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Merge pull request #1754 from hapifhir/2024-09-gg-sct-link 

2024 09 gg sct link
This commit is contained in:
Grahame Grieve 2024-09-23 12:17:27 -04:00 committed by GitHub
parent be8944ab94 b37073592b
commit 1a368ef8ac
No known key found for this signature in database
GPG Key ID: B5690EEEBB952194
9 changed files with 1051 additions and 1227 deletions
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30
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/conv40_50/resources40_50/Enumerations40_50.java
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@ -230,12 +230,6 @@ public class Enumerations40_50 {
case _4_3_0:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._4_3_0);
break;
case _4_3_0_CIBUILD:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._4_3_0CIBUILD);
break;
case _4_3_0_SNAPSHOT1:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._4_3_0SNAPSHOT1);
break;
case _5_0_0:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._5_0_0);
break;
@ -254,6 +248,15 @@ public class Enumerations40_50 {
case _5_0_0DRAFTFINAL:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._5_0_0DRAFTFINAL);
break;
case _6_0_0:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._6_0_0);
break;
case _6_0_0_BALLOT1:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._6_0_0_BALLOT1);
break;
case _6_0_0_BALLOT2:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion._6_0_0_BALLOT2);
break;
default:
tgt.setValue(org.hl7.fhir.r5.model.Enumerations.FHIRVersion.NULL);
break;
@ -342,12 +345,6 @@ public class Enumerations40_50 {
case _4_3_0:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._4_3_0);
break;
case _4_3_0CIBUILD:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._4_3_0_CIBUILD);
break;
case _4_3_0SNAPSHOT1:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._4_3_0_SNAPSHOT1);
break;
case _5_0_0:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._5_0_0);
break;
@ -366,6 +363,15 @@ public class Enumerations40_50 {
case _5_0_0DRAFTFINAL:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._5_0_0DRAFTFINAL);
break;
case _6_0_0:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._6_0_0);
break;
case _6_0_0_BALLOT1:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._6_0_0_BALLOT1);
break;
case _6_0_0_BALLOT2:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion._6_0_0_BALLOT2);
break;
default:
tgt.setValue(org.hl7.fhir.r4.model.Enumerations.FHIRVersion.NULL);

2117
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/Enumerations.java
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11
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
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@ -46,6 +46,7 @@ import org.hl7.fhir.r5.renderers.utils.RenderingContext.GenerationRules;
import org.hl7.fhir.r5.renderers.utils.RenderingContext.ResourceRendererMode;
import org.hl7.fhir.r5.renderers.utils.ResourceWrapper;
import org.hl7.fhir.r5.terminologies.JurisdictionUtilities;
import org.hl7.fhir.r5.terminologies.utilities.SnomedUtilities;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.r5.utils.ToolingExtensions;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
@ -1177,8 +1178,8 @@ public class DataRenderer extends Renderer implements CodeResolver {
}
private String getLinkForSystem(String system, String version) {
if ("http://snomed.info/sct".equals(system)) {
return "https://browser.ihtsdotools.org/";
if ("http://snomed.info/sct".equals(system)) {
return "https://browser.ihtsdotools.org/";
} else if ("http://loinc.org".equals(system)) {
return "https://loinc.org/";
} else if ("http://unitsofmeasure.org".equals(system)) {
@ -1198,11 +1199,7 @@ public class DataRenderer extends Renderer implements CodeResolver {
protected String getLinkForCode(String system, String version, String code) {
if ("http://snomed.info/sct".equals(system)) {
if (!Utilities.noString(code)) {
return "http://snomed.info/id/"+code;
} else {
return "https://browser.ihtsdotools.org/";
}
return SnomedUtilities.getSctLink(version, code, context.getContext().getExpansionParameters());
} else if ("http://loinc.org".equals(system)) {
if (!Utilities.noString(code)) {
return "https://loinc.org/"+code;

