honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Gg 202110 validation various (#634) 

* add explicit control over the User-Agent header, and make sure headers flow through properly to all calls

* #328 - wrong processing of markdown URLs

* test fixes for URL handling

* fix tests

* improved validation of UUIDs

* fix test case dependency

* Add Dicom Package builder
This commit is contained in:
Grahame Grieve 2021-10-30 07:26:50 +11:00 committed by GitHub
parent 69cee8b485
commit 1c65a9b261
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
43 changed files with 461 additions and 115 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

182
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/DicomPackageBuilder.java Normal file
View File

@ -0,0 +1,182 @@
package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.Date;
import java.util.HashSet;
import java.util.Set;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.utils.NPMPackageGenerator;
import org.hl7.fhir.r4.utils.NPMPackageGenerator.Category;
import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.xml.XMLUtil;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.xml.sax.SAXException;
import com.google.gson.JsonArray;
import com.google.gson.JsonObject;
public class DicomPackageBuilder {
private String version;
private String dest;
private String source;
public static void main(String[] args) throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
if (args.length == 0 || args[0].equals("-help")) {
System.out.println("Dicom Package Builder");
System.out.println("");
System.out.println("Before running, use FTP get the latest copy of ftp://medical.nema.org/MEDICAL/Dicom/Resources");
System.out.println("Then run with the following parameters (in order):");
System.out.println("1. the local folder that contains the copy of the FTP folder");
System.out.println("2. the local folder to put the package when it's created");
System.out.println("");
System.out.println("For help, see ");
return;
}
String source = args[0];
String dest = args[1];
DicomPackageBuilder self = new DicomPackageBuilder();
self.setSource(source);
self.setDest(dest);
self.execute();
}
private void execute() throws FileNotFoundException, ParserConfigurationException, SAXException, IOException {
CodeSystem cs = buildCodeSystem();
NPMPackageGenerator gen = new NPMPackageGenerator(Utilities.path(dest, "fhir.dicom#"+version+".tgz"), buildPackage());
int i = 2;
gen.addFile(Category.RESOURCE, "CodeSystem-"+cs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(cs));
ValueSet vs = buildAllValueSet();
gen.addFile(Category.RESOURCE, "ValueSet-"+vs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
Set<String> ids = new HashSet<>();
ids.add(vs.getId());
for (File f : new File(Utilities.path(source, "Resources", "valuesets", "fhir", "json")).listFiles()) {
vs = (ValueSet) JsonParser.loadFile(new FileInputStream(f));
vs.setVersion(version);
if (vs.getId().length() > 64) {
vs.setId(vs.getId().substring(0, 64));
}
if (ids.contains(vs.getId())) {
throw new Error("Duplicate Id once Ids cut off at 64 char: "+vs.getId());
}
ids.add(vs.getId());
gen.addFile(Category.RESOURCE, "ValueSet-"+vs.getId()+".json", new JsonParser().setOutputStyle(OutputStyle.NORMAL).composeBytes(vs));
i++;
}
gen.finish();
System.out.println("Finished - "+i+" resources");
}
private ValueSet buildAllValueSet() {
ValueSet vs = new ValueSet();
vs.setId("all");
vs.setUrl("http://dicom.nema.org/resources/ValueSet/all");
vs.setVersion(version);
vs.setName("All DICOMTerminologyDefinitions");
vs.setTitle("All DICOM Controlled Terminology Definitions");
vs.setStatus(PublicationStatus.ACTIVE);
