Merge pull request #804 from HL7/2023-11-gg-subscription-topic

2023 11 gg subscription topic
HL7 · Nov 7, 2023 · 62ce77c · 62ce77c
2 parents 6b76011 + b94f953
commit 62ce77c
Show file tree

Hide file tree

Showing 13 changed files with 225 additions and 29 deletions.
diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -1,17 +1,13 @@
-* TxClient: Remove "profile" from tx operations
-* Validator: Validate contextInvariant in extension definitions
-* Validator: Fix Typo in TI WG name
-* Validator: Handle unknown constants properly in FHIRPath
-* Validator: Fix handling of type ancestors at the root of FHIRPath expressions
-* Validator: CDA templates with no extension value use urn:oid: not urn:hl7ii:
-* Validator: Allow URL as a type of string in FHIRPath type checking
-* Validator: Fix semver validation
-* Validator: Fix problem resolving context in CDA invariants
-* Validator: Fix for FHIRPath constant handling
-* Renderer: SQL in FHIR Implementation of ViewDefinitions available as beta
-* Renderer: Fixes to Search Parameter rendering of multiples per FHIR-I decision
-* Renderer: Fix broken links in extension references done by [[[]]]
-* Renderer: Fix broken links in code system rendering of parents
-* Renderer: Support using names in [[[markdown]]] when rendering
-* Renderer: Fix [[[ and ]]] in markdown processing, and allow names
-* Test Cases: Add CDA to test IGs
+* General: Corrected spelling of 'supercedes' to 'supersedes' in IG…
+* Snapshot Generation: Support suppress examples when generating snapshots
+* Validator: Validate Vital signs Profiles when validating observations
+* Validator: Hack around problem with vs-1 constraint in R4
+* Validator: Check for retired status when multiple OID matches exist
+* Validator: Fix for validating extensions on R5 resources in R4 (R4 special case)
+* Validator: Minor fixes for standalone ViewDefinition validator
+* Renderer: Revised Capability Statement rendering (Thanks Vassil Peytchev)
+* Renderer: Fix bug rendering primitive types with an extension that provides a value alternative
+* Renderer: Add clickable links for references when rendering json and xml instances in IG publisher
+* Renderer: Fix bug generating profile spreadsheets
+* Cross-Version: Handle SubscriptionTopic in cross-version analysis
+* Internal QA: track memory during IG tests
diff --git a/...fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/IGKnowledgeProvider.java b/...fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/IGKnowledgeProvider.java
@@ -77,8 +77,9 @@ public class IGKnowledgeProvider implements ProfileKnowledgeProvider, ParserBase
   private Set<String> summaryRows = new HashSet<>();
   private String altCanonical;
   private XVerExtensionManager xver;
+  private List<FetchedFile> files;
 
-  public IGKnowledgeProvider(IWorkerContext context, String pathToSpec, String canonical, JsonObject igs, List<ValidationMessage> errors, boolean noXhtml, Template template, List<String> listedURLExemptions, String altCanonical) throws Exception {
+  public IGKnowledgeProvider(IWorkerContext context, String pathToSpec, String canonical, JsonObject igs, List<ValidationMessage> errors, boolean noXhtml, Template template, List<String> listedURLExemptions, String altCanonical, List<FetchedFile> files) throws Exception {
     super();
     this.context = context;
     this.pathToSpec = pathToSpec;
@@ -90,6 +91,7 @@ public IGKnowledgeProvider(IWorkerContext context, String pathToSpec, String can
     this.template = template;
     this.listedURLExemptions = listedURLExemptions;
     this.altCanonical = altCanonical;
+    this.files = files;
     if (igs != null) {
       loadPaths(igs);
     }
@@ -760,5 +762,30 @@ public Set<String> summaryRows() {
     return summaryRows ;
   }
 