30
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -51,6 +51,7 @@ import org.hl7.fhir.r5.terminologies.CodeSystemUtilities;
import org.hl7.fhir.r5.terminologies.ValueSetUtilities;
import org.hl7.fhir.r5.terminologies.expansion.ValueSetExpansionOutcome;
import org.hl7.fhir.r5.terminologies.utilities.CodingValidationRequest;
import org.hl7.fhir.r5.terminologies.utilities.SnomedUtilities;
import org.hl7.fhir.r5.terminologies.utilities.ValidationResult;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.r5.utils.ToolingExtensions;
@ -825,7 +826,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
String s = Utilities.padLeft("", '\u00A0', i*2);
td.attribute("style", "white-space:nowrap").addText(s);
addCodeToTable(c.getAbstract(), c.getSystem(), c.getCode(), c.getDisplay(), td);
addCodeToTable(c.getAbstract(), c.getSystem(), c.getVersion(), c.getCode(), c.getDisplay(), td);
td = tr.td();
td.addText(c.getSystem());
td = tr.td();
@ -863,7 +864,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
first = false;
XhtmlNode span = td.span(null, mapping.comp.getRelationship().toString());
span.addText(getCharForRelationship(mapping.comp));
addRefToCode(td, mapping.group.getTarget(), m.getLink(), mapping.comp.getCode());
addRefToCode(td, mapping.group.getTarget(), null, m.getLink(), mapping.comp.getCode());
if (!Utilities.noString(mapping.comp.getComment()))
td.i().tx("("+mapping.comp.getComment()+")");
}
@ -900,13 +901,13 @@ public class ValueSetRenderer extends TerminologyRenderer {
return true;
}
private void addCodeToTable(boolean isAbstract, String system, String code, String display, XhtmlNode td) {
private void addCodeToTable(boolean isAbstract, String system, String version, String code, String display, XhtmlNode td) {
CodeSystem e = getContext().getWorker().fetchCodeSystem(system);
if (e == null || (e.getContent() != org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode.COMPLETE && e.getContent() != org.hl7.fhir.r5.model.Enumerations.CodeSystemContentMode.FRAGMENT)) {
if (isAbstract)
td.i().setAttribute("title", context.formatPhrase(RenderingContext.VS_ABSTRACT_CODE_HINT)).addText(code);
else if ("http://snomed.info/sct".equals(system)) {
td.ah(context.prefixLocalHref(sctLink(code))).addText(code);
td.ah(context.prefixLocalHref(SnomedUtilities.getSctLink(version, code, context.getContext().getExpansionParameters()))).addText(code);
} else if ("http://loinc.org".equals(system)) {
td.ah(context.prefixLocalHref(LoincLinker.getLinkForCode(code))).addText(code);
} else
@ -928,15 +929,8 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
}
public String sctLink(String code) {
// if (snomedEdition != null)
// http://browser.ihtsdotools.org/?perspective=full&conceptId1=428041000124106&edition=us-edition&release=v20180301&server=https://prod-browser-exten.ihtsdotools.org/api/snomed&langRefset=900000000000509007
return "http://snomed.info/id/"+code;
}
private void addRefToCode(XhtmlNode td, String target, String vslink, String code) {
addCodeToTable(false, target, code, null, td);
private void addRefToCode(XhtmlNode td, String target, String vslink, String code, String version) {
addCodeToTable(false, target, version, code, null, td);
// CodeSystem cs = getContext().getWorker().fetchCodeSystem(target);
// String cslink = getCsRef(cs);
// String link = cslink != null ? cslink+"#"+cs.getId()+"-"+code : vslink+"#"+code;
@ -1212,10 +1206,10 @@ public class ValueSetRenderer extends TerminologyRenderer {
}
addMapHeaders(addTableHeaderRowStandard(t, false, true, hasDefinition, hasComments, false, false, null, langs, designations, doDesignations), maps);
for (ConceptReferenceComponent c : inc.getConcept()) {
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, c);
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, c, inc.getVersion());
}
for (Base b : VersionComparisonAnnotation.getDeleted(inc, "concept" )) {
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, (ConceptReferenceComponent) b);
renderConcept(inc, langs, doDesignations, maps, designations, definitions, t, hasComments, hasDefinition, (ConceptReferenceComponent) b, inc.getVersion());
}
}
if (inc.getFilter().size() > 0) {
@ -1312,11 +1306,11 @@ public class ValueSetRenderer extends TerminologyRenderer {
private void renderConcept(ConceptSetComponent inc, List<String> langs, boolean doDesignations,
List<UsedConceptMap> maps, Map<String, String> designations, Map<String, ConceptDefinitionComponent> definitions,
XhtmlNode t, boolean hasComments, boolean hasDefinition, ConceptReferenceComponent c) {
XhtmlNode t, boolean hasComments, boolean hasDefinition, ConceptReferenceComponent c, String version) {
XhtmlNode tr = t.tr();
XhtmlNode td = renderStatusRow(c, t, tr);
ConceptDefinitionComponent cc = definitions == null ? null : definitions.get(c.getCode());
addCodeToTable(false, inc.getSystem(), c.getCode(), c.hasDisplay()? c.getDisplay() : cc != null ? cc.getDisplay() : "", td);
addCodeToTable(false, inc.getSystem(), version, c.getCode(), c.hasDisplay()? c.getDisplay() : cc != null ? cc.getDisplay() : "", td);
td = tr.td();
if (!Utilities.noString(c.getDisplay()))
@ -1355,7 +1349,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
first = false;
XhtmlNode span = td.span(null, mapping.comp.getRelationship().toString());
span.addText(getCharForRelationship(mapping.comp));
addRefToCode(td, mapping.group.getTarget(), m.getLink(), mapping.comp.getCode());
addRefToCode(td, mapping.group.getTarget(), m.getLink(), mapping.comp.getCode(), version);
if (!Utilities.noString(mapping.comp.getComment()))
td.i().tx("("+mapping.comp.getComment()+")");
}

