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fix version bug generating snapshot

This commit is contained in:
Grahame Grieve 2019-11-12 09:07:54 +11:00
parent b3e95bd19f
commit 5fe2552a08
3 changed files with 166 additions and 122 deletions
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10
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/TextFile.java
View File

@ -107,6 +107,16 @@ public class TextFile {
sw.close();
}
public static void stringToStream(String content, OutputStream stream, boolean bom) throws IOException {
OutputStreamWriter sw = new OutputStreamWriter(stream, "UTF-8");
if (bom) {
sw.write('\ufeff'); // Unicode BOM, translates to UTF-8 with the configured outputstreamwriter
}
sw.write(content);
sw.flush();
sw.close();
}
public static byte[] stringToBytes(String content, boolean bom) throws IOException {
ByteArrayOutputStream bs = new ByteArrayOutputStream();
OutputStreamWriter sw = new OutputStreamWriter(bs, "UTF-8");

227
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/ValidationEngine.java
View File

@ -114,6 +114,7 @@ import org.hl7.fhir.r5.formats.FormatUtilities;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.RdfParser;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.Bundle;
import org.hl7.fhir.r5.model.Coding;
@ -803,60 +804,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
System.out.print("* load file: "+fn);
Resource r = null;
try {
if (version.startsWith("3.0")) {
org.hl7.fhir.dstu3.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
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_50.convertResource(res, false);
} else if (version.startsWith("4.0")) {
org.hl7.fhir.r4.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
res = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(t.getValue()), fn);
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_40_50.convertResource(res);
} else if (version.startsWith("1.4")) {
org.hl7.fhir.dstu2016may.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_14_50.convertResource(res);
} else if (version.startsWith("1.0")) {
org.hl7.fhir.dstu2.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(t.getValue()));
else
throw new Exception("Unsupported format for "+fn);
VersionConvertorAdvisor50 advisor = new org.hl7.fhir.convertors.IGR2ConvertorAdvisor5();
r = new VersionConvertor_10_50(advisor ).convertResource(res);
} else if (version.equals(Constants.VERSION)) {
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
r = new XmlParser().parse(new ByteArrayInputStream(t.getValue()));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
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.r5.utils.StructureMapUtilities(null).parse(new String(t.getValue()), fn);
else
throw new Exception("Unsupported format for "+fn);
} else
throw new Exception("Unsupported version "+version);
r = loadResourceByVersion(version, t.getValue(), fn);
if (debug)
System.out.println(" .. success");
} catch (Exception e) {
@ -879,6 +827,65 @@ public class ValidationEngine implements IValidatorResourceFetcher {
grabNatives(source, canonical);
}
public Resource loadResourceByVersion(String version, byte[] content, String fn) throws IOException, Exception {
Resource r;
if (version.startsWith("3.0")) {
org.hl7.fhir.dstu3.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.dstu3.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu3.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
res = new org.hl7.fhir.dstu3.utils.StructureMapUtilities(null).parse(new String(content));
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_30_50.convertResource(res, false);
} else if (version.startsWith("4.0")) {
org.hl7.fhir.r4.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.r4.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.r4.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
res = new org.hl7.fhir.r4.utils.StructureMapUtilities(null).parse(new String(content), fn);
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_40_50.convertResource(res);
} else if (version.startsWith("1.4")) {
org.hl7.fhir.dstu2016may.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new ByteArrayInputStream(content));
else
throw new Exception("Unsupported format for "+fn);
r = VersionConvertor_14_50.convertResource(res);
} else if (version.startsWith("1.0")) {
org.hl7.fhir.dstu2.model.Resource res;
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
res = new org.hl7.fhir.dstu2.formats.JsonParser().parse(new ByteArrayInputStream(content));
else
throw new Exception("Unsupported format for "+fn);
VersionConvertorAdvisor50 advisor = new org.hl7.fhir.convertors.IGR2ConvertorAdvisor5();
r = new VersionConvertor_10_50(advisor ).convertResource(res);
} else if (version.equals(Constants.VERSION)) {
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
r = new XmlParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
r = new JsonParser().parse(new ByteArrayInputStream(content));
else if (fn.endsWith(".txt"))
r = new StructureMapUtilities(context, null, null).parse(TextFile.bytesToString(content), fn);
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
r = new org.hl7.fhir.r5.utils.StructureMapUtilities(null).parse(new String(content), fn);
else
throw new Exception("Unsupported format for "+fn);
} else
throw new Exception("Unsupported version "+version);
return r;
}
private boolean exemptFile(String fn) {
return Utilities.existsInList(fn, "spec.internals", "version.info", "schematron.zip", "package.json");
}
@ -1249,34 +1256,17 @@ public class ValidationEngine implements IValidatorResourceFetcher {
return ResourceFactory.createResource(structureDefinition.getName());
