Merge pull request #934 from HL7/2024-08-gg-updates

2024 08 gg updates
HL7 · Aug 4, 2024 · 70ee556 · 70ee556
2 parents a9a0bfc + d1c7d7c
commit 70ee556
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Showing 8 changed files with 174 additions and 19 deletions.
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
@@ -688,7 +688,7 @@ private NodeChangeType checkLinks(LoadedFile lf, String s, String path, XhtmlNod
     if (nSelfChanged) {
       XhtmlNode a = new XhtmlNode(NodeType.Element);
       a.setName("a").setAttribute("name", nuid).addText("\u200B");
-      x.getChildNodes().add(0, a);
+      x.addChildNode(0, a);
     } 
     if (changed)
       return NodeChangeType.SELF;

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
@@ -1006,6 +1006,8 @@ public String getRelativePath() {
   }
 
   public void execute() throws Exception {
+    XhtmlNode.setCheckParaGeneral(true);
+
     tt = new TimeTracker();
     initialize();
     if (isBuildingTemplate) {
@@ -2123,7 +2125,7 @@ private void generateNarratives() throws Exception {
                 boolean regen = false;
                 for (Locale lang : langs) {
                 boolean first = true;
-                  RenderingContext lrc = rc.copy().setDefinitionsTarget(igpkp.getDefinitionsName(r));
+                  RenderingContext lrc = rc.copy(false).setDefinitionsTarget(igpkp.getDefinitionsName(r));
                   lrc.setLocale(lang);
                   lrc.setRules(GenerationRules.VALID_RESOURCE);
                   lrc.setDefinitionsTarget(igpkp.getDefinitionsName(r));
@@ -2151,7 +2153,8 @@ private void generateNarratives() throws Exception {
               } else {
                 boolean first = true;
                 for (Locale lang : langs) {
-                  RenderingContext lrc = rc.copy().setParser(getTypeLoader(f,r));
+                  RenderingContext lrc = rc.copy(false).setParser(getTypeLoader(f,r));
+                  lrc.clearAnchors();
                   lrc.setLocale(lang);
                   lrc.setRules(GenerationRules.VALID_RESOURCE);
                   lrc.setSecondaryLang(!first);
@@ -4373,7 +4376,7 @@ private boolean load() throws Exception {
         throw new Error("The version "+publishedIg.getVersion()+" is not a valid semantic version so cannot be published in the ci-build");
       } else {
         log("The version "+publishedIg.getVersion()+" is not a valid semantic version so cannot be published in the ci-build");
-        igf.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, "ImplementationGuide.version", "The version "+publishedIg.getVersion()+" is not a valid semantic version and will not be acceptible to the ci-build", IssueSeverity.ERROR));
+        igf.getErrors().add(new ValidationMessage(Source.Publisher, IssueType.EXCEPTION, "ImplementationGuide.version", "The version "+publishedIg.getVersion()+" is not a valid semantic version and will not be acceptible to the ci-build, nor will it be a valid vesion in the NPM package system", IssueSeverity.WARNING));
       }
     }
     String id = npmName;
@@ -8608,7 +8611,7 @@ private void generateSummaryOutputs(DBBuilder db) throws Exception {
 
     generateCanonicalSummary();
 