vs.setExperimental(false);
vs.setPublisher("FHIR Project on behalf of DICOM");
vs.setDate(new Date());
vs.setDescription("All DICOM Code Definitions (Coding Scheme Designator \"DCM\" Coding Scheme Version "+version);
vs.setPurpose("This value set is published as part of FHIR in order to make the codes available to FHIR terminology services and so implementers can easily leverage the codes");
vs.setCopyright("These codes are excerpted from Digital Imaging and Communications in Medicine (DICOM) Standard, Part 16: Content Mapping Resource, Copyright © 2011 by the National Electrical Manufacturers Association.");
vs.getCompose().getIncludeFirstRep().setSystem("http://dicom.nema.org/resources/ontology/DCM");
return vs;
}
private JsonObject buildPackage() {
JsonObject npm = new JsonObject();
npm.addProperty("tools-version", 3);
npm.addProperty("type", "fhir.ig");
npm.addProperty("license", "free");
npm.addProperty("author", "FHIR Project for DICOM");
npm.addProperty("name", "fhir.dicom");
npm.addProperty("url", "http://fhir.org/packages/fhir.dicom");
npm.addProperty("canonical", "http://fhir.org/packages/fhir.dicom");
npm.addProperty("version", version);
JsonArray fv = new JsonArray();
npm.add("fhirVersions", fv);
fv.add("4.0");
return npm;
}
private CodeSystem buildCodeSystem() throws ParserConfigurationException, FileNotFoundException, SAXException, IOException {
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
factory.setNamespaceAware(true);
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(new FileInputStream(Utilities.path(source, "Resources", "Ontology", "DCM", "dcm.owl")));
Element rdf = doc.getDocumentElement();
Element d = XMLUtil.getFirstChild(rdf);
version = processVersion(XMLUtil.getNamedChildText(d, "versionInfo"));
CodeSystem cs = new CodeSystem();
cs.setId("DCM");
cs.setUrl("http://dicom.nema.org/resources/ontology/DCM");
cs.setVersion(version);
cs.setName("DICOMTerminologyDefinitions");
cs.setTitle("DICOM Controlled Terminology Definitions");
cs.getIdentifier().add(new Identifier().setSystem("urn:ietf:rfc:3986").setValue("urn:oid:1.2.840.10008.2.16.4"));
cs.setStatus(PublicationStatus.ACTIVE);
cs.setExperimental(false);
cs.setPublisher("FHIR Project on behalf of DICOM");
cs.setDate(new Date());
cs.setDescription("DICOM Code Definitions (Coding Scheme Designator \"DCM\" Coding Scheme Version "+version);
cs.setPurpose("This code system is published as part of FHIR in order to make the codes available to FHIR terminology services and so implementers can easily leverage the codes");
cs.setCopyright("These codes are excerpted from Digital Imaging and Communications in Medicine (DICOM) Standard, Part 16: Content Mapping Resource, Copyright © 2011 by the National Electrical Manufacturers Association.");
cs.setCaseSensitive(true);
cs.setValueSet("http://dicom.nema.org/resources/ValueSet/all");
cs.setContent(CodeSystemContentMode.COMPLETE);
d = XMLUtil.getNextSibling(d);
while (d != null) {
String code = XMLUtil.getNamedChildText(d, "notation");
String display = XMLUtil.getNamedChildText(d, "prefLabel");
String definition = XMLUtil.getNamedChildText(d, "definition");
ConceptDefinitionComponent cc = new ConceptDefinitionComponent();
cs.getConcept().add(cc);
cc.setCode(code);
cc.setDisplay(display);
cc.setDefinition(definition);
d = XMLUtil.getNextSibling(d);
}
return cs;
}
private String processVersion(String s) {
String[] p = s.split("\\_");
return p[0].substring(0, 4)+"."+(1+(p[0].charAt(4) - 'a'))+"."+p[1];
}
private void setVersion(String version) {
this.version = version;
}
private void setDest(String dest) {
this.dest = dest;
}
private void setSource(String source) {
this.source = source;
}
}