74
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/utilities/SnomedUtilities.java Normal file
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@ -0,0 +1,74 @@
package org.hl7.fhir.r5.terminologies.utilities;
import org.hl7.fhir.r5.model.Parameters;
import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.utilities.Utilities;
//URL: http://snomed.info/sct/[module]/version/[e.g. 20150131]'
//International: 900000000000207008
//US: 731000124108
//Australia: 32506021000036107
//Belgium: 11000172109
//Canada: 20611000087101
//Spain: 449081005
//Denmark: 554471000005108
//Netherlands: 11000146104
//Sweden: 45991000052106
//Switzerland: 2011000195101
//UK: 83821000000107
//IPS: 827022005
public class SnomedUtilities {
public static String getVersionFromParameters(Parameters p, String version) {
for (ParametersParameterComponent pp : p.getParameter()) {
switch (pp.getName()) {
case "system-version" :
if (version == null) {
return pp.getValue().primitiveValue();
}
case "force-system-version":
return pp.getValue().primitiveValue();
}
}
return version;
}
public static String getEditionFromVersion(String version) {
if (version == null) {
return null;
}
if (version.startsWith("http://snomed.info/sct/")) {
version = version.substring(23);
}
if (version.contains("/")) {
version = version.substring(0, version.indexOf("/"));
}
if (Utilities.existsInList(version, "900000000000207008", "731000124108", "32506021000036107", "11000172109", "20611000087101",
"449081005", "554471000005108", "11000146104", "45991000052106", "2011000195101", "83821000000107", "827022005")) {
return version;
} else {
return null;
}
}
public static String getSctLink(String version, String code, Parameters p) {
if (!Utilities.noString(code)) {
version = SnomedUtilities.getVersionFromParameters(p, version);
String edId = SnomedUtilities.getEditionFromVersion(version);
if (edId != null) {
// if there's a version that's an edition, then:
// http://snomed.info/sct/11000172109/id//371305003
return "http://snomed.info/sct/"+edId+"/id/"+code;
} else {
// no, version:
return "http://snomed.info/id/"+code;
}
} else {
return "https://browser.ihtsdotools.org/";
}
}
}

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/formats/XmlLocationAnnotator.java
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@ -80,6 +80,15 @@ public class XmlLocationAnnotator extends XMLFilterImpl {
}
}
@Override
public Object getProperty(String name) throws SAXNotRecognizedException, SAXNotSupportedException {
if (!name.equals("http://javax.xml.xmlconstants/property/accessExternalDTD")) {
return null;
} else {
return super.getProperty(name);
}
}
@Override
public void setDocumentLocator(Locator locator) {
super.setDocumentLocator(locator);

3
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -1140,7 +1140,8 @@ TYPE_SPECIFIC_CHECKS_DT_XHTML_LITERAL_HREF = Hyperlink scheme ''{3}'' in ''{0}''
SM_TARGET_TYPE_UNKNOWN = The type of the target variable is not known: {0}
XHTML_XHTML_ATTRIBUTE_XML_SPACE = The attribute 'xml:space' is legal but has a fixed value of 'preserve'. It''s use is discouraged
VALIDATION_HL7_PUBLISHER_MULTIPLE_WGS = This resource has more than workgroup extension (http://hl7.org/fhir/StructureDefinition/structuredefinition-wg)
NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG = Wrong Display Name ''{0}'' for {1}#{2}. There are no valid display names found for language(s) ''{3}''. Default display is ''{4}''
NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_OK = There are no valid display names found for the code {1}#{2} for language(s) ''{3}''. The display is ''{4}'' the default language display
NO_VALID_DISPLAY_FOUND_NONE_FOR_LANG_ERR = Wrong Display Name ''{0}'' for {1}#{2}. There are no valid display names found for language(s) ''{3}''. Default display is ''{4}''
NO_VALID_DISPLAY_AT_ALL = Cannot validate display Name ''{0}'' for {1}#{2}: No displays are known
SD_BASE_EXPERIMENTAL = The definition builds on ''{0}'' which is experimental, but this definition is not labeled as experimental
SD_ED_EXPERIMENTAL_BINDING = The definition for the element ''{0}'' binds to the value set ''{1}'' which is experimental, but this structure is not labeled as experimental

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/model/CliContext.java
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@ -130,7 +130,7 @@ public class CliContext {
private boolean showTimes = false;
@JsonProperty("locale")
private String locale = Locale.ENGLISH.getDisplayLanguage();
private String locale = Locale.ENGLISH.toLanguageTag();
@JsonProperty("locations")
private Map<String, String> locations = new HashMap<String, String>();

2
pom.xml
View File

@ -21,7 +21,7 @@
<commons_compress_version>1.26.0</commons_compress_version>
<guava_version>32.0.1-jre</guava_version>
<hapi_fhir_version>6.4.1</hapi_fhir_version>
<validator_test_case_version>1.5.23</validator_test_case_version>
<validator_test_case_version>1.5.24-SNAPSHOT</validator_test_case_version>
<jackson_version>2.17.0</jackson_version>
<junit_jupiter_version>5.9.2</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>