-    CrossViewRenderer cvr = new CrossViewRenderer(igpkp.getCanonical(), altCanonical, context, igpkp.specPath(), rc.copy());
+    CrossViewRenderer cvr = new CrossViewRenderer(igpkp.getCanonical(), altCanonical, context, igpkp.specPath(), rc.copy(false));
     for (FetchedFile f : fileList) {
       for (FetchedResource r : f.getResources()) {
         if (r.getResource() != null && r.getResource() instanceof CanonicalResource) {
@@ -11403,7 +11406,7 @@ private void saveDirectResourceOutputs(FetchedFile f, FetchedResource r, Resourc
       long start = System.currentTimeMillis();
       XhtmlNode xhtml = getXhtml(f, r);
       if (xhtml == null && HistoryGenerator.allEntriesAreHistoryProvenance(r.getElement())) {
-        RenderingContext ctxt = rc.copy().setParser(getTypeLoader(f, r));
+        RenderingContext ctxt = rc.copy(false).setParser(getTypeLoader(f, r));
         List<ProvenanceDetails> entries = loadProvenanceForBundle(igpkp.getLinkFor(r, true), r.getElement(), f);
         xhtml = new HistoryGenerator(ctxt).generateForBundle(entries); 
         fragment(r.fhirType()+"-"+r.getId()+"-html", new XhtmlComposer(XhtmlComposer.XML).compose(xhtml), f.getOutputNames(), r, vars, null, start, "html", "Resource");
@@ -11432,7 +11435,7 @@ private void saveDirectResourceOutputs(FetchedFile f, FetchedResource r, Resourc
         fragment(r.fhirType()+"-"+r.getId()+"-html", html, f.getOutputNames(), r, vars, null, start, "html", "Resource");
       } else {
         if (xhtml == null) {
-          RenderingContext lrc = rc.copy();
+          RenderingContext lrc = rc.copy(false);
           if (r.getResource() != null && r.getResource() instanceof DomainResource) {
             xhtml = RendererFactory.factory(r.fhirType(), lrc).buildNarrative(ResourceWrapper.forResource(lrc, r.getResource()));
           } else {
@@ -11499,7 +11502,7 @@ private String saveDirectResourceOutputsContained(FetchedFile f, FetchedResource
       long start = System.currentTimeMillis();
       XhtmlNode xhtml = getXhtml(f, r, res);
       if (xhtml == null && HistoryGenerator.allEntriesAreHistoryProvenance(r.getElement())) {
-        RenderingContext ctxt = rc.copy().setParser(getTypeLoader(f, r));
+        RenderingContext ctxt = rc.copy(false).setParser(getTypeLoader(f, r));
         List<ProvenanceDetails> entries = loadProvenanceForBundle(igpkp.getLinkFor(r, true), r.getElement(), f);
         xhtml = new HistoryGenerator(ctxt).generateForBundle(entries); 
         fragment(res.fhirType()+"-"+prefixForContained+res.getId()+"-html", new XhtmlComposer(XhtmlComposer.XML).compose(xhtml), f.getOutputNames(), r, vars, prefixForContained, start, "html", "Resource");
@@ -12247,7 +12250,7 @@ private void generateOutputsLibrary(FetchedFile f, FetchedResource r, Library li
   }
 
   private void generateOutputsExampleScenario(FetchedFile f, FetchedResource r, ExampleScenario scen, Map<String,String> vars, String prefixForContainer) throws Exception {
-    ExampleScenarioRenderer er = new ExampleScenarioRenderer(context, checkAppendSlash(specPath), scen, Utilities.path(tempDir), igpkp, specMaps, pageTargets(), markdownEngine, packge, rc.copy().setDefinitionsTarget(igpkp.getDefinitionsName(r)), versionToAnnotate);
+    ExampleScenarioRenderer er = new ExampleScenarioRenderer(context, checkAppendSlash(specPath), scen, Utilities.path(tempDir), igpkp, specMaps, pageTargets(), markdownEngine, packge, rc.copy(false).setDefinitionsTarget(igpkp.getDefinitionsName(r)), versionToAnnotate);
     if (igpkp.wantGen(r, "actor-table")) {
       long start = System.currentTimeMillis();
       fragment("ExampleScenario-"+prefixForContainer+scen.getId()+"-actor-table", er.render(ExampleScenarioRendererMode.ACTORS), f.getOutputNames(), r, vars, null, start, "actor-table", "ExampleScenario");
@@ -12267,7 +12270,7 @@ private void generateOutputsExampleScenario(FetchedFile f, FetchedResource r, Ex
   }
 
