HL7 · dotasek · Sep 27, 2023 · Sep 27, 2023 · Sep 27, 2023 · Sep 27, 2023
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -0,0 +1,17 @@
+* Loader: Fix up parsing of logical models
+* Loader: Fix handling of CDA example fragments
+* Loader: Fix bug parsing extension with no value in JSON for the validator
+* Validator: Fix for issue parsing SHC and not recording line/col correctly
+* Validator: Fix issue validating CDA FHIR Path constraints
+* Validator: Better error handling validating codes in concept maps
+* Validator: Validate special resource rules on contained resources and Bundle entries
+* Validator: Improved error messages of observation bp
+* Validator: Fix up WG internal model for changes to workgroups
+* Validator: fix misleading error message inferring system when filters in play
+* Validator: Fix type handling for logical models (CDA fixes)
+* Version convertor: Fix version conversion issue between r4 and r5 charge definition issue
+* Renderer: Fix rendering extension and missed profile on Reference()
+* Renderer: fix wrong generation of logical models (for CDA)
+* Renderer: Don't create wrong phinvads references
+* Link Checker: Don't fail in link checking for illegal file references
+* Publication Process: exit code = 1 unless publication run is succesful
diff --git a/...hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/FetchedResource.java b/...hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/FetchedResource.java
@@ -82,6 +82,10 @@ public FetchedResource setElement(Element element) {
  return this;
  }
 
+ public void setType(String type) {
+ this.type = type;
+ }
+
  public String getId() {
  return id;
  }

diff --git a/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/HTMLInspector.java b/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/HTMLInspector.java
@@ -704,27 +704,35 @@ private boolean checkResolveLink(String filename, Location loc, String path, Str
  page = filename;
  } else if (page.contains("#")) {
  name = page.substring(page.indexOf("#")+1);
+ try {
  if (altRootFolder != null && filename.startsWith(altRootFolder))
  page = Utilities.path(altRootFolder, page.substring(0, page.indexOf("#")).replace("/", File.separator));
  else
  page = Utilities.path(rootFolder, page.substring(0, page.indexOf("#")).replace("/", File.separator));
+ } catch (Exception e) {
+ page = null;
+ }
  } else {
  String folder = Utilities.getDirectoryForFile(filename);
  page = Utilities.path(folder == null ? (altRootFolder != null && filename.startsWith(altRootFolder) ? altRootFolder : rootFolder) : folder, page.replace("/", File.separator));
  }
- LoadedFile f = cache.get(page);
- if (f != null) {
- if (Utilities.noString(name))
- resolved = true;
- else { 
- resolved = f.targets.contains(name);
- tgtList = " (valid targets: "+(f.targets.size() > 40 ? Integer.toString(f.targets.size())+" targets" : f.targets.toString())+")";
- for (String s : f.targets) {
- if (s.equalsIgnoreCase(name)) {
- tgtList = (" - case is wrong ('"+s+"')");
+ if (page != null) {
+ LoadedFile f = cache.get(page);
+ if (f != null) {
+ if (Utilities.noString(name))
+ resolved = true;
+ else { 
+ resolved = f.targets.contains(name);
+ tgtList = " (valid targets: "+(f.targets.size() > 40 ? Integer.toString(f.targets.size())+" targets" : f.targets.toString())+")";
+ for (String s : f.targets) {
+ if (s.equalsIgnoreCase(name)) {
+ tgtList = (" - case is wrong ('"+s+"')");
+ }
  }
  }
  }
+ } else {
+ resolved = false; 
  }
  }
  }

diff --git a/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java b/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java
@@ -1075,7 +1075,7 @@ private String makeTemplateJekyllIndexPage() {
  }
 
  private String makeTemplateQAPage() {
- String page = "<!DOCTYPE HTML><html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><head><title>Template QA Page</title></head><body><p><b>Template {{npm}} QA</b></p><p>No useful QA on templates - if you see this page, the template buitl ok.</p></body></html>";
+ String page = "<!DOCTYPE HTML><html xmlns=\"http://www.w3.org/1999/xhtml\" xml:lang=\"en\" lang=\"en\"><head><title>Template QA Page</title></head><body><p><b>Template {{npm}} QA</b></p><p>No useful QA on templates - if you see this page, the template built ok.</p></body></html>";
  return page.replace("{{npm}}", templateInfo.asString("name"));
  }
 
