Merge pull request #870 from HL7/2024-03-gg-auto-oid-root

2024 03 gg auto oid root

RELEASE_NOTES.md

@@ -0,0 +1,9 @@
+* Loader: Add support for auto-oid-root
+* Cross-Version Module: Further development
+* Validator: CodeSystem property validation improvements
+* Validator: More valueset validation improvements after real world testing
+* Validator: Fix processing of NotSelectable filters using in | not-in
+* Validator: Fix wrong collection type checking FHIRPath subsetOf parameter type
+* Generator: Put jurisdiction in NPM package file
+* Renderer: Rendering improvements for xver IG
+* Renderer: improved markdown support for [[[type.path]]]

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/Publisher.java

@@ -939,6 +939,8 @@ public void setNoSushi(boolean noSushi) {
   private List<String> viewDefinitions = new ArrayList<>();
   private int validationLogTime = 0;
   private long maxMemory = 0;
+  private String oidRoot;
+  private IniFile oidIni;
 
   long last = System.currentTimeMillis();
   private List<String> unknownParams = new ArrayList<>();
@@ -2945,7 +2947,25 @@ else if (p.getValue().equals("show-reference-messages"))
           fetcher.setReport(true);
         }
         break;
-      default: 
+      case "auto-oid-root":
+        oidRoot = p.getValue(); 
+        if (!Utilities.isValidOID(oidRoot)) {
+          throw new Error("Invalid oid found in assign-missing-oids-root: "+oidRoot);
+        }
+        oidIni = new IniFile(Utilities.path(Utilities.getDirectoryForFile(igName), "oids.ini"));
+        if (!oidIni.hasSection("Documentation")) {
+          oidIni.setStringProperty("Documentation", "information1", "This file stores the OID assignments for resources defined in this IG.", null);
+          oidIni.setStringProperty("Documentation", "information2", "It must be added to git and committed when resources are added or their id is changed", null);
+          oidIni.setStringProperty("Documentation", "information3", "You should not generally need to edit this file, but if you do:", null);
+          oidIni.setStringProperty("Documentation", "information4", " (a) you can change the id of a resource (left side) if you change it's actual id in your source, to maintain OID consistency", null);
+          oidIni.setStringProperty("Documentation", "information5", " (b) you can change the oid of the resource to an OID you assign manually. If you really know what you're doing with OIDs", null);
+          oidIni.setStringProperty("Documentation", "information6", "There is never a reason to edit anything else", null);
+          oidIni.save();
+        }
+        if (!hasOid(sourceIg.getIdentifier())) {
+          sourceIg.getIdentifier().add(new Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oidRoot));
+        }
+        default: 
         if (!template.isParameter(pc)) {
           unknownParams.add(pc+"="+p.getValue());
         }
@@ -4409,6 +4429,7 @@ private boolean load() throws Exception {
     rc.setParser(getTypeLoader(version));
     rc.addLink(KnownLinkType.SELF, targetOutput);
     rc.setFixedFormat(fixedFormat);
+    module.defineTypeMap(rc.getTypeMap());
     if (publishedIg.hasJurisdiction()) {
       Locale locale = null;
       try {
@@ -6266,6 +6287,11 @@ private void load(String type) throws Exception {
               if (new AdjunctFileLoader(binaryPaths, cql).replaceAttachments2(f, r)) {
                 altered = true;
               }
+              if (oidRoot != null && !hasOid(bc.getIdentifier())) {
+                String oid = getOid(r.fhirType(), bc.getIdBase());
+                bc.getIdentifier().add(new Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:"+oid));
+                altered = true;
+              }
               if (altered) {
                 if (Utilities.existsInList(r.fhirType(), "GraphDefinition")) {
                   f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.PROCESSING, bc.fhirType()+".where(url = '"+bc.getUrl()+"')", 
@@ -6315,6 +6341,75 @@ private void load(String type) throws Exception {
     }
   }
 