   private void generateOutputsQuestionnaire(FetchedFile f, FetchedResource r, Questionnaire q, Map<String,String> vars, String prefixForContainer) throws Exception {
-    QuestionnaireRenderer qr = new QuestionnaireRenderer(context, checkAppendSlash(specPath), q, Utilities.path(tempDir), igpkp, specMaps, pageTargets(), markdownEngine, packge, rc.copy().setDefinitionsTarget(igpkp.getDefinitionsName(r)), versionToAnnotate);
+    QuestionnaireRenderer qr = new QuestionnaireRenderer(context, checkAppendSlash(specPath), q, Utilities.path(tempDir), igpkp, specMaps, pageTargets(), markdownEngine, packge, rc.copy(false).setDefinitionsTarget(igpkp.getDefinitionsName(r)), versionToAnnotate);
     if (igpkp.wantGen(r, "summary")) {
       long start = System.currentTimeMillis();
       fragment("Questionnaire-"+prefixForContainer+q.getId()+"-summary", qr.summaryTable(r, igpkp.wantGen(r, "xml"), igpkp.wantGen(r, "json"), igpkp.wantGen(r, "ttl"), igpkp.summaryRows()), f.getOutputNames(), r, vars, null, start, "summary", "Questionnaire");
@@ -12330,7 +12333,7 @@ private String responsesForQuestionnaire(Questionnaire q) {
   }
 
   private void generateOutputsQuestionnaireResponse(FetchedFile f, FetchedResource r, Map<String,String> vars, String prefixForContainer) throws Exception {
-    RenderingContext lrc = rc.copy().setParser(getTypeLoader(f, r));
+    RenderingContext lrc = rc.copy(false).setParser(getTypeLoader(f, r));
     String qu = getQuestionnaireURL(r);
     if (qu != null) {
       Questionnaire q = context.fetchResource(Questionnaire.class, qu);
@@ -12387,7 +12390,7 @@ private XhtmlNode getXhtml(FetchedFile f, FetchedResource r) throws Exception {
       //        return new BundleRenderer(lrc).render(ResourceElement.forResource(lrc, r.getElement()));
       //      }
       if (r.getResource() != null && r.getResource() instanceof Bundle) {
-        RenderingContext lrc = rc.copy().setParser(getTypeLoader(f, r));
+        RenderingContext lrc = rc.copy(false).setParser(getTypeLoader(f, r));
         Bundle b = (Bundle) r.getResource();
         BundleRenderer br = new BundleRenderer(lrc);
         if (br.canRender(b)) {
@@ -12405,7 +12408,7 @@ private XhtmlNode getXhtml(FetchedFile f, FetchedResource r) throws Exception {
       return new ParametersRenderer(rc).buildNarrative(ResourceWrapper.forResource(rc, p));
     }
     if (r.fhirType().equals("Parameters")) {
-      RenderingContext lrc = rc.copy().setParser(getTypeLoader(f, r));
+      RenderingContext lrc = rc.copy(false).setParser(getTypeLoader(f, r));
       return new ParametersRenderer(lrc).buildNarrative(ResourceWrapper.forResource(lrc, r.getElement()));
     } else {
       return getHtmlForResource(r.getElement());
@@ -12426,7 +12429,7 @@ private XhtmlNode getXhtml(FetchedFile f, FetchedResource r, Resource resource)
       Parameters p = (Parameters) resource;
       return new ParametersRenderer(rc).buildNarrative(ResourceWrapper.forResource(rc, p));
     }
-    RenderingContext lrc = rc.copy().setParser(getTypeLoader(f, r));
+    RenderingContext lrc = rc.copy(false).setParser(getTypeLoader(f, r));
     return RendererFactory.factory(resource, lrc).buildNarrative(ResourceWrapper.forResource(rc, resource));
   }
 