+  @Override
+  public String resolveReference(String ref) {
+    if (ref == null) {
+      return null;
+    }
+    Resource res = context.fetchResource(Resource.class, ref);
+    if (res != null && res.hasWebPath()) {
+      return res.getWebPath();
+    }
+    if (ref.startsWith(canonical)) {
+      ref = Utilities.getRelativeUrlPath(canonical, ref);
+    }
+    String[] p = ref.split("/");
+    if (p.length == 2 && files != null) {
+      for (FetchedFile f : files) {
+        for (FetchedResource r : f.getResources()) {
+          if (p[0].equals(r.fhirType()) && p[1].equals(r.getId())) {
+            return getLinkFor(r, true);
+          }
+        }
+      }
+    }
+    return null;
+  }
+
 
 }
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
@@ -3016,7 +3016,7 @@ else if (vsCache == null) {
       checkTSVersion(vsCache, context.connectToTSServer(TerminologyClientFactory.makeClient("Tx-Server", webTxServer.getAddress(), "fhir/publisher", FhirPublication.fromCode(version)), txLog));
 
     loadPubPack();
-    igpkp = new IGKnowledgeProvider(context, checkAppendSlash(specPath), determineCanonical(sourceIg.getUrl(), "ImplementationGuide.url"), template.config(), errors, VersionUtilities.isR2Ver(version), template, listedURLExemptions, altCanonical);
+    igpkp = new IGKnowledgeProvider(context, checkAppendSlash(specPath), determineCanonical(sourceIg.getUrl(), "ImplementationGuide.url"), template.config(), errors, VersionUtilities.isR2Ver(version), template, listedURLExemptions, altCanonical, fileList);
     if (autoLoad) {
       igpkp.setAutoPath(true);
     }
@@ -3522,7 +3522,7 @@ else if (mode == IGBuildMode.AUTOBUILD)
 
     loadPubPack();
 
-    igpkp = new IGKnowledgeProvider(context, checkAppendSlash(specPath), cb.asString(), configuration, errors, VersionUtilities.isR2Ver(version), null, listedURLExemptions, altCanonical);
+    igpkp = new IGKnowledgeProvider(context, checkAppendSlash(specPath), cb.asString(), configuration, errors, VersionUtilities.isR2Ver(version), null, listedURLExemptions, altCanonical, fileList);
     igpkp.loadSpecPaths(specMaps.get(0));
     fetcher.setPkp(igpkp);
 

diff --git a/...hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/R4ToR4BAnalyser.java b/...hl7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/R4ToR4BAnalyser.java
@@ -11,6 +11,8 @@
 import java.util.Map;
 import java.util.Map.Entry;
 
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
+import org.hl7.fhir.convertors.factory.VersionConvertorFactory_43_50;
 import org.hl7.fhir.exceptions.FHIRException;
 import org.hl7.fhir.igtools.publisher.loaders.PublisherLoader;
 import org.hl7.fhir.r4b.model.Bundle;
@@ -80,7 +82,7 @@ public String present() {
   private static final List<String> R4BOnlyTypes = Collections.unmodifiableList(
       Arrays.asList(new String[] {"CodeableReference", "RatioRange", "NutritionProduct", 
           "AdministrableProductDefinition", "ClinicalUseDefinition", "PackagedProductDefinition", "ManufacturedItemDefinition", "RegulatedAuthorization",
-          "MedicinalProductDefinition", "Ingredient", "SubstanceDefinition", "Citation", "EvidenceReport", "SubscriptionStatus", "SubscriptionTopic"}));
+          "MedicinalProductDefinition", "Ingredient", "SubstanceDefinition", "Citation", "EvidenceReport", "SubscriptionStatus"/*, "SubscriptionTopic"*/}));
 
   private static final List<String> R4OnlyTypes = Collections.unmodifiableList(
       Arrays.asList(new String[] {"MedicinalProduct", "MedicinalProductIngredient", "SubstanceSpecification", "MedicinalProductAuthorization", 
@@ -269,17 +271,40 @@ public boolean canBeR4B() {
 
   public String generate(String pid, boolean inline) {
     if (VersionUtilities.isR4Ver(context.getVersion())) {
-      return gen(pid, "R4", "R4B", r4BOK, r4Problems, r4BProblems, r4Exemptions, r4BExemptions, inline);
+      return gen(pid, "R4", "R4B", r4OK, r4BOK, r4Problems, r4BProblems, r4Exemptions, r4BExemptions, inline);
     } else if (VersionUtilities.isR4BVer(context.getVersion())) {
-      return gen(pid, "R4B", "R4", r4OK, r4BProblems, r4Problems, r4BExemptions, r4Exemptions, inline);
+      return gen(pid, "R4B", "R4", r4BOK, r4OK, r4BProblems, r4Problems, r4BExemptions, r4Exemptions, inline);
     } else {
       return "";
     }
   }
 