+  private String getOid(String type, String id) {
+    String ot = oidNodeForType(type);
+    String oid = oidIni.getStringProperty(type, id);
+    if (oid != null) {
+      return oid;
+    }
+    Integer keyR = oidIni.getIntegerProperty("Key", type);
+    int key = keyR == null ? 0 : keyR.intValue();
+    key++;
+    oid = oidRoot+"."+ot+"."+key;
+    oidIni.setIntegerProperty("Key", type, key, null);
+    oidIni.setStringProperty(type, id, oid, null);
+    oidIni.save();
+    return oid;
+  }
+
+  private String oidNodeForType(String type) {
+    switch (type) {
+    case "ActivityDefinition" : return "11";
+    case "ActorDefinition" : return "12";
+    case "CapabilityStatement" : return "13";
+    case "ChargeItemDefinition" : return "14";
+    case "Citation" : return "15";
+    case "CodeSystem" : return "16";
+    case "CompartmentDefinition" : return "17";
+    case "ConceptMap" : return "18";
+    case "ConditionDefinition" : return "19";
+    case "EffectEvidenceSynthesis" : return "20";
+    case "EventDefinition" : return "21";
+    case "Evidence" : return "22";
+    case "EvidenceReport" : return "23";
+    case "EvidenceVariable" : return "24";
+    case "ExampleScenario" : return "25";
+    case "GraphDefinition" : return "26";
+    case "ImplementationGuide" : return "27";
+    case "Library" : return "28";
+    case "Measure" : return "29";
+    case "MessageDefinition" : return "30";
+    case "NamingSystem" : return "31";
+    case "ObservationDefinition" : return "32";
+    case "OperationDefinition" : return "33";
+    case "PlanDefinition" : return "34";
+    case "Questionnaire" : return "35";
+    case "Requirements" : return "36";
+    case "ResearchDefinition" : return "37";
+    case "ResearchElementDefinition" : return "38";
+    case "RiskEvidenceSynthesis" : return "39";
+    case "SearchParameter" : return "40";
+    case "SpecimenDefinition" : return "41";
+    case "StructureDefinition" : return "42";
+    case "StructureMap" : return "43";
+    case "SubscriptionTopic" : return "44";
+    case "TerminologyCapabilities" : return "45";
+    case "TestPlan" : return "46";
+    case "TestScript" : return "47";
+    case "ValueSet" : return "48";
+    default: return "10";
+    }
+  }
+
+  private boolean hasOid(List<Identifier> identifiers) {
+    for (Identifier id : identifiers) {
+      if ("urn:ietf:rfc:3986".equals(id.getSystem()) && id.hasValue() && id.getValue().startsWith("urn:oid:")) {
+        return true;
+      }
+    }
+    return false;
+  }
+
   private boolean canonicalUrlIsOk(CanonicalResource bc) {
     if (bc.getUrl().equals(Utilities.pathURL(igpkp.getCanonical(), bc.fhirType(), bc.getId()))) {
       return true;
@@ -6869,19 +6964,57 @@ private void checkURLsUnique() {
   }
 