diff --git a/...fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/PackagePacker.java b/...fhir.publisher.core/src/main/java/org/hl7/fhir/igtools/publisher/utils/PackagePacker.java
@@ -0,0 +1,25 @@
+package org.hl7.fhir.igtools.publisher.utils;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+
+import org.hl7.fhir.utilities.Utilities;
+import org.hl7.fhir.utilities.npm.NpmPackage;
+
+public class PackagePacker {
+
+  public static void main(String[] args) throws FileNotFoundException, IOException {
+   new PackagePacker().process("/Users/grahamegrieve/web/hl7.org/fhir/extensions/5.1.0-snapshot1/package-new");
+  }
+
+  private void process(String path) throws IOException {
+
+    System.out.println("Build Package");
+    NpmPackage npm = NpmPackage.fromFolder(path);
+    npm.loadAllFiles();
+    npm.save(new FileOutputStream("/Users/grahamegrieve/web/hl7.org/fhir/extensions/5.1.0-snapshot1/package.tgz"));
+
+  }
+}
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
@@ -44,6 +44,7 @@
 import org.hl7.fhir.r5.model.PackageInformation;
 import org.hl7.fhir.r5.model.PrimitiveType;
 import org.hl7.fhir.r5.model.Quantity;
+import org.hl7.fhir.r5.model.SearchParameter;
 import org.hl7.fhir.r5.model.StringType;
 import org.hl7.fhir.r5.model.StructureDefinition;
 import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionContextComponent;
@@ -2031,6 +2032,7 @@ public String references() throws FHIRFormatError, IOException {
     Map<String, String> refs = new HashMap<>();
     Map<String, String> trefs = new HashMap<>();
     Map<String, String> examples = new HashMap<>();
+    Map<String, String> searches = new HashMap<>();
     for (StructureDefinition sdt : context.fetchResourcesByType(StructureDefinition.class)) {
       if (refersToThisSD(sdt.getBaseDefinition())) {
         base.put(sdt.getWebPath(), sdt.present());
@@ -2084,6 +2086,13 @@ public String references() throws FHIRFormatError, IOException {
     for (FetchedFile f : files) {
       for (FetchedResource r : f.getResources()) {
         if (!r.fhirType().equals("ImplementationGuide")) {
+          if (r.fhirType().equals("SearchParameter")) {
+            SearchParameter sp = (SearchParameter) r.getResource();
+            String exp = sp.getExpression();
+            if (exp.contains("extension('"+sd.getUrl()+"')")) {
+              searches.put(igp.getLinkFor(r, true), r.getTitle());
+            }
+          }
           if (usesSD(r.getElement())) {
             String p = igp.getLinkFor(r, true);
             if (p != null) {
@@ -2123,12 +2132,18 @@ public String references() throws FHIRFormatError, IOException {
     if (!compliedWith.isEmpty()) {
       b.append(" <li>Comply with this profile " + type + ": " + refList(compliedWith, "compliedWith") + "</li>\r\n");
     }
-    if (!refs.isEmpty())
+    if (!refs.isEmpty()) {
       b.append(" <li>Use this " + type + ": " + refList(refs, "ref") + "</li>\r\n");
-    if (!trefs.isEmpty())
+    }
+    if (!trefs.isEmpty()) {
       b.append(" <li>Refer to this " + type + ": " + refList(trefs, "tref") + "</li>\r\n");
-    if (!examples.isEmpty())
+    }
+    if (!examples.isEmpty()) {
       b.append(" <li>Examples for this " + type + ": " + refList(examples, "ex") + "</li>\r\n");
+    }
+    if (!searches.isEmpty()) {
+      b.append(" <li>Search Parameters using this " + type + ": " + refList(searches, "sp") + "</li>\r\n");
+    }
     if (base.isEmpty() && refs.isEmpty() && trefs.isEmpty() && examples.isEmpty() & invoked.isEmpty() && imposed.isEmpty() && compliedWith.isEmpty()) {
       b.append(" <li>This " + type + " is not used by any profiles in this Implementation Guide</li>\r\n");
     }

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
@@ -61,6 +61,8 @@ private void testIg(String id, String path) throws Exception {
     pub.execute();
 
     System.out.println("===== Analysis ======================================================================");
+    System.out.println("-- output in "+Utilities.path(FhirSettings.getTestIgsPath(), "actual", id+".json")+" --");
+
     // to make diff programs easy to run
     IOUtils.copy(new FileInputStream(Utilities.path(FhirSettings.getTestIgsPath(), id, "output", "qa.json")), new FileOutputStream(Utilities.path(FhirSettings.getTestIgsPath(), "actual", id+".json")));
     IOUtils.copy(new FileInputStream(Utilities.path(FhirSettings.getTestIgsPath(), id, "output", "qa.compare.txt")), new FileOutputStream(Utilities.path(FhirSettings.getTestIgsPath(), "actual", id+".txt")));
@@ -172,7 +174,7 @@ private void writeMem(String name) {
     System.out.println(name+": "+usedMemory);
   }
 