@@ -6029,34 +6029,46 @@ private void loadAsElementModel(FetchedFile file, FetchedResource r, Implementat
 
  if (e != null) {
  try {
- if (!Utilities.noString(e.getIdBase())) {
- checkResourceUnique(e.fhirType()+"/"+e.getIdBase());
- }
+ String id;
  boolean altered = false;
-
- String id = e.getChildValue("id");
- if (Utilities.noString(id)) {
- if (e.hasChild("url")) {
- String url = e.getChildValue("url");
- String prefix = Utilities.pathURL(igpkp.getCanonical(), e.fhirType())+"/";
- if (url.startsWith(prefix)) {
- id = e.getChildValue("url").substring(prefix.length());
- e.setChildValue("id", id);
- altered = true;
- } 
- prefix = Utilities.pathURL(altCanonical, e.fhirType())+"/";
- if (url.startsWith(prefix)) {
- id = e.getChildValue("url").substring(prefix.length());
- e.setChildValue("id", id);
- altered = true;
- } 
- if (Utilities.noString(id)) {
- throw new Exception("Resource has no id in "+file.getPath()+" and canonical URL ("+url+") does not start with the IG canonical URL ("+prefix+")");
+ boolean binary = false;
+ if (!context.getResourceNamesAsSet().contains(e.fhirType())) {
+ File f = new File(file.getPath());
+ id = f.getName();
+ id = id.substring(0, id.indexOf("."));
+ checkResourceUnique("Binary/"+id);
+ r.setElement(e).setId(id).setType("Binary");
+ igpkp.findConfiguration(file, r);
+ binary = true;
+ } else {
+ id = e.getChildValue("id");
+ if (!Utilities.noString(e.getIdBase())) {
+ checkResourceUnique(e.fhirType()+"/"+e.getIdBase());
+ }
+
+ if (Utilities.noString(id)) {
+ if (e.hasChild("url")) {
+ String url = e.getChildValue("url");
+ String prefix = Utilities.pathURL(igpkp.getCanonical(), e.fhirType())+"/";
+ if (url.startsWith(prefix)) {
+ id = e.getChildValue("url").substring(prefix.length());
+ e.setChildValue("id", id);
+ altered = true;
+ } 
+ prefix = Utilities.pathURL(altCanonical, e.fhirType())+"/";
+ if (url.startsWith(prefix)) {
+ id = e.getChildValue("url").substring(prefix.length());
+ e.setChildValue("id", id);
+ altered = true;
+ } 
+ if (Utilities.noString(id)) {
+ throw new Exception("Resource has no id in "+file.getPath()+" and canonical URL ("+url+") does not start with the IG canonical URL ("+prefix+")");
+ }
  }
  }
+ r.setElement(e).setId(id);
+ igpkp.findConfiguration(file, r);
  }
- r.setElement(e).setId(id);
- igpkp.findConfiguration(file, r);
  if (!suppressLoading) {
  if (srcForLoad == null)
  srcForLoad = findIGReference(r.fhirType(), r.getId());
@@ -6116,8 +6128,9 @@ else if (file.getContentType().contains("xml"))
  if (new AdjunctFileLoader(binaryPaths, cql).replaceAttachments1(file, r, metadataResourceNames())) {
  altered = true;
  }
- if ((altered && r.getResource() != null) || (ver.equals(Constants.VERSION) && r.getResource() == null))
+ if (!binary && ((altered && r.getResource() != null) || (ver.equals(Constants.VERSION) && r.getResource() == null && context.getResourceNamesAsSet().contains(r.fhirType())))) {
  r.setResource(new ObjectConverter(context).convert(r.getElement()));
+ }
  if ((altered && r.getResource() == null)) {
  if (file.getContentType().contains("json")) {
  saveToJson(file, e);
@@ -6696,7 +6709,6 @@ private void generateSnapshot(FetchedFile f, FetchedResource r, StructureDefinit
  }
 