}
public DomainResource generate(String source) throws Exception {
public DomainResource generate(String source, String version) throws Exception {
Content cnt = loadContent(source, "validate");
Resource res;
if (cnt.cntType == FhirFormat.XML)
res = new XmlParser().parse(cnt.focus);
else if (cnt.cntType == FhirFormat.JSON)
res = new JsonParser().parse(cnt.focus);
else if (cnt.cntType == FhirFormat.TURTLE)
res = new RdfParser().parse(cnt.focus);
else
throw new Error("Not supported yet");
Resource res = loadResourceByVersion(version, cnt.focus, source);
new NarrativeGenerator("", "", context).generate((DomainResource) res, null);
return (DomainResource) res;
}
public StructureDefinition snapshot(String source) throws Exception {
public StructureDefinition snapshot(String source, String version) throws Exception {
Content cnt = loadContent(source, "validate");
Resource res;
if (cnt.cntType == FhirFormat.XML)
res = new XmlParser().parse(cnt.focus);
else if (cnt.cntType == FhirFormat.JSON)
res = new JsonParser().parse(cnt.focus);
else if (cnt.cntType == FhirFormat.TURTLE)
res = new RdfParser().parse(cnt.focus);
else
throw new Error("Not supported yet");
Resource res = loadResourceByVersion(version, cnt.focus, Utilities.getFileNameForName(source));
if (!(res instanceof StructureDefinition))
throw new Exception("Require a StructureDefinition for generating a snapshot");
StructureDefinition sd = (StructureDefinition) res;
@ -1606,5 +1596,90 @@ public class ValidationEngine implements IValidatorResourceFetcher {
return false;
}
public void handleOutput(Resource r, String output, String version) throws Exception {
if (output.startsWith("http://") || output.startsWith("http://")) {
ByteArrayOutputStream bs = new ByteArrayOutputStream();
handleOutputToStream(r, output, bs, version);
URL url = new URL(output);
HttpURLConnection c = (HttpURLConnection) url.openConnection();
c.setDoOutput(true);
c.setDoInput(true);
c.setRequestMethod("POST");
c.setRequestProperty( "Content-type", "application/fhir+xml");
c.setRequestProperty( "Accept", "application/fhir+xml" );
c.getOutputStream().write(bs.toByteArray());
c.getOutputStream().close();
if (c.getResponseCode() >= 300) {
// String line;
// BufferedReader reader = new BufferedReader(new InputStreamReader(c.getInputStream()));
// while ((line = reader.readLine()) != null) {
// System.out.println(line);
// }
// reader.close();
throw new IOException("Unable to PUT to "+output+": "+c.getResponseMessage());
}
} else {
FileOutputStream s = new FileOutputStream(output);
handleOutputToStream(r, output, s, version);
}
}
private void handleOutputToStream(Resource r, String fn, OutputStream s, String version) throws Exception {
if (fn.endsWith(".html") || fn.endsWith(".htm") && r instanceof DomainResource)
new XhtmlComposer(XhtmlComposer.HTML, true).compose(s, ((DomainResource) r).getText().getDiv());
else if (version.startsWith("3.0")) {
org.hl7.fhir.dstu3.model.Resource res = VersionConvertor_30_50.convertResource(r, false);
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
new org.hl7.fhir.dstu3.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.dstu3.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu3.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
TextFile.stringToStream(org.hl7.fhir.dstu3.utils.StructureMapUtilities.render((org.hl7.fhir.dstu3.model.StructureMap) res), s, false);
else
throw new Exception("Unsupported format for "+fn);
} else if (version.startsWith("4.0")) {
org.hl7.fhir.r4.model.Resource res = VersionConvertor_40_50.convertResource(r);
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
new org.hl7.fhir.r4.formats.XmlParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(org.hl7.fhir.r4.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
TextFile.stringToStream(org.hl7.fhir.r4.utils.StructureMapUtilities.render((org.hl7.fhir.r4.model.StructureMap) res), s, false);
else
throw new Exception("Unsupported format for "+fn);
} else if (version.startsWith("1.4")) {
org.hl7.fhir.dstu2016may.model.Resource res = VersionConvertor_14_50.convertResource(r);
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
new org.hl7.fhir.dstu2016may.formats.XmlParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.dstu2016may.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu2016may.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else
throw new Exception("Unsupported format for "+fn);
} else if (version.startsWith("1.0")) {
VersionConvertorAdvisor50 advisor = new org.hl7.fhir.convertors.IGR2ConvertorAdvisor5();
org.hl7.fhir.dstu2.model.Resource res = new VersionConvertor_10_50(advisor ).convertResource(r);
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
new org.hl7.fhir.dstu2.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new org.hl7.fhir.dstu2.formats.JsonParser().setOutputStyle(org.hl7.fhir.dstu2.formats.IParser.OutputStyle.PRETTY).compose(s, res);
else
throw new Exception("Unsupported format for "+fn);
} else if (version.equals(Constants.VERSION)) {
if (fn.endsWith(".xml") && !fn.endsWith("template.xml"))
new XmlParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
else if (fn.endsWith(".json") && !fn.endsWith("template.json"))
new JsonParser().setOutputStyle(org.hl7.fhir.r5.formats.IParser.OutputStyle.PRETTY).compose(s, r);
else if (fn.endsWith(".txt") || fn.endsWith(".map") )
TextFile.stringToStream(org.hl7.fhir.r5.utils.StructureMapUtilities.render((org.hl7.fhir.r5.model.StructureMap) r), s, false);
else
throw new Exception("Unsupported format for "+fn);
} else
throw new Exception("Unsupported version "+version);
s.close();
}
}