   private void checkOIDsUnique() {
+    if (oidRoot != null) {
+      try {
+        JsonObject json = org.hl7.fhir.utilities.json.parser.JsonParser.parseObjectFromUrl("https://raw.githubusercontent.com/FHIR/ig-registry/master/oid-assignments.json");
+        JsonObject assignments = json.getJsonObject("assignments");
+        String ig = null;
+        String oid = null;
+        if (assignments.has(oidRoot)) {
+          ig = assignments.getJsonObject(oidRoot).asString("id");
+        }
+        for (JsonProperty p : assignments.getProperties()) {
+          if (p.getValue().isJsonObject() && sourceIg.getPackageId().equals(p.getValue().asJsonObject().asString("id"))) {
+            oid = p.getName();
+          }
+        }
+        if (oid == null && ig == null) {
+          errors.add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "ImplementationGuide", "The assigned auto-oid-root value '"+oidRoot+"' is not registered in https://github.com/FHIR/ig-registry/blob/master/oid-assignments.json so isn't known to be valid", IssueSeverity.WARNING));          
+        } else if (oid != null && !oid.equals(oidRoot)) {
+          throw new FHIRException("The assigned auto-oid-root value '"+oidRoot+"' does not match the value of '"+oidRoot+"' registered in https://github.com/FHIR/ig-registry/blob/master/oid-assignments.json so cannot proceed");                    
+        } else if (ig != null && !ig.equals(sourceIg.getPackageId())) {
+          throw new FHIRException("The assigned auto-oid-root value '"+oidRoot+"' is already registered to the IG '"+ig+"' in https://github.com/FHIR/ig-registry/blob/master/oid-assignments.json so cannot proceed");                    
+        }
+      } catch (Exception e) {
+        errors.add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "ImplementationGuide", "Unable to check auto-oid-root because "+e.getMessage(), IssueSeverity.INFORMATION));
+      }
+    }
+    String oidHint = " (OIDs are easy to assign - see https://build.fhir.org/ig/FHIR/fhir-tools-ig/CodeSystem-ig-parameters.html#ig-parameters-auto-oid-root)";
     Map<String, FetchedResource> oidMap = new HashMap<>();
     for (FetchedFile f : fileList) {
       for (FetchedResource r : f.getResources()) {
         if (r.getResource() != null && r.getResource() instanceof CanonicalResource) {
           List<String> oids = loadOids(((CanonicalResource) r.getResource())); 
-          for (String oid : oids) {
-            if (oidMap.containsKey(oid)) {
-              FetchedResource rs = oidMap.get(oid);
-              FetchedFile fs = findFileForResource(rs);
-              f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "The OID '"+oid+"' has already been used by "+rs.getId()+" in "+fs.getName(), IssueSeverity.ERROR));
-              fs.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "The OID '"+oid+"' is also used by "+r.getId()+" in "+f.getName(), IssueSeverity.ERROR));
+          if (oids.isEmpty()) {
+            if (Utilities.existsInList(r.getResource().fhirType(), "CodeSystem", "ValueSet")) {
+              if (forHL7orFHIR()) {
+                f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "This resource must have an OID assigned to cater for possible e.g. CDA usage"+oidHint, IssueSeverity.ERROR));
+              } else {
+                f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "This resource should have an OID assigned to cater for possible e.g. CDA usage"+oidHint, IssueSeverity.WARNING));                
+              }
             } else {
-              oidMap.put(oid, r);
+              f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "This resource could usefully have an OID assigned"+oidHint, IssueSeverity.INFORMATION));
+            }
+          } else {
+            for (String oid : oids) {
+              if (oidMap.containsKey(oid)) {
+                FetchedResource rs = oidMap.get(oid);
+                FetchedFile fs = findFileForResource(rs);
+                f.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "The OID '"+oid+"' has already been used by "+rs.getId()+" in "+fs.getName(), IssueSeverity.ERROR));
+                fs.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.BUSINESSRULE, "Resource", "The OID '"+oid+"' is also used by "+r.getId()+" in "+f.getName(), IssueSeverity.ERROR));
+              } else {
+                oidMap.put(oid, r);
+              }
             }
           }
         }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/CrossVersionModule.java

@@ -18,7 +18,6 @@
 import org.hl7.fhir.igtools.publisher.modules.xver.ElementDefinitionLink;
 import org.hl7.fhir.igtools.publisher.modules.xver.ElementDefinitionPair;
 import org.hl7.fhir.igtools.publisher.modules.xver.SourcedElementDefinition;
-import org.hl7.fhir.igtools.publisher.modules.xver.SourcedElementDefinitionSorter;
 import org.hl7.fhir.igtools.publisher.modules.xver.StructureDefinitionColumn;
 import org.hl7.fhir.igtools.publisher.modules.xver.XVerAnalysisEngine;
 import org.hl7.fhir.igtools.publisher.modules.xver.XVerAnalysisEngine.MakeLinkMode;
@@ -32,10 +31,10 @@
 import org.hl7.fhir.r5.model.CodeSystem;
 import org.hl7.fhir.r5.model.ConceptMap;
 import org.hl7.fhir.r5.model.ElementDefinition;
-import org.hl7.fhir.r5.model.Extension;
-import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
 import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
+import org.hl7.fhir.r5.model.Extension;
+import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionContextComponent;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
 import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
@@ -48,11 +47,11 @@
 import org.hl7.fhir.r5.utils.ToolingExtensions;
 import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
 import org.hl7.fhir.utilities.MarkDownProcessor;
+import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
 import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.VersionUtilities;
 import org.hl7.fhir.utilities.ZipGenerator;
-import org.hl7.fhir.utilities.MarkDownProcessor.Dialect;
 import org.hl7.fhir.utilities.xhtml.NodeType;
 import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@@ -102,15 +101,16 @@ public boolean preProcess(String path) {
         }
 
         engine.logProgress("Generating extensions");
+        Utilities.createDirectory(Utilities.path(path, "temp", "xver", "extensions"));
         for (StructureDefinition sd : engine.getExtensions()) {
-          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "input", "extensions", "StructureDefinition-"+sd.getId()+".json")), sd);
+          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "temp", "xver", "extensions", "StructureDefinition-"+sd.getId()+".json")), sd);
           genExtensionPage(path, sd);
         }  
         for (ValueSet vs : engine.getNewValueSets().values()) {
-          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "input", "extensions", "ValueSet-"+vs.getId()+".json")), vs);
+          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "temp", "xver", "extensions", "ValueSet-"+vs.getId()+".json")), vs);
         }
         for (CodeSystem cs : engine.getNewCodeSystems().values()) {
-          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "input", "extensions", "CodeSystem-"+cs.getId()+".json")), cs);
+          new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(path, "temp", "xver", "extensions", "CodeSystem-"+cs.getId()+".json")), cs);
         }
         genSummaryPages(path);
         genZips(path);
@@ -161,6 +161,10 @@ private void cleanup(String path) throws IOException {
   }
 
