Merge pull request #1426 from hapifhir/2023-09-gg-imposes-profile

2023 09 gg imposes profile

org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java

@@ -1,5 +1,8 @@
 package org.hl7.fhir.convertors.analytics;
 
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -42,7 +45,8 @@ public class PackageVisitor {
   private boolean current;
   private IPackageVisitorProcessor processor;
   private FilesystemPackageCacheManager pcm;
-  private PackageClient pc;  
+  private PackageClient pc;
+  private String cache;  
   
   public List<String> getResourceTypes() {
     return resourceTypes;
@@ -76,6 +80,14 @@ public class PackageVisitor {
 
 
 
+  public String getCache() {
+    return cache;
+  }
+
+  public void setCache(String cache) {
+    this.cache = cache;
+  }
+
   public void setCorePackages(boolean corePackages) {
     this.corePackages = corePackages;
   }
@@ -109,6 +121,8 @@ public class PackageVisitor {
     System.out.println("Finding packages");
     pc = new PackageClient(PackageServer.primaryServer());
     pcm = new FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
+  
+    Set<String> pidList = getAllPackages();
     
     Map<String, String> cpidMap = getAllCIPackages();
     Set<String> cpidSet = new HashSet<>();
@@ -118,7 +132,7 @@ public class PackageVisitor {
       processCurrentPackage(s, cpidMap.get(s), cpidSet, i, cpidMap.size()); 
       i++;
     }
-    Set<String> pidList = getAllPackages();
+    
     System.out.println("Go: "+pidList.size()+" published packages");
     i = 0;
     for (String pid : pidList) {    
@@ -161,11 +175,21 @@ public class PackageVisitor {
 
   private void processCurrentPackage(String url, String pid, Set<String> cpidSet, int i, int t) {
     try {
+      long ms1 = System.currentTimeMillis();
       String[] p = url.split("\\/");
       String repo = "https://build.fhir.org/ig/"+p[0]+"/"+p[1];
-      NpmPackage npm = NpmPackage.fromUrl(repo+"/package.tgz");
+      JsonObject manifest = JsonParser.parseObjectFromUrl(repo+"/package.manifest.json");
+      File co = new File(Utilities.path(cache, pid+"."+manifest.asString("date")+".tgz"));
+      if (!co.exists()) {
+        SimpleHTTPClient fetcher = new SimpleHTTPClient();
+        HTTPResult res = fetcher.get(repo+"/package.tgz?nocache=" + System.currentTimeMillis());
+        res.checkThrowException();
+        TextFile.bytesToFile(res.getContent(), co);
+      }
+      NpmPackage npm = NpmPackage.fromPackage(new FileInputStream(co));          
       String fv = npm.fhirVersion();
       cpidSet.add(pid);
+      long ms2 = System.currentTimeMillis();
       
       if (corePackages || !corePackage(npm)) {
         int c = 0;
@@ -182,7 +206,7 @@ public class PackageVisitor {
             }
           }
         }    
-        System.out.println("Processed: "+pid+"#current: "+c+" resources ("+i+" of "+t+")");  
+        System.out.println("Processed: "+pid+"#current: "+c+" resources ("+i+" of "+t+", "+(ms2-ms1)+"/"+(System.currentTimeMillis()-ms2)+"ms)");  
       }
     } catch (Exception e) {      
       System.out.println("Unable to process: "+pid+"#current: "+e.getMessage());      