51
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
View File

@ -549,18 +549,16 @@ public class Validator {
e.printStackTrace();
}
} else if (mode == EngineMode.NARRATIVE) {
DomainResource r = validator.generate(sources.get(0));
DomainResource r = validator.generate(sources.get(0), sv);
System.out.println(" ...generated narrative successfully");
if (output != null) {
handleOutput(r, output);
validator.handleOutput(r, output, sv);
}
} else if (mode == EngineMode.SNAPSHOT) {
if (definitions == null)
throw new Exception("Must provide a defn when generating a snapshot");
StructureDefinition r = validator.snapshot(sources.get(0));
} else if (mode == EngineMode.SNAPSHOT) {
StructureDefinition r = validator.snapshot(sources.get(0), sv);
System.out.println(" ...generated snapshot successfully");
if (output != null) {
handleOutput(r, output);
validator.handleOutput(r, output, sv);
}
} else {
if (definitions == null)
@ -621,45 +619,6 @@ public class Validator {
return "??";
}
private static void handleOutput(Resource r, String output) throws IOException {
if (output.startsWith("http://") || output.startsWith("http://")) {
ByteArrayOutputStream bs = new ByteArrayOutputStream();
handleOutputToStream(r, output, bs);
URL url = new URL(output);
HttpURLConnection c = (HttpURLConnection) url.openConnection();
c.setDoOutput(true);
c.setDoInput(true);
c.setRequestMethod("POST");
c.setRequestProperty( "Content-type", "application/fhir+xml");
c.setRequestProperty( "Accept", "application/fhir+xml" );
c.getOutputStream().write(bs.toByteArray());
c.getOutputStream().close();
if (c.getResponseCode() >= 300) {
// String line;
// BufferedReader reader = new BufferedReader(new InputStreamReader(c.getInputStream()));
// while ((line = reader.readLine()) != null) {
// System.out.println(line);
// }
// reader.close();
throw new IOException("Unable to PUT to "+output+": "+c.getResponseMessage());
}
} else {
FileOutputStream s = new FileOutputStream(output);
handleOutputToStream(r, output, s);
}
}
private static void handleOutputToStream(Resource r, String output, OutputStream s) throws IOException {
if (output.endsWith(".html") || output.endsWith(".htm") && r instanceof DomainResource)
new XhtmlComposer(XhtmlComposer.HTML, true).compose(s, ((DomainResource) r).getText().getDiv());
else if (output.endsWith(".json"))
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, r);
else
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, r);
s.close();
}
private static int displayOO(OperationOutcome oo) {
int error = 0;
int warn = 0;