   private void genExtensionPage(String path, StructureDefinition sd) throws IOException {
+    String fn = Utilities.path(path, "temp", "xver-qa", "StructureDefinition-"+sd.getId()+".html");
+    if (new File(fn).exists()) {
+      throw new FHIRException("Duplicate id: "+sd.getId());
+    }
     XhtmlNode body = new XhtmlNode(NodeType.Element, "div");  
     body.h1().tx(sd.getTitle());
     var tbl = body.table("grid");
@@ -200,7 +204,7 @@ private void genExtensionPage(String path, StructureDefinition sd) throws IOExce
     body.hr();
 
     body.pre().tx(new JsonParser().setOutputStyle(OutputStyle.PRETTY).composeString(sd));
-    TextFile.stringToFile(new XhtmlComposer(false, false).compose(wrapPage(body, sd.getName())), Utilities.path(path, "temp", "xver-qa", "StructureDefinition-"+sd.getId()+".html"));
+    TextFile.stringToFile(new XhtmlComposer(false, false).compose(wrapPage(body, sd.getName())), fn);
   }
 
   private void renderVersionRange(XhtmlNode x, Extension ext) {
@@ -713,4 +717,10 @@ public boolean prependLinks() {
   public String getLinkForUrl(String corePath, String s) {
     throw new NotImplementedError();
   }
+
+  @Override
+  public void defineTypeMap(Map<String, String> typeMap) {
+    typeMap.putAll(engine.getTypeMap());
+
+  }
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/IPublisherModule.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.igtools.publisher.modules;
 
+import java.util.Map;
+
 // modules are triggered from ig.ini 
 public interface IPublisherModule {
 
@@ -17,4 +19,7 @@ public interface IPublisherModule {
   // should be documented clearly in the console output
   // all the actions will be taken on the files in the path (which is the root of the IG that contains ig.ini)
   public boolean preProcess(String path);
+
+  // if the module lnows of type aliases, define them for the rendering system
+  public void defineTypeMap(Map<String, String> typeMap);
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/NullModule.java

@@ -1,5 +1,7 @@
 package org.hl7.fhir.igtools.publisher.modules;
 
+import java.util.Map;
+
 public class NullModule implements IPublisherModule {
 
   public boolean preProcess(String path) {
@@ -22,4 +24,10 @@ public boolean useRoutine(String name) {
     return false;
   }
 
+  @Override
+  public void defineTypeMap(Map<String, String> typeMap) {
+    // TODO Auto-generated method stub
+
+  }
+
 }

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/xver/SourcedElementDefinition.java

@@ -4,7 +4,6 @@
 import java.util.HashSet;
 import java.util.Set;
 
-import org.hl7.fhir.igtools.publisher.modules.xver.SourcedElementDefinition.ElementValidState;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ElementDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition;
@@ -13,7 +12,7 @@
 
 public class SourcedElementDefinition {
   public enum ElementValidState {
-    FULL_VALID, CARDINALITY, NEW_TYPES, NEW_TARGETS, NOT_VALID, CODES
+    FULL_VALID, CARDINALITY, NEW_TYPES, NEW_TARGETS, NOT_VALID, CODES, REMOVED_TYPES, PARENT
   }
 
   private StructureDefinition sd;
@@ -51,7 +50,11 @@ public ElementDefinition getEd() {
   }
 
   public String getStatusReason() {
-    return statusReasons.length() == 0 ? "No Change" : statusReasons.toString();
+    if (statusReasons.length() == 0) {
+      return validState == ElementValidState.FULL_VALID ? "Made up reason" : "No Change"; 
+    } else {
+      return statusReasons.toString();
+    }
   }
 
   void addStatusReason(String statusReason) {

org.hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/modules/xver/VSPair.java

@@ -2,11 +2,9 @@
 
 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.model.CodeSystem;
 import org.hl7.fhir.r5.model.Coding;
 import org.hl7.fhir.r5.model.ValueSet;