-  //---- todo: this class is only run by Grahame, so these ahts are hard-coded
+  //---- todo: this class is only run by Grahame, so these paths are hard-coded
 
   private File syncDateFile() {
     return new File("/Users/grahamegrieve/work/test-igs/date.txt");

diff --git a/pom.xml b/pom.xml
@@ -24,7 +24,7 @@
     <version>1.6.19-SNAPSHOT</version> <!-- See the note above -->
 
     <properties>
-        <core_version>6.3.18</core_version>
+        <core_version>6.3.19-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
@@ -26,3 +26,4 @@ Version,example.fhir.uv.myig,fhir.base.template.ig,hl7.base.template.ig,hl7.cda.
 1.6.14,71441,955,83,223167,614957,3717,1754846,1025347,,40427,106638,636638,890027,141549,293706
 1.6.15,63766,1083,103,122252,279932,1204,1339037,579431,675157,33625,85427,578334,516740,62492,201274
 1.6.17,68693,949,96,121108,280290,893,1300165,600615,688971,37985,86649,592377,535137,69995,202884
+1.6.19,64172,942,95,113448,297926,1716,714801,595112,655001,32330,98325,476742,398608,59608,190433
diff --git a/test-statistics.json b/test-statistics.json
@@ -2823,5 +2823,114 @@
       "time" : 688971,
       "memory" : 6002722160
     }
+  },
+  "1.6.19" : {
+    "sync-date" : "2024-06-30",
+    "date" : "2024-08-04",
+    "hl7.fhir.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 1716,
+      "memory" : 17503264
+    },
+    "hl7.cda.uv.core" : {
+      "errors" : 0,
+      "warnings" : 140,
+      "hints" : 0,
+      "time" : 113448,
+      "memory" : 3593127096
+    },
+    "hl7.fhir.us.ecr" : {
+      "errors" : 4596,
+      "warnings" : 330,
+      "hints" : 113,
+      "time" : 595112,
+      "memory" : 8621362000
+    },
+    "hl7.fhir.uv.ipa" : {
+      "errors" : 24,
+      "warnings" : 8,
+      "hints" : 38,
+      "time" : 98325,
+      "memory" : 2780264320
+    },
+    "hl7.fhir.uv.ips" : {
+      "errors" : 0,
+      "warnings" : 12,
+      "hints" : 47,
+      "time" : 476742,
+      "memory" : 2348868008
+    },
+    "ihe.mhd.fhir" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 2,
+      "time" : 190433,
+      "memory" : 2439781224
+    },
+    "hl7.base.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 95,
+      "memory" : 4055888
+    },
+    "hl7.fhir.uv.howto" : {
+      "errors" : 1,
+      "warnings" : 2,
+      "hints" : 1,
+      "time" : 32330,
+      "memory" : 1450879784
+    },
+    "fhir.base.template.ig" : {
+      "errors" : 0,
+      "warnings" : 0,
+      "hints" : 0,
+      "time" : 942,
+      "memory" : 183851704
+    },
+    "hl7.fhir.au.base" : {
+      "errors" : 1,
+      "warnings" : 123,
+      "hints" : 57,
+      "time" : 297926,
+      "memory" : 2962810728
+    },
+    "example.fhir.uv.myig" : {
+      "errors" : 21,
+      "warnings" : 19,
+      "hints" : 4,
+      "time" : 64172,
+      "memory" : 1796660992
+    },
+    "hl7.fhir.uv.extensions" : {
+      "errors" : 1094,
+      "warnings" : 772,
+      "hints" : 1606,
+      "time" : 655001,
+      "memory" : 8339311752
+    },
+    "hl7.fhir.us.core" : {
+      "errors" : 56,
+      "warnings" : 3,
+      "hints" : 3,
+      "time" : 714801,
+      "memory" : 14458910008
+    },
+    "hl7.fhir.uv.sdc" : {
+      "errors" : 45,
+      "warnings" : 67,
+      "hints" : 368,
+      "time" : 398608,
+      "memory" : 2522271816
+    },
+    "hl7.fhir.uv.tools" : {
+      "errors" : 0,
+      "warnings" : 2,
+      "hints" : 0,
+      "time" : 59608,
+      "memory" : 3115180560
+    }
   }
 }