIg(n, true);
}
}
}
if (content.has("crumb-trail")) {

4
pom.xml
View File

@ -14,12 +14,12 @@
HAPI FHIR.
-->
<artifactId>org.hl7.fhir.core</artifactId>
<version>5.1.17-SNAPSHOT</version>
<version>5.1.18-SNAPSHOT</version>
<packaging>pom</packaging>
<properties>
<hapi_fhir_version>5.1.0</hapi_fhir_version>
<validator_test_case_version>1.1.45</validator_test_case_version>
<validator_test_case_version>1.1.46</validator_test_case_version>
<junit_jupiter_version>5.6.2</junit_jupiter_version>
<maven_surefire_version>3.0.0-M4</maven_surefire_version>
<jacoco_version>0.8.5</jacoco_version>