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Auto-update extension min- slicing + fix handling of summary extension + update markdown element url handling + update url detection in markdown

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This commit is contained in:
Grahame Grieve 2023-06-21 09:21:05 +10:00
parent 52abef6f2c
commit 04f7805be4
1 changed files with 122 additions and 47 deletions
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169
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
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@ -79,6 +79,7 @@ import org.hl7.fhir.r5.model.ExpressionNode.Kind;
import org.hl7.fhir.r5.model.ExpressionNode.Operation;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.MarkdownType;
import org.hl7.fhir.r5.model.Resource;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
@ -216,6 +217,7 @@ public class ProfileUtilities extends TranslatingUtilities {
"http://hl7.org/fhir/StructureDefinition/structuredefinition-normative-version",
"http://hl7.org/fhir/tools/StructureDefinition/obligation-profile",
"http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status-reason",
ToolingExtensions.EXT_SUMMARY,
ToolingExtensions.EXT_OBLIGATION);
@ -357,6 +359,7 @@ public class ProfileUtilities extends TranslatingUtilities {
private XVerExtensionManager xver;
private boolean wantFixDifferentialFirstElementType;
private Set<String> masterSourceFileNames;
private Set<String> localFileNames;
private Map<ElementDefinition, SourcedChildDefinitions> childMapCache = new HashMap<>();
private AllowUnknownProfile allowUnknownProfile = AllowUnknownProfile.ALL_TYPES;
private MappingMergeModeOption mappingMergeMode = MappingMergeModeOption.APPEND;
@ -639,8 +642,8 @@ public class ProfileUtilities extends TranslatingUtilities {
checkDifferential(derived.getDifferential().getElement(), derived.getTypeName(), derived.getUrl());
checkDifferentialBaseType(derived);
copyInheritedExtensions(base, derived);
copyInheritedExtensions(base, derived, webUrl);
findInheritedObligationProfiles(derived);
// so we have two lists - the base list, and the differential list
// the differential list is only allowed to include things that are in the base list, but
@ -895,10 +898,16 @@ public class ProfileUtilities extends TranslatingUtilities {
private void copyInheritedExtensions(StructureDefinition base, StructureDefinition derived) {
private void copyInheritedExtensions(StructureDefinition base, StructureDefinition derived, String webUrl) {
for (Extension ext : base.getExtension()) {
if (!Utilities.existsInList(ext.getUrl(), NON_INHERITED_ED_URLS) && !derived.hasExtension(ext.getUrl())) {
derived.getExtension().add(ext.copy());
Extension next = ext.copy();
if (ext.hasValueMarkdownType()) {
MarkdownType md = ext.getValueMarkdownType();
md.setValue(processRelativeUrls(md.getValue(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
derived.getExtension().add(next);
}
}
@ -1796,79 +1805,137 @@ public class ProfileUtilities extends TranslatingUtilities {
if (webUrl != null) {
// also, must touch up the markdown
if (element.hasDefinition()) {
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
if (element.hasComment()) {
element.setComment(processRelativeUrls(element.getComment(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
element.setComment(processRelativeUrls(element.getComment(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
if (element.hasRequirements()) {
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
if (element.hasMeaningWhenMissing()) {
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
if (element.hasBinding() && element.getBinding().hasDescription()) {
element.getBinding().setDescription(processRelativeUrls(element.getBinding().getDescription(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, false));
element.getBinding().setDescription(processRelativeUrls(element.getBinding().getDescription(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
for (Extension ext : element.getExtension()) {
if (ext.hasValueMarkdownType()) {
MarkdownType md = ext.getValueMarkdownType();
md.setValue(processRelativeUrls(md.getValue(), webUrl, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, false));
}
}
}
}
return element;
}
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames, Set<String> baseFilenames, Set<String> localFilenames, boolean processRelatives) {
if (markdown == null) {
return "";
}
Set<String> anchorRefs = new HashSet<>();
markdown = markdown+" ";
StringBuilder b = new StringBuilder();
int i = 0;
int left = -1;
boolean processingLink = false;
int linkLeft = -1;
while (i < markdown.length()) {
if (i < markdown.length()-3 && markdown.substring(i, i+2).equals("](")) {
int j = i + 2;
while (j < markdown.length() && markdown.charAt(j) != ')')
j++;
if (j < markdown.length()) {
String url = markdown.substring(i+2, j);
if (!Utilities.isAbsoluteUrl(url) && !url.startsWith("..")) {
//
// In principle, relative URLs are supposed to be converted to absolute URLs in snapshots.
