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Merge pull request #704 from lmckenzi/Add_map_compile 

Add map compile
This commit is contained in:
Grahame Grieve 2022-02-01 11:50:41 +11:00 committed by GitHub
parent 5b66d3fe42 817b0d19de
commit 96538ba249
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GPG Key ID: 4AEE18F83AFDEB23
8 changed files with 47 additions and 4 deletions
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2
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/context/BaseWorkerContext.java
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@ -385,7 +385,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if ((packageInfo == null || !packageInfo.isExamplesPackage()) || !map.containsKey(r.getId())) {
map.put(r.getId(), new ResourceProxy(r));
} else {
System.out.println("Ingore "+r.fhirType()+"/"+r.getId()+" from package "+packageInfo.toString());
System.out.println("Ignore "+r.fhirType()+"/"+r.getId()+" from package "+packageInfo.toString());
}
if (r instanceof CodeSystem || r instanceof NamingSystem) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -390,7 +390,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if ((packageInfo == null || !packageInfo.isExamplesPackage()) || !map.containsKey(r.getId())) {
map.put(r.getId(), new ResourceProxy(r));
} else {
System.out.println("Ingore "+r.fhirType()+"/"+r.getId()+" from package "+packageInfo.toString());
System.out.println("Ignore "+r.fhirType()+"/"+r.getId()+" from package "+packageInfo.toString());
}
if (r instanceof CodeSystem || r instanceof NamingSystem) {

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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@ -498,7 +498,7 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
// nup, don't have it locally (or it's expired)
FilesystemPackageCacheManager.InputStreamWithSrc source;
if ("current".equals(version) || version.startsWith("current$")) {
if ("current".equals(version) || (version!= null && version.startsWith("current$"))) {
// special case - fetch from ci-build server
source = loadFromCIBuild(id, version.startsWith("current$") ? version.substring(8) : null);
} else {

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
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@ -426,6 +426,11 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
return transform(cnt.focus, cnt.cntType, map);
}
public StructureMap compile(String mapUri) throws FHIRException, IOException {
StructureMap map = context.getTransform(mapUri);
return map;
}
public org.hl7.fhir.r5.elementmodel.Element transform(byte[] source, FhirFormat cntType, String mapUri) throws FHIRException, IOException {
List<Base> outputs = new ArrayList<>();
StructureMapUtilities scu = new StructureMapUtilities(context, new TransformSupportServices(outputs, mapLog, context));
@ -642,7 +647,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
else
throw new FHIRException("Unsupported format for " + fn);
} else
throw new FHIRException("Encounted unsupported configured version " + version + " loading " + fn);
throw new FHIRException("Encountered unsupported configured version " + version + " loading " + fn);
s.close();
}

3
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidatorCli.java
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@ -241,6 +241,9 @@ public class ValidatorCli {
case TRANSFORM:
validationService.transform(cliContext, validator);
break;
case COMPILE:
validationService.compile(cliContext, validator);
break;
case NARRATIVE:
validationService.generateNarrative(cliContext, validator);
break;

30
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
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@ -253,6 +253,36 @@ public class ValidationService {
}
}
public void compile(CliContext cliContext, ValidationEngine validator) throws Exception {
if (cliContext.getSources().size() > 0)
throw new Exception("Cannot specify sources when compling transform (found " + cliContext.getSources() + ")");
if (cliContext.getMap() == null)
throw new Exception("Must provide a map when compiling a transform");
if (cliContext.getOutput() == null)
throw new Exception("Must provide an output name when compiling a transform");
try {
List<StructureDefinition> structures = validator.getContext().allStructures();
for (StructureDefinition sd : structures) {
if (!sd.hasSnapshot()) {
if (sd.getKind() != null && sd.getKind() == StructureDefinitionKind.LOGICAL) {
validator.getContext().generateSnapshot(sd, true);
} else {
validator.getContext().generateSnapshot(sd, false);
}
}
}
validator.setMapLog(cliContext.getMapLog());
StructureMap map = validator.compile(cliContext.getMap());
if (map == null)
throw new Exception("Unable to locate map " + cliContext.getMap());
validator.handleOutput(map, cliContext.getOutput(), validator.getVersion());
System.out.println(" ...success");
} catch (Exception e) {
System.out.println(" ...Failure: " + e.getMessage());
e.printStackTrace();
}
}
public void transformVersion(CliContext cliContext, ValidationEngine validator) throws Exception {
if (cliContext.getSources().size() > 1) {
throw new Exception("Can only have one source when converting versions (found " + cliContext.getSources() + ")");

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/EngineMode.java
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@ -2,6 +2,7 @@ package org.hl7.fhir.validation.cli.utils;
public enum EngineMode {
VALIDATION,
COMPILE,
TRANSFORM,
NARRATIVE,
SNAPSHOT,

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Params.java
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@ -31,6 +31,7 @@ public class Params {
public static final String TO_VERSION = "-to-version";
public static final String DO_NATIVE = "-do-native";
public static final String NO_NATIVE = "-no-native";
public static final String COMPILE = "-compile";
public static final String TRANSFORM = "-transform";
public static final String NARRATIVE = "-narrative";
public static final String SNAPSHOT = "-snapshot";
@ -192,6 +193,9 @@ public class Params {
} else if (args[i].equals(TRANSFORM)) {
cliContext.setMap(args[++i]);
cliContext.setMode(EngineMode.TRANSFORM);
} else if (args[i].equals(COMPILE)) {
cliContext.setMap(args[++i]);
cliContext.setMode(EngineMode.COMPILE);
} else if (args[i].equals(NARRATIVE)) {
cliContext.setMode(EngineMode.NARRATIVE);
} else if (args[i].equals(SPREADSHEET)) {