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Merge pull request #929 from hapifhir/gg-2022-09-cs_vs 

Gg 2022 09 cs vs
This commit is contained in:
Grahame Grieve 2022-09-23 12:14:22 -04:00 committed by GitHub
parent c51f7c2327 695a8610a2
commit 0b40db7f0b
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GPG Key ID: 4AEE18F83AFDEB23
9 changed files with 129 additions and 29 deletions
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41
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/analytics/PackageVisitor.java
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@ -116,28 +116,53 @@ public class PackageVisitor {
Map<String, String> cpidMap = getAllCIPackages();
Set<String> cpidSet = new HashSet<>();
System.out.println("Go: "+cpidMap.size()+" current packages");
int i = 0;
for (String s : cpidMap.keySet()) {
processCurrentPackage(s, cpidMap.get(s), cpidSet);
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) {
if (!cpidSet.contains(pid)) {
cpidSet.add(pid);
List<String> vList = listVersions(pid);
if (oldVersions) {
for (String v : vList) {
processPackage(pid, v);
processPackage(pid, v, i, pidList.size());
}
} else if (vList.isEmpty()) {
System.out.println("No Packages for "+pid);
} else {
processPackage(pid, vList.get(vList.size() - 1));
processPackage(pid, vList.get(vList.size() - 1), i, pidList.size());
}
}
}
i++;
}
JsonObject json = JsonTrackingParser.fetchJson("https://raw.githubusercontent.com/FHIR/ig-registry/master/fhir-ig-list.json");
i = 0;
List<JsonObject> objects = JsonUtilities.objects(json, "guides");
for (JsonObject o : objects) {
String pid = JsonUtilities.str(o, "npm-name");
if (pid != null && !cpidSet.contains(pid)) {
cpidSet.add(pid);
List<String> vList = listVersions(pid);
if (oldVersions) {
for (String v : vList) {
processPackage(pid, v, i, objects.size());
}
} else if (vList.isEmpty()) {
System.out.println("No Packages for "+pid);
} else {
processPackage(pid, vList.get(vList.size() - 1), i, objects.size());
}
}
i++;
}
}
private void processCurrentPackage(String url, String pid, Set<String> cpidSet) {
private void processCurrentPackage(String url, String pid, Set<String> cpidSet, int i, int t) {
try {
String[] p = url.split("\\/");
String repo = "https://build.fhir.org/ig/"+p[0]+"/"+p[1];
@ -160,7 +185,7 @@ public class PackageVisitor {
}
}
}
System.out.println("Processed: "+pid+"#current: "+c+" resources");
System.out.println("Processed: "+pid+"#current: "+c+" resources ("+i+" of "+t+")");
}
} catch (Exception e) {
System.out.println("Unable to process: "+pid+"#current: "+e.getMessage());
@ -228,7 +253,7 @@ public class PackageVisitor {
}
private void processPackage(String pid, String v) throws IOException {
private void processPackage(String pid, String v, int i, int t) throws IOException {
NpmPackage npm = null;
String fv = null;
try {
@ -252,7 +277,7 @@ public class PackageVisitor {
}
}
}
System.out.println("Processed: "+pid+"#"+v+": "+c+" resources");
System.out.println("Processed: "+pid+"#"+v+": "+c+" resources ("+i+" of "+t+")");
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/CapabilityStatementRenderer.java
View File

@ -41,7 +41,9 @@ public class CapabilityStatementRenderer extends ResourceRenderer {
if (conf.getRest().size() > 0) {
CapabilityStatementRestComponent rest = conf.getRest().get(0);
XhtmlNode t = x.table(null);
addTableRow(t, "Mode", rest.getMode().toString());
if (rest.hasMode()) {
addTableRow(t, "Mode", rest.getMode().toString());
}
addMarkdown(addTableRow(t, "Description"), rest.getDocumentation());
addTableRow(t, "Transaction", showOp(rest, SystemRestfulInteraction.TRANSACTION));