  if (changed || (!r.getElement().hasChild("snapshot") && sd.hasSnapshot())) {
- // for big snapshots, this can take considerable time, and there's really no reason to do it 
  r.setElement(convertToElement(r, sd));
  }
  r.getElement().setUserData("profileutils.snapshot.errors", messages); 
@@ -6925,28 +6937,32 @@ private void validate() throws Exception {
  try {
  logDebugMessage(LogCategory.PROGRESS, " .. validate "+f.getName());
  logDebugMessage(LogCategory.PROGRESS, " .. "+f.getName());
- for (FetchedResource r : f.getResources()) {
- if (!r.isValidated()) {
- logDebugMessage(LogCategory.PROGRESS, " validating "+r.getTitle());
- validate(f, r);
- }
- }
- FetchedResource r = f.getResources().get(0);
- if (f.getLogical() != null && f.getResources().size() == 1 && r.fhirType().equals("Binary")) {
- Binary bin = (Binary) r.getResource();
- StructureDefinition profile = context.fetchResource(StructureDefinition.class, f.getLogical());
- List<ValidationMessage> errs = new ArrayList<ValidationMessage>();
- if (profile == null) {
- errs.add(new ValidationMessage(Source.InstanceValidator, IssueType.NOTFOUND, "file", context.formatMessage(I18nConstants.Bundle_BUNDLE_Entry_NO_LOGICAL_EXPL, r.getId(), f.getLogical()), IssueSeverity.ERROR));
- } else {
- FhirFormat fmt = FhirFormat.readFromMimeType(bin.getContentType()); 
- Session tts = tt.start("validation");
- List<StructureDefinition> profiles = new ArrayList<>();
- profiles.add(profile);
- validate(f, r, bin, errs, fmt, profiles); 
- tts.end();
+ FetchedResource r0 = f.getResources().get(0);
+ if (f.getLogical() != null && f.getResources().size() == 1 && !r0.fhirType().equals("Binary")) {
+ throw new Error("Not done yet");
+ } else {
+ for (FetchedResource r : f.getResources()) {
+ if (!r.isValidated()) {
+ logDebugMessage(LogCategory.PROGRESS, " validating "+r.getTitle());
+ validate(f, r);
+ }
+ }
+ if (f.getLogical() != null && f.getResources().size() == 1 && r0.fhirType().equals("Binary")) {
+ Binary bin = (Binary) r0.getResource();
+ StructureDefinition profile = context.fetchResource(StructureDefinition.class, f.getLogical());
+ List<ValidationMessage> errs = new ArrayList<ValidationMessage>();
+ if (profile == null) {
+ errs.add(new ValidationMessage(Source.InstanceValidator, IssueType.NOTFOUND, "file", context.formatMessage(I18nConstants.Bundle_BUNDLE_Entry_NO_LOGICAL_EXPL, r0.getId(), f.getLogical()), IssueSeverity.ERROR));
+ } else {
+ FhirFormat fmt = FhirFormat.readFromMimeType(bin.getContentType()); 
+ Session tts = tt.start("validation");
+ List<StructureDefinition> profiles = new ArrayList<>();
+ profiles.add(profile);
+ validate(f, r0, bin, errs, fmt, profiles); 
+ tts.end();
+ }
+ processValidationOutcomes(f, r0, errs);
  }
- processValidationOutcomes(f, r, errs);
  }
  } finally {
  f.finish("validate"); 
@@ -6990,6 +7006,17 @@ private void validate(FetchedFile f, FetchedResource r, List<ValidationMessage>
  }
  }
 