2
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
View File

@ -29,7 +29,7 @@ public class VSACImporter extends OIDBasedValueSetImporter {
CSVReader csv = new CSVReader(new FileInputStream(source));
csv.readHeaders();
FHIRToolingClient fhirToolingClient = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir");
FHIRToolingClient fhirToolingClient = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", "fhir/vsac");
fhirToolingClient.setUsername(username);
fhirToolingClient.setPassword(password);

28
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientFactory.java
View File

@ -39,42 +39,42 @@ import java.net.URISyntaxException;
public class TerminologyClientFactory {
public static TerminologyClient makeClient(String url, FhirPublication v) throws URISyntaxException {
public static TerminologyClient makeClient(String url, String userAgent, FhirPublication v) throws URISyntaxException {
if (v == null)
return new TerminologyClientR5(checkEndsWith("/r4", url));
return new TerminologyClientR5(checkEndsWith("/r4", url), userAgent);
switch (v) {
case DSTU2016May:
return new TerminologyClientR3(checkEndsWith("/r3", url)); // r3 is the least worst match
return new TerminologyClientR3(checkEndsWith("/r3", url), userAgent); // r3 is the least worst match
case DSTU1:
throw new Error("The version " + v + " is not currently supported");
case DSTU2:
return new TerminologyClientR2(checkEndsWith("/r2", url));
return new TerminologyClientR2(checkEndsWith("/r2", url), userAgent);
case R4:
return new TerminologyClientR5(checkEndsWith("/r4", url));
return new TerminologyClientR5(checkEndsWith("/r4", url), userAgent);
case R5:
return new TerminologyClientR5(checkEndsWith("/r4", url)); // r4 for now, since the terminology is currently the same
return new TerminologyClientR5(checkEndsWith("/r4", url), userAgent); // r4 for now, since the terminology is currently the same
case STU3:
return new TerminologyClientR3(checkEndsWith("/r3", url));
return new TerminologyClientR3(checkEndsWith("/r3", url), userAgent);
default:
throw new Error("The version " + v + " is not currently supported");
}
}
public static TerminologyClient makeClient(String url, String v) throws URISyntaxException {
public static TerminologyClient makeClient(String url, String userAgent, String v) throws URISyntaxException {
if (v == null)
return new TerminologyClientR5(checkEndsWith("/r4", url));
return new TerminologyClientR5(checkEndsWith("/r4", url), userAgent);
v = VersionUtilities.getMajMin(v);
switch (v) {
case "1.0":
return new TerminologyClientR2(checkEndsWith("/r2", url));
return new TerminologyClientR2(checkEndsWith("/r2", url), userAgent);
case "1.4":
return new TerminologyClientR3(checkEndsWith("/r3", url)); // r3 is the least worst match
return new TerminologyClientR3(checkEndsWith("/r3", url), userAgent); // r3 is the least worst match
case "3.0":
return new TerminologyClientR3(checkEndsWith("/r3", url));
return new TerminologyClientR3(checkEndsWith("/r3", url), userAgent);
case "4.0":
return new TerminologyClientR4(checkEndsWith("/r4", url));
return new TerminologyClientR4(checkEndsWith("/r4", url), userAgent);
case "4.5":
return new TerminologyClientR5(checkEndsWith("/r4", url)); // r4 for now, since the terminology is currently the same
return new TerminologyClientR5(checkEndsWith("/r4", url), userAgent); // r4 for now, since the terminology is currently the same
default:
throw new Error("The version " + v + " is not currently supported");
}

10
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java
View File

@ -48,8 +48,8 @@ public class TerminologyClientR2 implements TerminologyClient {
private final FHIRToolingClient client; // todo: use the R2 client
public TerminologyClientR2(String address) throws URISyntaxException {
client = new FHIRToolingClient(address);
public TerminologyClientR2(String address, String userAgent) throws URISyntaxException {
client = new FHIRToolingClient(address, userAgent);
}
@Override
@ -153,4 +153,10 @@ public class TerminologyClientR2 implements TerminologyClient {
public TerminologyClient setClientHeaders(ClientHeaders clientHeaders) {
return null;
}
@Override
public TerminologyClient setUserAgent(String userAgent) {
client.setUserAgent(userAgent);
return this;
}
}

14
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
View File

@ -49,13 +49,13 @@ public class TerminologyClientR3 implements TerminologyClient {
private final FHIRToolingClient client; // todo: use the R2 client
private ClientHeaders clientHeaders;
public TerminologyClientR3(String address) throws URISyntaxException {
client = new FHIRToolingClient(address);
public TerminologyClientR3(String address, String userAgent) throws URISyntaxException {
client = new FHIRToolingClient(address, userAgent);
setClientHeaders(new ClientHeaders());
}
public TerminologyClientR3(String address, ClientHeaders clientHeaders) throws URISyntaxException {
client = new FHIRToolingClient(address);
public TerminologyClientR3(String address, String userAgent, ClientHeaders clientHeaders) throws URISyntaxException {
client = new FHIRToolingClient(address, userAgent);
setClientHeaders(clientHeaders);
}
@ -162,4 +162,10 @@ public class TerminologyClientR3 implements TerminologyClient {
this.client.setClientHeaders(this.clientHeaders.headers());
return this;
}
@Override
public TerminologyClient setUserAgent(String userAgent) {
client.setUserAgent(userAgent);
return this;
}
}