53
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/CodeSystemUtilities.java
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@ -41,6 +41,7 @@ import java.util.Set;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.CanonicalResource;
import org.hl7.fhir.r5.model.CanonicalType;
@ -67,6 +68,35 @@ import org.hl7.fhir.utilities.Utilities;
public class CodeSystemUtilities {
public static class SystemReference {
private String link;
private String text;
private boolean local;
public SystemReference(String text, String link) {
super();
this.link = link;
this.text = text;
}
public SystemReference(String text, String link, boolean local) {
super();
this.link = link;
this.text = text;
this.local = local;
}
public String getLink() {
return link;
}
public String getText() {
return text;
}
public boolean isLocal() {
return local;
}
}
public static class ConceptDefinitionComponentSorter implements Comparator<ConceptDefinitionComponent> {
@Override
@ -619,5 +649,26 @@ public class CodeSystemUtilities {
return jurisdiction == null || !jurisdiction.contains("#") ? null : new Coding().setCode(jurisdiction.substring(jurisdiction.indexOf("#")+1)).setSystem(jurisdiction.substring(0, jurisdiction.indexOf("#")));
}
public static SystemReference getSystemReference(String system, IWorkerContext ctxt) {
if (system == null) {
return null;
} if ("http://snomed.info/sct".equals(system)) {
return new SystemReference("SNOMED CT", "https://browser.ihtsdotools.org/");
} else if ("http://loinc.org".equals(system)) {
return new SystemReference("LOINC", "https://loinc.org/");
} else if ("http://unitsofmeasure.org".equals(system)) {
return new SystemReference("UCUM", "http://ucum.org");
} else if (system.equals("http://www.nlm.nih.gov/research/umls/rxnorm")) {
return new SystemReference("RxNorm", "http://www.nlm.nih.gov/research/umls/rxnorm");
} else if (ctxt != null) {
CodeSystem cs = ctxt.fetchCodeSystem(system);
if (cs != null && cs.hasUserData("path")) {
return new SystemReference(cs.present(), cs.getUserString("path"), Utilities.isAbsoluteUrl(cs.getUserString("path")));
} else if (cs != null) {
return new SystemReference(cs.present(), null);
}
}
return null;
}
}
}

14
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/ValueSetUtilities.java
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@ -51,6 +51,7 @@ import org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r5.model.CodeType;
import org.hl7.fhir.r5.model.ValueSet.ConceptReferenceComponent;
import org.hl7.fhir.r5.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetComposeComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionContainsComponent;
import org.hl7.fhir.r5.model.ValueSet.ValueSetExpansionPropertyComponent;
import org.hl7.fhir.r5.terminologies.CodeSystemUtilities.ConceptDefinitionComponentSorter;
@ -272,5 +273,18 @@ public class ValueSetUtilities {
Collections.sort(inc.getConcept(), new ConceptReferenceComponentSorter());
}
public static String getAllCodesSystem(ValueSet vs) {
if (vs.hasCompose()) {
ValueSetComposeComponent c = vs.getCompose();
if (c.getExclude().isEmpty() && c.getInclude().size() == 1) {
ConceptSetComponent i = c.getIncludeFirstRep();
if (i.hasSystem() && !i.hasValueSet() && !i.hasConcept() && !i.hasFilter()) {
return i.getSystem();
}
}
}
return null;
}
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
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@ -631,6 +631,10 @@ public class I18nConstants {
public static final String VALUESET_SHAREABLE_MISSING_HL7 = "VALUESET_SHAREABLE_MISSING_HL7";
public static final String VALUESET_SHAREABLE_EXTRA_MISSING_HL7 = "VALUESET_SHAREABLE_EXTRA_MISSING_HL7";
public static final String VALUESET_SHAREABLE_EXTRA_MISSING = "VALUESET_SHAREABLE_EXTRA_MISSING";
public static final String CODESYSTEM_SHAREABLE_MISSING = "CODESYSTEM_SHAREABLE_MISSING";
public static final String CODESYSTEM_SHAREABLE_MISSING_HL7 = "CODESYSTEM_SHAREABLE_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = "CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7";
public static final String CODESYSTEM_SHAREABLE_EXTRA_MISSING = "CODESYSTEM_SHAREABLE_EXTRA_MISSING";
public static final String VALUESET_UNC_SYSTEM_WARNING = "VALUESET_UNC_SYSTEM_WARNING";
public static final String VALUESET_UNC_SYSTEM_WARNING_VER = "VALUESET_UNC_SYSTEM_WARNING_VER";
public static final String VALUESET_IMPORT_UNION_INTERSECTION = "VALUESET_IMPORT_UNION_INTERSECTION";