+ private void validate(FetchedFile f, FetchedResource r, List<ValidationMessage> errs, Binary bin, StructureDefinition sd) {
+ long ts = System.currentTimeMillis();
+ List<StructureDefinition> profiles = new ArrayList<StructureDefinition>();
+ profiles.add(sd);
+ validator.validate(r.getElement(), errs, new ByteArrayInputStream(bin.getContent()), FhirFormat.readFromMimeType(bin.getContentType()), profiles);
+ long tf = System.currentTimeMillis();
+ if (tf-ts > validationLogTime && validationLogTime > 0) {
+ reportLongValidation(f, r, tf-ts);
+ }
+ }
+
  private void validate(FetchedFile f, FetchedResource r, List<ValidationMessage> errs, Resource ber) {
  long ts = System.currentTimeMillis();
  validator.validate(r.getElement(), errs, ber, ber.getUserString("profile"));
@@ -7218,6 +7245,10 @@ private void validate(FetchedFile file, FetchedResource r) throws Exception {
  } else if (res.hasUserData("profile")) {
  validate(file, r, errs, res);
  }
+ } else if (r.getResource() != null && r.getResource() instanceof Binary && file.getLogical() != null && context.hasResource(StructureDefinition.class, file.getLogical())) {
+ StructureDefinition sd = context.fetchResource(StructureDefinition.class, file.getLogical());
+ Binary bin = (Binary) r.getResource();
+ validate(file, r, errs, bin, sd); 
  } else if (r.getResource() != null && r.getResource() instanceof Binary && r.getExampleUri() != null) {
  Binary bin = (Binary) r.getResource();
  validate(file, r, errs, bin); 
@@ -7747,7 +7778,8 @@ private Element convertToElement(FetchedResource r, Resource res) throws Excepti
  org.hl7.fhir.r5.formats.JsonParser jp = new org.hl7.fhir.r5.formats.JsonParser();
  jp.compose(bs, res);
  }
- ByteArrayInputStream bi = new ByteArrayInputStream(bs.toByteArray());
+ byte[] cnt = bs.toByteArray();
+ ByteArrayInputStream bi = new ByteArrayInputStream(cnt);
  Element e = new org.hl7.fhir.r5.elementmodel.JsonParser(context).parseSingle(bi, null);
  if (xhtml != null) {
  Element div = e.getNamedChild("text").getNamedChild("div");

diff --git a/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/SpecMapManager.java b/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/SpecMapManager.java
@@ -181,10 +181,23 @@ public String getPath(String url, String def, String rt, String id) throws FHIRE
  if (special != null) {
  switch (special) {
  case Simplifier: return "https://simplifier.net/resolve?scope="+pi.name()+"@"+pi.version()+"&canonical="+url;
- case PhinVads: if (url.startsWith(base)) 
- return "??phinvads??"; 
- else 
- break;
+ case PhinVads: 
+ try {
+ if (url.startsWith(base)) {
+ final String fileName = Utilities.urlTail(url) + "json";
+
+ if ((isValidFilename(fileName) && pi.hasFile("package", fileName))
+ || pi.hasCanonical(url)) {
+ return "phinvads_broken_link.html"; 
+ } else {
+ return null;
+ }
+
+ } else 
+ break;
+ } catch (IOException e) {
+ return null;
+ }
  case Vsac: if (url.contains("cts.nlm.nih.gov")) {
  return url.replace("http://cts.nlm.nih.gov/fhir/ValueSet/", "https://vsac.nlm.nih.gov/valueset/")+"/expansion";
  }

