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Fix markdown relative link issues + start working on additional bindings extension

This commit is contained in:
Grahame Grieve 2022-02-12 07:53:23 +11:00
parent b49e791cd1
commit 0fa757b426
7 changed files with 106 additions and 7 deletions
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5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/BaseLoaderR5.java
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@ -38,6 +38,11 @@ public abstract class BaseLoaderR5 implements IContextResourceLoader {
public void setPath(Resource r) {
String path = lkp.getResourcePath(r);
if (lkp.getWebRoot() != null) {
r.setUserData("webroot", lkp.getWebRoot());
} else {
r.setUserData("webroot", "");
}
if (path != null) {
r.setUserData("path", path);
}

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/ILoaderKnowledgeProviderR5.java
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@ -16,4 +16,6 @@ public interface ILoaderKnowledgeProviderR5 {
String getResourcePath(Resource resource);
ILoaderKnowledgeProviderR5 forNewPackage(NpmPackage npm) throws JsonSyntaxException, IOException;
String getWebRoot();
}

5
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/loaders/loaderR5/NullLoaderKnowledgeProviderR5.java
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@ -13,4 +13,9 @@ public class NullLoaderKnowledgeProviderR5 implements ILoaderKnowledgeProviderR5
public ILoaderKnowledgeProviderR5 forNewPackage(NpmPackage npm) {
return this;
}
@Override
public String getWebRoot() {
return null;
}
}

47
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -104,6 +104,7 @@ import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionMappingCompo
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionSnapshotComponent;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.model.ValueSet;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
@ -2480,19 +2481,19 @@ public class ProfileUtilities extends TranslatingUtilities {
if (webUrl != null) {
// also, must touch up the markdown
if (element.hasDefinition())
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasComment())
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasRequirements())
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
if (element.hasMeaningWhenMissing())
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames));
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
}
}
return element;
}
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames, Set<String> filenames) {
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames, Set<String> filenames, boolean processRelatives) {
StringBuilder b = new StringBuilder();
int i = 0;
while (i < markdown.length()) {
@ -2520,7 +2521,13 @@ public class ProfileUtilities extends TranslatingUtilities {
} else {
b.append("](");
// disabled 7-Dec 2021 GDG - we don't want to fool with relative URLs at all?
// b.append(webUrl);
// re-enabled 11-Feb 2022 GDG - we do want to do this. At least, $assemble in davinci-dtr, where the markdown comes from the SDC IG, and an SDC local reference must be changed to point to SDC. in this case, it's called when generating snapshots
// added processRelatives parameter to deal with this (well, to try)
if (processRelatives) {
b.append(webUrl);
} else {
System.out.println("Not making "+url+" relative to '"+webUrl+"'");
}
i = i + 1;
}
} else
@ -2778,7 +2785,9 @@ public class ProfileUtilities extends TranslatingUtilities {
profile = source.getType().size() == 1 && source.getTypeFirstRep().hasProfile() ? context.fetchResource(StructureDefinition.class, source.getTypeFirstRep().getProfile().get(0).getValue()) : null;
if (profile != null) {
ElementDefinition e = profile.getSnapshot().getElement().get(0);
base.setDefinition(e.getDefinition());
String webroot = profile.getUserString("webroot");
base.setDefinition(processRelativeUrls(e.getDefinition(), webroot, baseSpecUrl(), context.getResourceNames(), masterSourceFileNames, true));
base.setShort(e.getShort());
if (e.hasCommentElement())
base.setCommentElement(e.getCommentElement());
@ -4688,6 +4697,13 @@ public class ProfileUtilities extends TranslatingUtilities {
c.getPieces().add(gen.new Piece(null, ": ", null));
c.addMarkdownNoPara(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement()).asStringValue(), checkForNoChange(PublicationHacker.fixBindingDescriptions(context, binding.getDescriptionElement())));
}
if (binding.hasExtension(ToolingExtensions.EXT_BINDING_ADDITIONAL)) {
c.addPiece(gen.new Piece("br"));
c.getPieces().add(checkForNoChange(binding, gen.new Piece(null, translate("sd.table", "Additional Bindings")+": ", null).addStyle("font-weight:bold")));
for (Extension ext : binding.getExtensionsByUrl(ToolingExtensions.EXT_BINDING_ADDITIONAL)) {
renderAdditionalBinding(gen, c, ext);
}
}
}
for (ElementDefinitionConstraintComponent inv : definition.getConstraint()) {
if (!inv.hasSource() || profile == null || inv.getSource().equals(profile.getUrl()) || allInvariants) {
@ -4767,6 +4783,23 @@ public class ProfileUtilities extends TranslatingUtilities {
return c;
}
private void renderAdditionalBinding(HierarchicalTableGenerator gen, Cell c, Extension ext) {
// <nsbp>2 <sp> purpose <sp> value-set-link ([context]) {documentation}
// String purpose = ext.getExtensionString("purpose");
// String valueSet = ext.getExtensionString("valueSet");
// String doco = ext.getExtensionString("documentation");
// UsageContext usage = (ext.hasExtension("usage")) ? ext.getExtensionByUrl("usage").getValueUsageContext() : null;
//
// purpose: code - defines how the binding is used
// usage : UsageContext - defines the contexts in which this binding is used for it's purpose
// valueSet : canonical(ValueSet)
// documentation : markdown
// !!
// c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, inv.getKey()+": ", null).addStyle("font-weight:bold")));
// c.getPieces().add(checkForNoChange(inv, gen.new Piece(null, gt(inv.getHumanElement()), null)));
}
private BindingResolution makeNullBr(ElementDefinitionBindingComponent binding) {
BindingResolution br = new BindingResolution();
br.url = "http://none.none/none";