14
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java
View File

@ -49,13 +49,13 @@ public class TerminologyClientR4 implements TerminologyClient {
private final FHIRToolingClient client; // todo: use the R2 client
private ClientHeaders clientHeaders;
public TerminologyClientR4(String address) throws URISyntaxException {
this.client = new FHIRToolingClient(address);
public TerminologyClientR4(String address, String userAgent) throws URISyntaxException {
this.client = new FHIRToolingClient(address, userAgent);
setClientHeaders(new ClientHeaders());
}
public TerminologyClientR4(String address, ClientHeaders clientHeaders) throws URISyntaxException {
this.client = new FHIRToolingClient(address);
public TerminologyClientR4(String address, String userAgent, ClientHeaders clientHeaders) throws URISyntaxException {
this.client = new FHIRToolingClient(address, userAgent);
setClientHeaders(clientHeaders);
}
@ -162,4 +162,10 @@ public class TerminologyClientR4 implements TerminologyClient {
this.client.setClientHeaders(this.clientHeaders.headers());
return this;
}
@Override
public TerminologyClient setUserAgent(String userAgent) {
client.setUserAgent(userAgent);
return this;
}
}

14
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR5.java
View File

@ -46,13 +46,13 @@ public class TerminologyClientR5 implements TerminologyClient {
private final FHIRToolingClient client;
private ClientHeaders clientHeaders;
public TerminologyClientR5(String address) throws URISyntaxException {
this.client = new FHIRToolingClient(address);
public TerminologyClientR5(String address, String userAgent) throws URISyntaxException {
this.client = new FHIRToolingClient(address, userAgent);
setClientHeaders(new ClientHeaders());
}
public TerminologyClientR5(String address, ClientHeaders clientHeaders) throws URISyntaxException {
this.client = new FHIRToolingClient(address);
public TerminologyClientR5(String address, String userAgent, ClientHeaders clientHeaders) throws URISyntaxException {
this.client = new FHIRToolingClient(address, userAgent);
setClientHeaders(clientHeaders);
}
@ -148,4 +148,10 @@ public class TerminologyClientR5 implements TerminologyClient {
this.client.setClientHeaders(this.clientHeaders.headers());
return this;
}
@Override
public TerminologyClient setUserAgent(String userAgent) {
client.setUserAgent(userAgent);
return this;
}
}

2
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/BatchLoader.java
View File

@ -117,7 +117,7 @@ public class BatchLoader {
private static int loadBundle(String server, Bundle b, int size, int start, int end) throws URISyntaxException {
System.out.println("Post to "+server+". size = "+Integer.toString(size)+", start = "+Integer.toString(start)+", total = "+Integer.toString(b.getEntry().size()));
FHIRToolingClient client = new FHIRToolingClient(server);
FHIRToolingClient client = new FHIRToolingClient(server, "fhir/batch-loader");
int c = start;
if (end == -1)
end = b.getEntry().size();

4
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/SimpleWorkerContext.java
View File

@ -111,8 +111,8 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
return res;
}
public void connectToTSServer(String url) throws URISyntaxException {
txServer = new FHIRToolingClient(url);
public void connectToTSServer(String url, String userAgent) throws URISyntaxException {
txServer = new FHIRToolingClient(url, userAgent);
}
private void loadFromFile(InputStream stream, String name) throws IOException, FHIRException {

13
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/ClientUtils.java
View File

@ -105,6 +105,7 @@ public class ClientUtils {
private String password;
private ToolingClientLogger logger;
private int retryCount;
private String userAgent;
public HttpHost getProxy() {
return proxy;
@ -258,7 +259,9 @@ public class ClientUtils {
* @param request
*/
protected void configureFhirRequest(HttpRequest request, String format, List<Header> headers) {
request.addHeader("User-Agent", "Java FHIR Client for FHIR");
if (!Utilities.noString(userAgent)) {
request.addHeader("User-Agent", userAgent);
}
if (format != null) {
request.addHeader("Accept",format);
@ -663,5 +666,13 @@ public class ClientUtils {
this.retryCount = retryCount;
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
}
}

12
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/FHIRToolingClient.java
View File