diff --git a/...lisher.core/src/main/java/org/hl7/fhir/igtools/renderers/StructureDefinitionRenderer.java b/...lisher.core/src/main/java/org/hl7/fhir/igtools/renderers/StructureDefinitionRenderer.java
@@ -453,7 +453,7 @@ public String snapshot(String defnFile, Set<String> outputTracker, boolean toTab
  return "";
  else {
  sdr.getContext().setStructureMode(mode);
- return new XhtmlComposer(XhtmlComposer.HTML).compose(sdr.generateTable(defnFile, sd, false, destDir, false, sd.getId(), true, corePath, "", false, false, outputTracker, false, gen, toTabs ? ANCHOR_PREFIX_SNAP : ANCHOR_PREFIX_SNAP));
+ return new XhtmlComposer(XhtmlComposer.HTML).compose(sdr.generateTable(defnFile, sd, false, destDir, false, sd.getId(), true, corePath, "", sd.getKind() == StructureDefinitionKind.LOGICAL, false, outputTracker, false, gen, toTabs ? ANCHOR_PREFIX_SNAP : ANCHOR_PREFIX_SNAP));
  }
  }
 
@@ -466,7 +466,7 @@ public String byKey(String defnFile, Set<String> outputTracker, boolean toTabs,
 
  sdCopy.getSnapshot().setElement(getKeyElements());
  sdr.getContext().setStructureMode(mode);
- org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", false, false, outputTracker, true, gen, toTabs ? ANCHOR_PREFIX_KEY : ANCHOR_PREFIX_SNAP);
+ org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", sd.getKind() == StructureDefinitionKind.LOGICAL, false, outputTracker, true, gen, toTabs ? ANCHOR_PREFIX_KEY : ANCHOR_PREFIX_SNAP);
 
  return composer.compose(table);
  }
@@ -481,7 +481,7 @@ public String byMustSupport(String defnFile, Set<String> outputTracker, boolean
  sdr.getContext().setStructureMode(mode);
 
  sdCopy.getSnapshot().setElement(getMustSupportElements());
- org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", false, false, outputTracker, true, gen, toTabs ? ANCHOR_PREFIX_MS : ANCHOR_PREFIX_SNAP);
+ org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", sd.getKind() == StructureDefinitionKind.LOGICAL, false, outputTracker, true, gen, toTabs ? ANCHOR_PREFIX_MS : ANCHOR_PREFIX_SNAP);
 
  return composer.compose(table);
  }
@@ -524,7 +524,7 @@ public String byKeyElements(String defnFile, Set<String> outputTracker) throws I
  List<ElementDefinition> keyElements = getKeyElements();
 
  sdCopy.getSnapshot().setElement(keyElements);
- org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", false, false, outputTracker, true, gen, ANCHOR_PREFIX_KEY);
+ org.hl7.fhir.utilities.xhtml.XhtmlNode table = sdr.generateTable(defnFile, sdCopy, false, destDir, false, sdCopy.getId(), true, corePath, "", sd.getKind() == StructureDefinitionKind.LOGICAL, false, outputTracker, true, gen, ANCHOR_PREFIX_KEY);
 
  return composer.compose(table);
  }

diff --git a/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/web/PublicationProcess.java b/org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/web/PublicationProcess.java
@@ -48,6 +48,8 @@
 
 public class PublicationProcess {
 
+ private int exitCode = 1;
+
  /*
  * checks that must be run prior to runing this:
  * 
@@ -131,6 +133,7 @@ public void publish(String source, String web, String date, String registrySourc
  e.printStackTrace();
  }
  System.out.println("Full log in "+logger.getFilename());
+ System.exit(exitCode);
  }
 
  private static String removePassword(String[] args, int i) {
@@ -578,6 +581,7 @@ private void doPublish(File fSource, File fOutput, JsonObject qa, String destina
  System.out.println("No!");
  System.out.print("Changes not applied. Finished");
  }
+ exitCode = 0;
  }
 
  private List<String> loadSubPackageList(String path) throws JsonException, IOException {

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
  <version>1.4.9-SNAPSHOT</version> <!-- See the note above -->
 
  <properties>
- <core_version>6.1.8</core_version>
+ <core_version>6.1.9-SNAPSHOT</core_version>
  <maven_surefire_version>3.0.0-M5</maven_surefire_version>
  <apache_poi_version>5.2.1</apache_poi_version>
  <okhttp.version>4.11.0</okhttp.version>