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -200,6 +200,7 @@ public class ToolingExtensions {
public static final String EXT_VALUESET_SYSTEM = "http://hl7.org/fhir/StructureDefinition/valueset-system";
public static final String EXT_EXPAND_RULES = "http://hl7.org/fhir/StructureDefinition/valueset-expand-rules";
public static final String EXT_EXPAND_GROUP = "http://hl7.org/fhir/StructureDefinition/valueset-expand-group";
public static final String EXT_BINDING_ADDITIONAL = "http://hl7.org/fhir/tools/StructureDefinition/additional-binding";
// specific extension helpers

45
org.hl7.fhir.r5/src/test/resources/txCache/loinc.cache Normal file
View File

@ -0,0 +1,45 @@
-------------------------------------------------------------------------------------
{"hierarchical" : false, "valueSet" :{
"resourceType" : "ValueSet",
"compose" : {
"include" : [{
"system" : "http://loinc.org",
"concept" : [{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "A."
}],
"code" : "LA20752-4",
"display" : "Within 24 hours"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "B."
}],
"code" : "LA20753-2",
"display" : "After 24 hours but before 3 days"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "C."
}],
"code" : "LA20754-0",
"display" : "Three days or later"
},
{
"extension" : [{
"url" : "http://hl7.org/fhir/StructureDefinition/valueset-label",
"valueString" : "D."
}],
"code" : "LA4489-6",
"display" : "Unknown"
}]
}]
}
}}####
e: {
"error" : "Cannot invoke \"org.hl7.fhir.r5.terminologies.TerminologyClient.expandValueset(org.hl7.fhir.r5.model.ValueSet, org.hl7.fhir.r5.model.Parameters, java.util.Map)\" because \"this.txClient\" is null"
}
-------------------------------------------------------------------------------------

8
org.hl7.fhir.validation/src/test/resources/txCache/4.0.1/all-systems.cache
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@ -1591,3 +1591,11 @@ v: {
"error" : "Unable to find code 10821000202101 in http://snomed.info/sct (version http://snomed.info/sct/900000000000207008/version/20210731); The code \"10821000202101\" is not valid in the system http://snomed.info/sct; The code provided (http://snomed.info/sct#10821000202101) is not valid in the value set 'no-colonoscopy-sedation-level' (from http://tx.fhir.org/r4)"
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "pdf"
}, "url": "http://hl7.org/fhir/ValueSet/mimetypes", "version": "4.0.1", "lang":"null", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "versionFlexible":"false"}####
v: {
"severity" : "error",
"error" : "The code \"pdf\" is not valid in the system urn:ietf:bcp:13; The code provided (urn:ietf:bcp:13#pdf) is not valid in the value set 'Mime Types' (from http://tx.fhir.org/r4)"
}
-------------------------------------------------------------------------------------