@ -100,14 +100,16 @@ public class FHIRToolingClient {
private ClientUtils utils = new ClientUtils();
//Pass enpoint for client - URI
public FHIRToolingClient(String baseServiceUrl) throws URISyntaxException {
public FHIRToolingClient(String baseServiceUrl, String userAgent) throws URISyntaxException {
preferredResourceFormat = ResourceFormat.RESOURCE_XML;
utils.setUserAgent(userAgent);
detectProxy();
initialize(baseServiceUrl);
}
public FHIRToolingClient(String baseServiceUrl, String username, String password) throws URISyntaxException {
public FHIRToolingClient(String baseServiceUrl, String userAgent, String username, String password) throws URISyntaxException {
preferredResourceFormat = ResourceFormat.RESOURCE_XML;
utils.setUserAgent(userAgent);
utils.setUsername(username);
utils.setPassword(password);
detectProxy();
@ -857,5 +859,11 @@ public class FHIRToolingClient {
utils.setRetryCount(retryCount);
}
public String getUserAgent() {
return utils.getUserAgent();
}
public void setUserAgent(String userAgent) {
utils.setUserAgent(userAgent);
}
}

4
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/context/SimpleWorkerContext.java
View File

@ -218,8 +218,8 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
loadBytes(name, stream);
}
public String connectToTSServer(String url) throws URISyntaxException {
txServer = new FHIRToolingClient(url);
public String connectToTSServer(String url, String userAgent) throws URISyntaxException {
txServer = new FHIRToolingClient(url, userAgent);
txServer.setTimeout(30000);
return txServer.getCapabilitiesStatementQuick().getSoftware().getVersion();
}

2
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/BatchLoader.java
View File

@ -80,7 +80,7 @@ public class BatchLoader {
private static void LoadDirectory(String server, String folder, int size) throws IOException, Exception {
System.out.print("Connecting to "+server+".. ");
FHIRToolingClient client = new FHIRToolingClient(server);
FHIRToolingClient client = new FHIRToolingClient(server, "fhir/batch-loader");
System.out.println("Done");
IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));

17
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/FHIRToolingClient.java
View File

@ -66,10 +66,12 @@ public class FHIRToolingClient {
private ArrayList<Header> headers = new ArrayList<>();
private String username;
private String password;
private String userAgent;
//Pass endpoint for client - URI
public FHIRToolingClient(String baseServiceUrl) throws URISyntaxException {
public FHIRToolingClient(String baseServiceUrl, String userAgent) throws URISyntaxException {
preferredResourceFormat = ResourceFormat.RESOURCE_XML;
this.userAgent = userAgent;
initialize(baseServiceUrl);
}
@ -280,7 +282,7 @@ public class FHIRToolingClient {
if (client.getLogger() != null) {
client.getLogger().logRequest("POST", url.toString(), null, body);
}
result = client.issuePostRequest(url, body, getPreferredResourceFormat(),
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
} else {
if (client.getLogger() != null) {
@ -555,6 +557,9 @@ public class FHIRToolingClient {
if(this.headers != null) {
this.headers.forEach(header -> builder.add(header.toString()));
}
if (!Utilities.noString(userAgent)) {
builder.add("User-Agent: "+userAgent);
}
return builder.build();
}
@ -567,5 +572,13 @@ public class FHIRToolingClient {
String base64usernamePassword = Base64.getEncoder().encodeToString(usernamePassword.getBytes());
return new Header("Authorization", "Basic " + base64usernamePassword);
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
}
}

10
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/network/FhirRequestBuilder.java
View File

@ -63,7 +63,7 @@ public class FhirRequestBuilder {
* @param headers Any additional {@link Headers} to add to the request.
*/
protected static void formatHeaders(Request.Builder request, String format, Headers headers) {
addDefaultHeaders(request);
addDefaultHeaders(request, headers);
if (format != null) addResourceFormatHeaders(request, format);
if (headers != null) addHeaders(request, headers);
}
@ -75,8 +75,10 @@ public class FhirRequestBuilder {
*
* @param request {@link Request.Builder} to add default headers to.
*/
protected static void addDefaultHeaders(Request.Builder request) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
protected static void addDefaultHeaders(Request.Builder request, Headers headers) {
if (headers == null || !headers.names().contains("User-Agent")) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
}
request.addHeader("Accept-Charset", DEFAULT_CHARSET);
}
@ -203,7 +205,7 @@ public class FhirRequestBuilder {
}
public <T extends Resource> ResourceRequest<T> execute() throws IOException {
formatHeaders(httpRequest, resourceFormat, null);
formatHeaders(httpRequest, resourceFormat, headers);
Response response = getHttpClient().newCall(httpRequest.build()).execute();
T resource = unmarshalReference(response, resourceFormat);
return new ResourceRequest<T>(resource, response.code(), getLocationHeader(response.headers()));