-  private String gen(String pid, String src, String dst, boolean dstOk, List<String> srcProblems, List<String> dstProblems, Map<String, ResPointer> srcExempt, Map<String, ResPointer> dstExempt, boolean inline) {
+  private String gen(String pid, String src, String dst, boolean srcOk, boolean dstOk, List<String> srcProblems, List<String> dstProblems, Map<String, ResPointer> srcExempt, Map<String, ResPointer> dstExempt, boolean inline) {
     StringBuilder b = new StringBuilder();
-    if (dstOk) {
+    if (!srcOk) {
+      if (!inline) {
+        b.append("<p>");
+      }
+      b.append("Something went wrong with the cross-version analysis because: \r\n");
+      if (!inline) {
+        b.append("</p>\r\n");
+        b.append("<ul>\r\n");
+      }
+      boolean first = true;
+      for (String s : srcProblems) {
+        if (!inline) {
+          b.append("<li>");
+        }
+        if (first) first = false; else if (inline) b.append(", ");
+        b.append(s);
+        if (!inline) {
+          b.append("</li>\r\n");
+        }
+      }
+      if (!inline) {
+        b.append("</ul>\r\n");
+      }
+    } else if (dstOk) {
       if (!inline) {
         b.append("<p>");
       }
@@ -503,6 +528,11 @@ private void processFileOther(NPMPackageGenerator gen, String folder, String fil
     if (Utilities.existsInList(folder, "package", "example")) {
       if (!Utilities.existsInList(filename, "package.json", ".index.json", ".index.db")) {
         org.hl7.fhir.r4b.model.Resource res = new org.hl7.fhir.r4b.formats.JsonParser().parse(content);
+        if (VersionUtilities.isR4Ver(context.getVersion()) && "Basic".equals(res.fhirType())) {
+          org.hl7.fhir.r4.model.Resource r4 =  new org.hl7.fhir.r4.formats.JsonParser().parse(content);
+          org.hl7.fhir.r5.model.Resource r5 = VersionConvertorFactory_40_50.convertResource(r4);
+          res = VersionConvertorFactory_43_50.convertResource(r5);
+        }
         boolean exempt = (exemptions.containsKey(res.fhirType()+"/"+res.getId()) ||
             ((res instanceof org.hl7.fhir.r4b.model.CanonicalResource) && exemptions.containsKey(((org.hl7.fhir.r4b.model.CanonicalResource) res).getUrl())));
         if (!exempt) {

diff --git a/...isher.core/src/main/java/org/hl7/fhir/igtools/publisher/SuppressedMessageInformation.java b/...isher.core/src/main/java/org/hl7/fhir/igtools/publisher/SuppressedMessageInformation.java
@@ -67,6 +67,10 @@ public int getUseCount() {
     }
 
     public boolean matches(String msg) {
+      return matchesInner(msg) || matchesInner(msg.replace(" (this may not be a problem, but you should check that it's not intended to match a slice)", ""));
+    }
+
+    private boolean matchesInner(String msg) {
       switch (compType) {
        case 0: return msg.equals(messageComp);
        case 1: return msg.startsWith(messageComp);

