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org.hl7.fhir.core
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fixes for validation loading

This commit is contained in:
Grahame Grieve 2019-03-04 15:30:33 +11:00
parent 5a1dfba236
commit 88c145a00c
12 changed files with 31 additions and 17 deletions
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2
org.hl7.fhir.convertors/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_10_50.java
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@ -11574,7 +11574,7 @@ public org.hl7.fhir.dstu2.model.ValueSet.ConceptDefinitionDesignationComponent c
if (src.hasExtension("http://hl7.org/fhir/StructureDefinition/valueset-extensible"))
tgt.setExtensible(((BooleanType) src.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/valueset-extensible").getValue()).booleanValue());
org.hl7.fhir.r5.model.CodeSystem srcCS = (CodeSystem) src.getUserData("r2-cs");
if (srcCS == null)
if (srcCS == null && advisor != null)
srcCS = advisor.getCodeSystem(src);
if (srcCS != null) {
tgt.getCodeSystem().setSystem(srcCS.getUrl());

2
org.hl7.fhir.dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu2016may/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation.cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
org.hl7.fhir.validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>org.hl7.fhir.core</artifactId>
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

26
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r4/validation/ValidationEngine.java
View File

@ -463,7 +463,7 @@ public class ValidationEngine {
if (stream != null)
return readZip(stream);
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
FhirFormat fmt = checkIsResource(stream);
FhirFormat fmt = checkIsResource(stream, src);
if (fmt != null) {
Map<String, byte[]> res = new HashMap<String, byte[]>();
res.put(Utilities.changeFileExt(src, "."+fmt.getExtension()), TextFile.fileToBytes(src));
@ -488,15 +488,21 @@ public class ValidationEngine {
private Map<String, byte[]> scanDirectory(File f) throws FileNotFoundException, IOException {
Map<String, byte[]> res = new HashMap<String, byte[]>();
for (File ff : f.listFiles()) {
FhirFormat fmt = checkIsResource(ff.getAbsolutePath());
if (fmt != null) {
res.put(Utilities.changeFileExt(ff.getName(), "."+fmt.getExtension()), TextFile.fileToBytes(ff.getAbsolutePath()));
if (!isIgnoreFile(ff)) {
FhirFormat fmt = checkIsResource(ff.getAbsolutePath());
if (fmt != null) {
res.put(Utilities.changeFileExt(ff.getName(), "."+fmt.getExtension()), TextFile.fileToBytes(ff.getAbsolutePath()));
}
}
}
return res;
}
private boolean isIgnoreFile(File ff) {
return Utilities.existsInList(ff.getName(), ".DS_Store");
}
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws FileNotFoundException, IOException {
return loadPackage(pcm.extractLocally(stream, name));
}
@ -585,7 +591,8 @@ public class ValidationEngine {
this.noInvariantChecks = value;
}
private FhirFormat checkIsResource(InputStream stream) {
private FhirFormat checkIsResource(InputStream stream, String filename) {
System.out.println(" ..Detect format for "+filename);
try {
Manager.parse(context, stream, FhirFormat.XML);
return FhirFormat.XML;
@ -606,6 +613,7 @@ public class ValidationEngine {
return FhirFormat.TEXT;
} catch (Exception e) {
}
System.out.println(" .. not a resource: "+filename);
return null;
}
@ -622,7 +630,7 @@ public class ValidationEngine {
if (Utilities.existsInList(ext, "txt"))
return FhirFormat.TEXT;
return checkIsResource(new FileInputStream(path));
return checkIsResource(new FileInputStream(path), path);
}
public void connectToTSServer(String url, String log, FhirPublication version) throws URISyntaxException, FHIRException {
@ -667,6 +675,8 @@ public class ValidationEngine {
res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
res = new org.hl7.fhir.dstu3.utils.StructureMapUtilities(null).parse(new String(t.getValue()));
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_30_40.convertResource(res, false);
@ -696,6 +706,8 @@ public class ValidationEngine {
r = new JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".txt"))
r = new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(t.getValue()), fn);
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
r = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(t.getValue()), fn);
else
throw new Exception("Unsupported format for "+fn);
} else
@ -764,6 +776,8 @@ public class ValidationEngine {
res.cntType = FhirFormat.XML;
else if (t.getKey().endsWith(".ttl"))
res.cntType = FhirFormat.TURTLE;
else if (t.getKey().endsWith(".txt") || t.getKey().endsWith(".map"))
res.cntType = FhirFormat.TEXT;
else
throw new Exception("Todo: Determining resource type is not yet done");
}

2
pom.xml
View File

@ -13,7 +13,7 @@
each other. It is fine to bump the point version of this POM without affecting
HAPI FHIR.
-->
<version>3.7.7-SNAPSHOT</version>
<version>3.7.8-SNAPSHOT</version>
<properties>
<hapi_fhir_version>3.7.0-SNAPSHOT</hapi_fhir_version>