// that's what this code is doing.
//
// But that hasn't always happened and there's packages out there where the snapshots
// contain relative references that actually are references to the main specification
//
// This code is trying to guess which relative references are actually to the
// base specification.
//
if (markdown.charAt(i) == '[') {
if (left == -1) {
left = i;
} else {
left = Integer.MAX_VALUE;
}
}
if (markdown.charAt(i) == ']') {
if (left != -1 && left != Integer.MAX_VALUE && markdown.length() > i && markdown.charAt(i+1) != '(') {
String n = markdown.substring(left+1, i);
if (anchorRefs.contains(n) && markdown.length() > i && markdown.charAt(i+1) == ':') {
processingLink = true;
} else {
anchorRefs.add(n);
}
}
left = -1;
}
if (processingLink) {
char ch = markdown.charAt(i);
if (linkLeft == -1) {
if (ch != ']' && ch != ':' && !Character.isWhitespace(ch)) {
linkLeft = i;
} else {
b.append(ch);
}
} else {
if (Character.isWhitespace(ch)) {
// found the end of the processible link:
String url = markdown.substring(linkLeft, i);
if (isLikelySourceURLReference(url, resourceNames, baseFilenames, localFilenames)) {
b.append("](");
b.append(basePath);
if (!Utilities.noString(basePath) && !basePath.endsWith("/")) {
b.append("/");
}
i = i + 1;
} else {
b.append("](");
// disabled 7-Dec 2021 GDG - we don't want to fool with relative URLs at all?
// 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 && webUrl != null && !issLocalFileName(url, localFilenames)) {
// System.out.println("Making "+url+" relative to '"+webUrl+"'");
b.append(webUrl);
} else {
// System.out.println("Not making "+url+" relative to '"+webUrl+"'");
}
i = i + 1;
}
} else
b.append(markdown.charAt(i));
} else
b.append(markdown.charAt(i));
b.append(url);
b.append(ch);
linkLeft = -1;
}
}
} else {
b.append(markdown.charAt(i));
if (i < markdown.length()-3 && markdown.substring(i, i+2).equals("](")) {
int j = i + 2;
while (j < markdown.length() && markdown.charAt(j) != ')')
j++;
if (j < markdown.length()) {
String url = markdown.substring(i+2, j);
if (!Utilities.isAbsoluteUrl(url) && !url.startsWith("..")) {
//
// In principle, relative URLs are supposed to be converted to absolute URLs in snapshots.
// that's what this code is doing.
//
// But that hasn't always happened and there's packages out there where the snapshots
// contain relative references that actually are references to the main specification
//
// This code is trying to guess which relative references are actually to the
// base specification.
//
if (isLikelySourceURLReference(url, resourceNames, baseFilenames, localFilenames)) {
b.append("](");
b.append(basePath);
if (!Utilities.noString(basePath) && !basePath.endsWith("/")) {
b.append("/");
}
i = i + 1;
} else {
b.append("](");
// disabled 7-Dec 2021 GDG - we don't want to fool with relative URLs at all?
// 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 && webUrl != null && !issLocalFileName(url, localFilenames)) {
// System.out.println("Making "+url+" relative to '"+webUrl+"'");
b.append(webUrl);
} else {
// System.out.println("Not making "+url+" relative to '"+webUrl+"'");
}
i = i + 1;
}
} else
b.append(markdown.charAt(i));
} else
b.append(markdown.charAt(i));
} else {
b.append(markdown.charAt(i));
}
}
i++;
}
return b.toString();
String s = b.toString();
return Utilities.rightTrim(s);
}
private static boolean issLocalFileName(String url, Set<String> localFilenames) {
@ -2209,7 +2276,7 @@ public class ProfileUtilities extends TranslatingUtilities {
String webroot = profile.getUserString("webroot");
if (e.hasDefinition()) {
base.setDefinition(processRelativeUrls(e.getDefinition(), webroot, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, null, true));
base.setDefinition(processRelativeUrls(e.getDefinition(), webroot, context.getSpecUrl(), context.getResourceNames(), masterSourceFileNames, localFileNames, true));
}
base.setShort(e.getShort());
if (e.hasCommentElement())
@ -4215,6 +4282,14 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public Set<String> getLocalFileNames() {
return localFileNames;
}
public void setLocalFileNames(Set<String> localFileNames) {
this.localFileNames = localFileNames;
}
public ProfileKnowledgeProvider getPkp() {
return pkp;
}