diff --git a/...ublisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/IpaComparator.java b/...ublisher.core/src/main/java/org/hl7/fhir/igtools/publisher/comparators/IpaComparator.java
@@ -186,7 +186,7 @@ public void startChecks(ImplementationGuide ig) {
           vi.context.setLocale(context.getLocale());
           vi.context.setLogger(context.getLogger());
           vi.context.loadFromPackageAndDependencies(current, new PublisherLoader(current, SpecMapManager.fromPackage(current), current.getWebLocation(), null).makeLoader(), pcm);
-          vi.pkp = new IGKnowledgeProvider(vi.context, current.getWebLocation(), current.canonical(), null, null, false, null, null, null);
+          vi.pkp = new IGKnowledgeProvider(vi.context, current.getWebLocation(), current.canonical(), null, null, false, null, null, null, null);
         } catch (Exception e) {
           vi.errMsg = "Unable to find load package "+pid+"#"+vi.version+" ("+e.getMessage()+" on file "+filename+")";
           e.printStackTrace();

diff --git a/...e/src/main/java/org/hl7/fhir/igtools/publisher/comparators/PreviousVersionComparator.java b/...e/src/main/java/org/hl7/fhir/igtools/publisher/comparators/PreviousVersionComparator.java
@@ -208,7 +208,7 @@ public void startChecks(ImplementationGuide ig) {
           vi.context.setLocale(context.getLocale());
           vi.context.setLogger(context.getLogger());
           vi.context.loadFromPackageAndDependencies(current, new PublisherLoader(current, SpecMapManager.fromPackage(current), current.getWebLocation(), null).makeLoader(), pcm);
-          vi.pkp = new IGKnowledgeProvider(vi.context, current.getWebLocation(), current.canonical(), null, null, false, null, null, null);
+          vi.pkp = new IGKnowledgeProvider(vi.context, current.getWebLocation(), current.canonical(), null, null, false, null, null, null, null);
         } catch (Exception e) {
           vi.errMsg = "Unable to find load package "+pid+"#"+vi.version+" ("+e.getMessage()+" on file "+filename+")";
           e.printStackTrace();

diff --git a/...7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/JsonXhtmlRenderer.java b/...7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/JsonXhtmlRenderer.java
@@ -215,5 +215,10 @@ public void anchor(String name) {
     b.append("<a name=\""+name+"\"></a>");
   }
 
+  @Override
+  public void externalLink(String ref) {
+    b.append("<a href=\""+Utilities.escapeXml(ref)+"\" style=\"color: Maroon\">&#x1F517;</a> ");
+  }
+
 
 }
diff --git a/...l7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/XmlXHtmlRenderer.java b/...l7.fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/renderers/XmlXHtmlRenderer.java
@@ -785,4 +785,18 @@ public void decorate(ElementDecoration decoration) throws IOException {
   @Override
   public void setSchemaLocation(String s, String s1) throws IOException {
   }
+
+
+  @Override
+  public void externalLink(String ref) throws IOException {
+    if (pendingClose) { 
+      b.append("&gt;");
+      writeDecorations();
+      writePendingComment();
+      pendingClose = false;
+    }
+    b.append("<a href=\""+Utilities.escapeXml(ref)+"\" style=\"color: Maroon\">&#x1F517;</a> ");
+  }
+
+
 }
diff --git a/org.hl7.fhir.publisher.core/src/test/java/tests/AllGuidesTests.java b/org.hl7.fhir.publisher.core/src/test/java/tests/AllGuidesTests.java
@@ -46,6 +46,7 @@ private void testIg(String id, String path) throws Exception {
     String version = readVersion();
     File statsFile = determineStatsFile();
     long time = System.currentTimeMillis();
+    long startingMem = getCurrentmem();
 
     System.out.println("=======================================================================================");
     String p = (path == null ? Utilities.path(FhirSettings.getTestIgsPath(), id) : Utilities.path(FhirSettings.getTestIgsPath(), id, path));
@@ -84,7 +85,7 @@ private void testIg(String id, String path) throws Exception {
     si.set("warnings", cWarn);
     si.set("hints", cHint);
     si.set("time", System.currentTimeMillis() - time);
-    si.set("memory", pub.getMaxMemory());
+    si.set("memory", pub.getMaxMemory() - startingMem);
     JsonParser.compose(stats, statsFile, true);
 
     Map<String, Map<String, String>> statsMap = new HashMap<>();
@@ -134,6 +135,15 @@ private void testIg(String id, String path) throws Exception {
     dumpMem(id);
   }
 