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java

@@ -2839,10 +2839,11 @@ public class ProfileUtilities extends TranslatingUtilities {
     boolean ok = false;
     CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
     String t = ts.getWorkingCode();
+    String tDesc = ts.toString();
     for (TypeRefComponent td : base.getType()) {;
       boolean matchType = false;
       String tt = td.getWorkingCode();
-      b.append(tt);
+      b.append(td.toString());
       if (td.hasCode() && (tt.equals(t))) {
         matchType = true;
       }
@@ -2869,20 +2870,7 @@ public class ProfileUtilities extends TranslatingUtilities {
           // check that any derived target has a reference chain back to one of the base target profiles
           for (UriType u : ts.getTargetProfile()) {
             String url = u.getValue();
-            boolean tgtOk = !td.hasTargetProfile() || td.hasTargetProfile(url);
+            boolean tgtOk = !td.hasTargetProfile() || sdConformsToTargets(path, derived.getPath(), url, td);            
-            while (url != null && !tgtOk) {
-              StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
-              if (sd == null) {
-                if (messages != null) {
-                  messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, path, "Cannot check whether the target profile " + url + " on "+derived.getPath()+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
-                }
-                url = null;
-                tgtOk = true; // suppress error message
-              } else {
-                url = sd.getBaseDefinition();
-                tgtOk = td.hasTargetProfile(url);
-              }
-            }
             if (tgtOk) {
               ok = true;
             } else {
@@ -2899,11 +2887,34 @@ public class ProfileUtilities extends TranslatingUtilities {
       }
     }
     if (!ok) {
-      throw new DefinitionException(context.formatMessage(I18nConstants.STRUCTUREDEFINITION__AT__ILLEGAL_CONSTRAINED_TYPE__FROM__IN_, purl, derived.getPath(), t, b.toString(), srcSD.getUrl()));
+      throw new DefinitionException(context.formatMessage(I18nConstants.STRUCTUREDEFINITION__AT__ILLEGAL_CONSTRAINED_TYPE__FROM__IN_, purl, derived.getPath(), tDesc, b.toString(), srcSD.getUrl()));
     }
   }
 
 
+  private boolean sdConformsToTargets(String path, String dPath, String url, TypeRefComponent td) {
+    if (td.hasTargetProfile(url)) {
+      return true;
+    }
+    StructureDefinition sd = context.fetchResource(StructureDefinition.class, url);
+    if (sd == null) {
+      if (messages != null) {
+        messages.add(new ValidationMessage(Source.InstanceValidator, IssueType.BUSINESSRULE, path, "Cannot check whether the target profile " + url + " on "+dPath+" is valid constraint on the base because it is not known", IssueSeverity.WARNING));
+      }
+      return true;
+    } else {
+      if (sd.hasBaseDefinition() && sdConformsToTargets(path, dPath, sd.getBaseDefinition(), td)) {
+        return true;
+      }
+      for (Extension ext : sd.getExtensionsByUrl(ToolingExtensions.EXT_SD_IMPOSE_PROFILE)) {
+        if (sdConformsToTargets(path, dPath, ext.getValueCanonicalType().asStringValue(), td)) {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
+
   private void checkTypeOk(ElementDefinition dest, String ft, StructureDefinition sd, String fieldName) {
     boolean ok = false;
     Set<String> types = new HashSet<>();

org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ElementDefinition.java

@@ -2587,7 +2587,7 @@ public boolean hasTarget() {
       res = res + "}";
     }
     if (hasTargetProfile()) {
-      res = res + "->(";
+      res = res + "(";
       boolean first = true;
       for (CanonicalType s : getTargetProfile()) {
         if (first) first = false; else res = res + "|";

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/MarkDownProcessor.java

@@ -42,6 +42,7 @@ import org.commonmark.node.Node;
 import org.commonmark.parser.Parser;
 import org.commonmark.renderer.html.HtmlRenderer;
 
+import com.github.rjeschke.txtmark.Configuration;
 import com.github.rjeschke.txtmark.Processor;
 
 public class MarkDownProcessor {
@@ -65,7 +66,8 @@ public class MarkDownProcessor {
       return "";
     }
     switch (dialect) {
-    case DARING_FIREBALL : return Processor.process(source); 
+    case DARING_FIREBALL : 
+      return Processor.process(source, Configuration.builder().enableSafeMode().enablePanicMode().build()); 
     case COMMON_MARK : return processCommonMark(preProcess(source)); 
     default: throw new Error("Unknown Markdown Dialect: "+dialect.toString()+" at "+context); 
     }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java

