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changes for version 3.4.3 #139

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merged 10 commits into from
Sep 20, 2023
Merged

changes for version 3.4.3 #139

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9ed3f0b
FML: Contained ConceptMap in StructureMap #137
oliveregger Sep 19, 2023
8f5ba57
adjust capability statement #133
oliveregger Sep 19, 2023
99b5133
#129 and #133 update
oliveregger Sep 19, 2023
0960a69
context.version set with xver instead of r4 #135
oliveregger Sep 20, 2023
f81fcad
validation R5 extension support #137
oliveregger Sep 20, 2023
040f089
matchbox dynamic app location #128
oliveregger Sep 20, 2023
ce09cba
display values warnings #132
oliveregger Sep 20, 2023
9d6a643
display values should only be warnings #132
oliveregger Sep 20, 2023
534563b
#138 #135 lab validation problems
oliveregger Sep 20, 2023
c13e1c4
FHIR Validation problem #135 xver
oliveregger Sep 20, 2023
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1 change: 1 addition & 0 deletions matchbox-engine/src/main/java/ch/ahdis/matchbox/engine/cli/MatchboxService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -407,6 +407,7 @@ public String initializeValidator(CliContext cliContext, String definitions, Tim
validator.setLanguage(cliContext.getLang());
validator.setLocale(cliContext.getLocale());
validator.setSnomedExtension(cliContext.getSnomedCTCode());
validator.setDisplayWarnings(cliContext.isDisplayWarnings());
validator.setAssumeValidRestReferences(cliContext.isAssumeValidRestReferences());
validator.setShowMessagesFromReferences(cliContext.isShowMessagesFromReferences());
validator.setDoImplicitFHIRPathStringConversion(cliContext.isDoImplicitFHIRPathStringConversion());
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3 changes: 1 addition & 2 deletions ...engine/src/main/java/ch/ahdis/matchbox/mappinglanguage/MatchboxStructureMapUtilities.java
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Expand Up @@ -117,8 +117,7 @@ public Base translate(TransformContext context, StructureMap map, Base source, S
ConceptMap cmap = null;
if (conceptMapUrl.startsWith("#")) {
for (Resource r : map.getContained()) {
// if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl)) { FIXME: looks like a simpleworkercontext issue
if (r instanceof ConceptMap && r.getId().equals(conceptMapUrl.substring(1))) {
if (r instanceof ConceptMap && (r.getId().equals(conceptMapUrl.substring(1)) || r.getId().equals(conceptMapUrl))) {
cmap = (ConceptMap) r;
su = map.getUrl() + "#" + conceptMapUrl;
}
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41 changes: 36 additions & 5 deletions matchbox-engine/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -116,6 +116,9 @@ public interface IPackageProvider {
private boolean suppressErrors;
private boolean minimalMemory;

private final static String VER_XVER_PROVIDED = "0.0.13";



public FilesystemPackageCacheManager(boolean userMode) throws IOException {
init(userMode ? FilesystemPackageCacheMode.USER : FilesystemPackageCacheMode.SYSTEM);
Expand Down Expand Up @@ -293,16 +296,27 @@ private void listSpecs(Map<String, String> specList, PackageServer server) throw

protected InputStreamWithSrc loadFromPackageServer(String id, String version) {

// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
if (CommonPackages.ID_XVER.equals(id)) {
version = "0.0.13";
// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
if (CommonPackages.ID_XVER.equals(id)) {
ourLog.info("loading " +id+ " form classpath");
version = VER_XVER_PROVIDED;
InputStream stream = getClass().getResourceAsStream("/"+id+"#"+version+".tgz");
if (stream==null) {
ourLog.error("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
throw new FHIRException("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
}
return new InputStreamWithSrc(stream, "http://fhir.org/packages/hl7.fhir.xver-extensions", version);
}
}

if ("hl7.fhir.r5.core".equals(id)) {
ourLog.info("loading hl7.fhir.r5.core form classpath");
InputStream stream = getClass().getResourceAsStream("/"+id+".tgz");
if (stream==null) {
ourLog.error("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
throw new FHIRException("Unable to find/resolve/read from classpath (we dont' want go to the package server) for :" + id+"#"+version+".tgz");
}
return new InputStreamWithSrc(stream, "https://hl7.org/fhir/R5/hl7.fhir.r5.core.tgz", version);
}

InputStreamWithSrc retVal = super.loadFromPackageServer(id, version);
if (retVal != null) {
Expand Down Expand Up @@ -464,7 +478,7 @@ public NpmPackage loadPackageFromCacheOnly(String id, String version) throws IOE
public NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException {
// matchbox-engine PATCH, we do not want to load from a package server for hl7.fhir.xver-extension :
if (CommonPackages.ID_XVER.equals(id)) {
version = "0.0.13";
version = VER_XVER_PROVIDED;
NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream, sourceDesc, true);
return npm;
}
Expand Down Expand Up @@ -586,6 +600,23 @@ public void listAllIds(Map<String, String> specList) throws IOException {
@Override
public NpmPackage loadPackage(String id, String version) throws FHIRException, IOException {
//ok, try to resolve locally

if (CommonPackages.ID_XVER.equals(id)) {
version = VER_XVER_PROVIDED;
InputStreamWithSrc packageTgzInputStream = this.loadFromPackageServer(id, version);
NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream.stream);
// org.hl7.fhir.exceptions.FHIRException: Unknown FHIRVersion code '0.0.13'
// https://github.com/ahdis/matchbox/issues/135
npm.getNpm().set("version", "4.0");
return npm;
}

if ("hl7.fhir.r5.core".equals(id)) {
InputStreamWithSrc packageTgzInputStream = this.loadFromPackageServer(id, version);
NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream.stream);
return npm;
}

if (!Utilities.noString(version) && version.startsWith("file:")) {
return loadPackageFromFile(id, version.substring(5));
}
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