+  private long getCurrentmem() {
+
+    Runtime runtime = Runtime.getRuntime();
+    long totalMemory = runtime.totalMemory();
+    long freeMemory = runtime.freeMemory();
+    long usedMemory = totalMemory - freeMemory;
+    return usedMemory;
+  }
+
   private void dumpMem(String id) throws IOException {
     File f = new File(Utilities.path("[tmp]", "memory-dump-"+id+".hprof"));
     f.delete();

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
     <version>1.5.2-SNAPSHOT</version> <!-- See the note above -->
 
     <properties>
-        <core_version>6.2.1</core_version>
+        <core_version>6.2.2-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>

diff --git a/test-statistics.csv b/test-statistics.csv
@@ -3,3 +3,4 @@
 1.4.17,45405,1152,90,,333893,713,576428,510291,688062,20062,77921,292184,255657,49109,182535
 1.5.0,48649,1349,129,128937,254417,1494,385606,446970,760444,42358,73453,185270,225642,59841,200877
 1.5.1,47973,1120,75,108608,331701,595,566979,500812,702868,32185,76394,300885,258990,49734,191994
+1.5.2,65891,1056,80,109119,545761,594,892711,392719,675203,32335,113522,538889,389926,51564,207463
diff --git a/test-statistics.json b/test-statistics.json
@@ -407,5 +407,114 @@
       "time" : 702868,
       "memory" : 5103103688
     }
+  },
+  "1.5.2" : {
+    "sync-date" : "2023-10-28",
+    "date" : "2023-11-07",
+    "hl7.fhir.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 594,
+      "memory" : 9868864
+    },
+    "hl7.cda.uv.core" : {
+      "errors" : 0,
+      "warnings" : 1,
+      "hints" : 2,
+      "time" : 109119,
+      "memory" : 4793043584
+    },
+    "hl7.fhir.us.ecr" : {
+      "errors" : 6,
+      "warnings" : 27,
+      "hints" : 0,
+      "time" : 392719,
+      "memory" : 8445073096
+    },
+    "hl7.fhir.uv.ipa" : {
+      "errors" : 25,
+      "warnings" : 8,
+      "hints" : 32,
+      "time" : 113522,
+      "memory" : 1874596080
+    },
+    "hl7.fhir.uv.ips" : {
+      "errors" : 0,
+      "warnings" : 31,
+      "hints" : 17,
+      "time" : 538889,
+      "memory" : 2607124480
+    },
+    "ihe.mhd.fhir" : {
+      "errors" : 0,
+      "warnings" : 21,
+      "hints" : 21,
+      "time" : 207463,
+      "memory" : 2264503184
+    },
+    "hl7.fhir.uv.sdc" : {
+      "errors" : 125,
+      "warnings" : 38,
+      "hints" : 153,
+      "time" : 389926,
+      "memory" : 2254545928
+    },
+    "hl7.fhir.uv.tools" : {
+      "errors" : 68,
+      "warnings" : 4,
+      "hints" : 3,
+      "time" : 51564,
+      "memory" : 1694438320
+    },
+    "hl7.base.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 80,
+      "memory" : 8390664
+    },
+    "hl7.fhir.uv.howto" : {
+      "errors" : 1,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 32335,
+      "memory" : 1050476360
+    },
+    "fhir.base.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 1056,
+      "memory" : 92963024
+    },
+    "hl7.fhir.au.base" : {
+      "errors" : 10,
+      "warnings" : 187,
+      "hints" : 78,
+      "time" : 545761,
+      "memory" : 4179752904
+    },
+    "example.fhir.uv.myig" : {
+      "errors" : 18,
+      "warnings" : 11,
+      "hints" : 7,
+      "time" : 65891,
+      "memory" : 1492180160
+    },
+    "hl7.fhir.us.core" : {
+      "errors" : 8,
+      "warnings" : 7,
+      "hints" : 211,
+      "time" : 892711,
+      "memory" : 9977895608
+    },
+    "hl7.fhir.uv.extensions" : {
+      "errors" : 126,
+      "warnings" : 92,
+      "hints" : 211,
+      "time" : 675203,
+      "memory" : 7181111928
+    }
   }
 }