@@ -647,6 +647,10 @@ public class Utilities {
     return PathBuilder.getPathBuilder().buildPath(args);
   }
 
+  public static File pathFile(String... args) throws IOException {
+    return new File(PathBuilder.getPathBuilder().buildPath(args));
+  }
+
   public static String path(File f, String... args) throws IOException {
     String[] a = new String[args.length+1];
     a[0] = f.getAbsolutePath();

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/parser/JsonParser.java

@@ -1,6 +1,7 @@
 package org.hl7.fhir.utilities.json.parser;
 
 import java.io.File;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -167,6 +168,12 @@ public class JsonParser {
     compose(element, stream, false);    
   }
   
+  public static void compose(JsonElement element, File file) throws IOException {
+    FileOutputStream fo = new FileOutputStream(file);
+    compose(element, fo, false);
+    fo.close();
+  }
+  
   public static byte[] composeBytes(JsonElement element) {
     return composeBytes(element, false);    
   }
@@ -179,6 +186,12 @@ public class JsonParser {
     byte[] cnt = composeBytes(element, pretty);
     stream.write(cnt);
   }
+  public static void compose(JsonElement element, File file, boolean pretty) throws IOException {
+    byte[] cnt = composeBytes(element, pretty);
+    FileOutputStream fo = new FileOutputStream(file);
+    fo.write(cnt);
+    fo.close();
+  }
 
   public static byte[] composeBytes(JsonElement element, boolean pretty) {
     String s = compose(element, pretty); 

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageList.java

@@ -5,7 +5,9 @@ import java.io.IOException;
 import java.text.ParseException;
 import java.time.Instant;
 import java.util.ArrayList;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.hl7.fhir.utilities.FhirPublication;
 import org.hl7.fhir.utilities.TextFile;
@@ -67,6 +69,10 @@ public class PackageList {
       json.set("date", date);      
     }
 
+    public String name() {
+      return json.asString("name");
+    }
+    
     public List<String> subPackages() {
       List<String> list = new ArrayList<>();
       if (json.has("sub-packages")) {
@@ -169,6 +175,7 @@ public class PackageList {
       }
       setDate(date);
     }
+
   }
   
   private String source;
@@ -334,5 +341,15 @@ public class PackageList {
     return json.asString("introduction");
   }
 
+  public List<PackageListEntry> milestones() {
+    List<PackageListEntry> list = new ArrayList<>();
+    for (PackageListEntry t : versions) {
+      if (t.name() != null) {
+        list.add(t);
+      }
+    }
+    return list;
+  }
+
 
 }

org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlParser.java

@@ -47,6 +47,7 @@ import java.util.Set;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.exceptions.FHIRFormatError;
 import org.hl7.fhir.utilities.StringPair;
+import org.hl7.fhir.utilities.TextFile;
 import org.hl7.fhir.utilities.Utilities;
 import org.hl7.fhir.utilities.i18n.I18nConstants;
 import org.hl7.fhir.utilities.xhtml.XhtmlNode.Location;
@@ -59,6 +60,7 @@ import org.xmlpull.v1.XmlPullParserException;
 public class XhtmlParser {
   public static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
   private static final char END_OF_CHARS = (char) -1;
+  private static final boolean DEBUG = false;
 
   public class NamespaceNormalizationMap {
 
@@ -1285,7 +1287,14 @@ public class XhtmlParser {
 
   public XhtmlNode parseFragment(String source) throws IOException, FHIRException  {
     rdr = new StringReader(source);
-    return parseFragment();
+    try {
+      return parseFragment();
+    } catch (Exception e) {
+      if (DEBUG) {
+        TextFile.stringToFile(source, Utilities.path("[tmp]", "html-fail.xhtml"));
+      }
+      throw e;
+    }
   }
 
   public XhtmlNode parseFragment(InputStream input) throws IOException, FHIRException  {