4
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/TerminologyClientR4.java
View File

@ -46,8 +46,8 @@ public class TerminologyClientR4 implements TerminologyClient {
private FHIRToolingClient client;
public TerminologyClientR4(String address) throws URISyntaxException {
client = new FHIRToolingClient(address);
public TerminologyClientR4(String address, String userAgent) throws URISyntaxException {
client = new FHIRToolingClient(address, userAgent);
}
@Override

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/BatchLoader.java
View File

@ -80,7 +80,7 @@ public class BatchLoader {
private static void LoadDirectory(String server, String folder, int size) throws IOException, Exception {
System.out.print("Connecting to "+server+".. ");
FHIRToolingClient client = new FHIRToolingClient(server);
FHIRToolingClient client = new FHIRToolingClient(server, "fhir/batch-loader");
System.out.println("Done");
IniFile ini = new IniFile(Utilities.path(folder, "batch-load-progress.ini"));

17
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/FHIRToolingClient.java
View File

@ -63,10 +63,12 @@ public class FHIRToolingClient {
private ArrayList<Header> headers = new ArrayList<>();
private String username;
private String password;
private String userAgent;
//Pass endpoint for client - URI
public FHIRToolingClient(String baseServiceUrl) throws URISyntaxException {
public FHIRToolingClient(String baseServiceUrl, String userAgent) throws URISyntaxException {
preferredResourceFormat = ResourceFormat.RESOURCE_XML;
this.userAgent = userAgent;
initialize(baseServiceUrl);
}
@ -277,7 +279,7 @@ public class FHIRToolingClient {
if (client.getLogger() != null) {
client.getLogger().logRequest("POST", url.toString(), null, body);
}
result = client.issuePostRequest(url, body, getPreferredResourceFormat(),
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
} else {
if (client.getLogger() != null) {
@ -528,6 +530,9 @@ public class FHIRToolingClient {
if(this.headers != null) {
this.headers.forEach(header -> builder.add(header.toString()));
}
if (!Utilities.noString(userAgent)) {
builder.add("User-Agent: "+userAgent);
}
return builder.build();
}
@ -540,5 +545,13 @@ public class FHIRToolingClient {
String base64usernamePassword = Base64.getEncoder().encodeToString(usernamePassword.getBytes());
return new Header("Authorization", "Basic " + base64usernamePassword);
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
}
}

10
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/FhirRequestBuilder.java
View File

@ -63,7 +63,7 @@ public class FhirRequestBuilder {
* @param headers Any additional {@link Headers} to add to the request.
*/
protected static void formatHeaders(Request.Builder request, String format, Headers headers) {
addDefaultHeaders(request);
addDefaultHeaders(request, headers);
if (format != null) addResourceFormatHeaders(request, format);
if (headers != null) addHeaders(request, headers);
}
@ -75,8 +75,10 @@ public class FhirRequestBuilder {
*
* @param request {@link Request.Builder} to add default headers to.
*/
protected static void addDefaultHeaders(Request.Builder request) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
protected static void addDefaultHeaders(Request.Builder request, Headers headers) {
if (headers == null || !headers.names().contains("User-Agent")) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
}
request.addHeader("Accept-Charset", DEFAULT_CHARSET);
}
@ -203,7 +205,7 @@ public class FhirRequestBuilder {
}
public <T extends Resource> ResourceRequest<T> execute() throws IOException {
formatHeaders(httpRequest, resourceFormat, null);
formatHeaders(httpRequest, resourceFormat, headers);
Response response = getHttpClient().newCall(httpRequest.build()).execute();
T resource = unmarshalReference(response, resourceFormat);
return new ResourceRequest<T>(resource, response.code(), getLocationHeader(response.headers()));