1
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JsonUtilities.java
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@ -165,5 +165,4 @@ public class JsonUtilities {
}
return res;
}
}

4
org.hl7.fhir.utilities/src/main/resources/Messages.properties
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@ -726,3 +726,7 @@ VALUESET_SHAREABLE_MISSING = The ShareableValueSet profile says that the {0} ele
VALUESET_SHAREABLE_EXTRA_MISSING = The ShareableValueSet profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableValueSet profile
VALUESET_SHAREABLE_MISSING_HL7 = The ShareableValueSet profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
VALUESET_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableValueSet profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableValueSet profile
CODESYSTEM_SHAREABLE_MISSING = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not present. Published value sets SHOULD conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_MISSING_HL7 = The ShareableCodeSystem profile says that the {0} element is mandatory, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile
CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7 = The ShareableCodeSystem profile recommends that the {0} element is populated, but it is not found. HL7 Published value sets SHALL conform to the ShareableCodeSystem profile

36
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/CodeSystemValidator.java
View File

@ -91,28 +91,28 @@ public class CodeSystemValidator extends BaseValidator {
private void checkShareableCodeSystem(List<ValidationMessage> errors, Element cs, NodeStack stack) {
if (parent.isForPublication()) {
if (isHL7(cs)) {
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "url");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "version");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.VALUESET_SHAREABLE_EXTRA_MISSING_HL7, "name");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "status");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "experimental");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "description");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "content");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "url");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "version");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.CODESYSTEM_SHAREABLE_EXTRA_MISSING_HL7, "name");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "status");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "experimental");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "description");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "content");
if (!"supplement".equals(cs.getChildValue("content"))) {
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.VALUESET_SHAREABLE_MISSING_HL7, "caseSensitive");
rule(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING_HL7, "caseSensitive");
}
} else {
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.VALUESET_SHAREABLE_MISSING, "url");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.VALUESET_SHAREABLE_MISSING, "version");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.VALUESET_SHAREABLE_MISSING, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.VALUESET_SHAREABLE_EXTRA_MISSING, "name");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.VALUESET_SHAREABLE_MISSING, "status");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.VALUESET_SHAREABLE_MISSING, "experimental");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.VALUESET_SHAREABLE_MISSING, "description");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.VALUESET_SHAREABLE_MISSING, "content");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("url"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "url");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("version"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "version");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("title"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "title");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("name"), I18nConstants.CODESYSTEM_SHAREABLE_EXTRA_MISSING, "name");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("status"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "status");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("experimental"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "experimental");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("description"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "description");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("content"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "content");
if (!"supplement".equals(cs.getChildValue("content"))) {
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.VALUESET_SHAREABLE_MISSING, "caseSensitive");
warning(errors, IssueType.REQUIRED, cs.line(), cs.col(), stack.getLiteralPath(), cs.hasChild("caseSensitive"), I18nConstants.CODESYSTEM_SHAREABLE_MISSING, "caseSensitive");
}
}
}

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/StructureDefinitionValidator.java
View File

@ -78,6 +78,7 @@ public class StructureDefinitionValidator extends BaseValidator {
List<ValidationMessage> msgs = new ArrayList<>();
ProfileUtilities pu = new ProfileUtilities(context, msgs, null);
pu.setXver(xverManager);
pu.setNewSlicingProcessing(!sd.hasFhirVersion() || VersionUtilities.isR4Plus(sd.getFhirVersion().toCode()));
pu.generateSnapshot(base, sd, sd.getUrl(), "http://hl7.org/fhir/R4/", sd.getName());
if (msgs.size() > 0) {
for (ValidationMessage msg : msgs) {