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ValueSetComparer.java
View File

@ -394,7 +394,7 @@ public class ValueSetComparer extends CanonicalResourceComparer {
private void compareExpansions(ValueSet left, ValueSet right, ValueSetComparison res) {
ValueSet expL = left.hasExpansion() ? left : expand(left, res, "left", session.getContextLeft());
ValueSet expR = left.hasExpansion() ? left : expand(right, res, "right", session.getContextRight());
ValueSet expR = right.hasExpansion() ? right : expand(right, res, "right", session.getContextRight());
if (expL != null && expR != null) {
// ignore the parameters for now
compareConcepts(expL.getExpansion().getContains(), expR.getExpansion().getContains(), res.forceExpansion(), res.getUnion().getExpansion().getContains(), res.getIntersection().getExpansion().getContains(), "ValueSet.expansion.contains", res);

38
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -2452,19 +2452,19 @@ public class ProfileUtilities extends TranslatingUtilities {
if (webUrl != null) {
// also, must touch up the markdown
if (element.hasDefinition())
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl()));
element.setDefinition(processRelativeUrls(element.getDefinition(), webUrl, baseSpecUrl(), context.getResourceNames()));
if (element.hasComment())
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl()));
element.setComment(processRelativeUrls(element.getComment(), webUrl, baseSpecUrl(), context.getResourceNames()));
if (element.hasRequirements())
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl()));
element.setRequirements(processRelativeUrls(element.getRequirements(), webUrl, baseSpecUrl(), context.getResourceNames()));
if (element.hasMeaningWhenMissing())
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl()));
element.setMeaningWhenMissing(processRelativeUrls(element.getMeaningWhenMissing(), webUrl, baseSpecUrl(), context.getResourceNames()));
}
}
return element;
}
public static String processRelativeUrls(String markdown, String webUrl, String basePath) {
public static String processRelativeUrls(String markdown, String webUrl, String basePath, List<String> resourceNames) {
StringBuilder b = new StringBuilder();
int i = 0;
while (i < markdown.length()) {
@ -2485,7 +2485,7 @@ public class ProfileUtilities extends TranslatingUtilities {
// This code is trying to guess which relative references are actually to the
// base specification.
//
if (isLikelySourceURLReference(url)) {
if (isLikelySourceURLReference(url, resourceNames)) {
b.append("](");
b.append(basePath);
i = i + 1;
@ -2507,14 +2507,36 @@ public class ProfileUtilities extends TranslatingUtilities {
}
public static boolean isLikelySourceURLReference(String url) {
public static boolean isLikelySourceURLReference(String url, List<String> resourceNames) {
if (resourceNames != null) {
for (String n : resourceNames) {
if (url.startsWith(n.toLowerCase()+".html")) {
return true;
}
if (url.startsWith(n.toLowerCase()+"-definitions.html")) {
return true;
}
}
}
return
url.startsWith("extensibility.html") ||
url.startsWith("terminologies.html") ||
url.startsWith("observation.html") ||
url.startsWith("codesystem.html") ||
url.startsWith("fhirpath.html") ||
url.startsWith("datatypes.html") ||
url.startsWith("operations.html") ||
url.startsWith("resource.html") ||
url.startsWith("elementdefinition.html") ||
url.startsWith("element-definitions.html") ||
url.startsWith("snomedct.html") ||
url.startsWith("loinc.html") ||
url.startsWith("http.html") ||
url.startsWith("references") ||
url.startsWith("narrative.html") ||
(url.startsWith("extension-") || url.contains(".html")) ||
url.startsWith("search.html") ||
url.startsWith("patient-operation-match.html") ||
(url.startsWith("extension-") && url.contains(".html")) ||
url.startsWith("resource-definitions.html");
}

11
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
View File

@ -207,6 +207,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
protected TimeTracker clock;
private boolean tlogging = true;
private ICanonicalResourceLocator locator;
protected String userAgent;
public BaseWorkerContext() throws FileNotFoundException, IOException, FHIRException {
txCache = new TerminologyCache(lock, null);
@ -2100,4 +2101,14 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
this.locator = locator;
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
if (txClient != null)
txClient.setUserAgent(userAgent);
}
}

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -296,6 +296,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
txLog = new HTMLClientLogger(log);
}
txClient.setLogger(txLog);
txClient.setUserAgent(userAgent);
CapabilityStatement cps = txClient.getCapabilitiesStatementQuick();
setTxCaps(txClient.getTerminologyCapabilities());
return cps.getSoftware().getVersion();

1
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/TerminologyClient.java
View File

@ -54,4 +54,5 @@ public interface TerminologyClient {
CanonicalResource read(String type, String id);
ClientHeaders getClientHeaders();
TerminologyClient setClientHeaders(ClientHeaders clientHeaders);
TerminologyClient setUserAgent(String userAgent);
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/BatchLoader.java
View File

@ -117,7 +117,7 @@ public class BatchLoader {
private static int loadBundle(String server, Bundle b, int size, int start, int end) throws URISyntaxException {
System.out.println("Post to "+server+". size = "+Integer.toString(size)+", start = "+Integer.toString(start)+", total = "+Integer.toString(b.getEntry().size()));
FHIRToolingClient client = new FHIRToolingClient(server);
FHIRToolingClient client = new FHIRToolingClient(server, "fhir/batch-loader");
int c = start;
if (end == -1)
end = b.getEntry().size();

23
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java
View File

@ -95,10 +95,12 @@ public class FHIRToolingClient {
private ArrayList<Header> headers = new ArrayList<>();
private String username;
private String password;
private String userAgent;
//Pass endpoint for client - URI
public FHIRToolingClient(String baseServiceUrl) throws URISyntaxException {
public FHIRToolingClient(String baseServiceUrl, String userAgent) throws URISyntaxException {
preferredResourceFormat = ResourceFormat.RESOURCE_XML;
this.userAgent = userAgent;
initialize(baseServiceUrl);
}
@ -309,7 +311,7 @@ public class FHIRToolingClient {
if (client.getLogger() != null) {
client.getLogger().logRequest("POST", url.toString(), null, body);
}
result = client.issuePostRequest(url, body, getPreferredResourceFormat(),
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
} else {
if (client.getLogger() != null) {
@ -336,7 +338,9 @@ public class FHIRToolingClient {
public Bundle transaction(Bundle batch) {
Bundle transactionResult = null;
try {
transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(), ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), "transaction", TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(), ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(),
"transaction", TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -560,6 +564,9 @@ public class FHIRToolingClient {
if(this.headers != null) {
this.headers.forEach(header -> builder.add(header.toString()));
}
if (!Utilities.noString(userAgent)) {
builder.add("User-Agent: "+userAgent);
}
return builder.build();
}
@ -572,5 +579,15 @@ public class FHIRToolingClient {
String base64usernamePassword = Base64.getEncoder().encodeToString(usernamePassword.getBytes());
return new Header("Authorization", "Basic " + base64usernamePassword);
}
public String getUserAgent() {
return userAgent;
}
public void setUserAgent(String userAgent) {
this.userAgent = userAgent;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/network/Client.java
View File

@ -149,6 +149,7 @@ public class Client {
public Bundle postBatchRequest(URI resourceUri,
byte[] payload,
String resourceFormat,
Headers headers,
String message,
int timeout) throws IOException {
if (payload == null) throw new EFhirClientException("POST requests require a non-null payload");
@ -157,7 +158,7 @@ public class Client {
.url(resourceUri.toURL())
.post(body);
return executeBundleRequest(request, resourceFormat, new Headers.Builder().build(), message, retryCount, timeout);
return executeBundleRequest(request, resourceFormat, headers, message, retryCount, timeout);
}
public <T extends Resource> Bundle executeBundleRequest(Request.Builder request,

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilder.java
View File

@ -63,7 +63,7 @@ public class FhirRequestBuilder {
* @param headers Any additional {@link Headers} to add to the request.
*/
protected static void formatHeaders(Request.Builder request, String format, Headers headers) {
addDefaultHeaders(request);
addDefaultHeaders(request, headers);
if (format != null) addResourceFormatHeaders(request, format);
if (headers != null) addHeaders(request, headers);
}
@ -75,8 +75,10 @@ public class FhirRequestBuilder {
*
* @param request {@link Request.Builder} to add default headers to.
*/
protected static void addDefaultHeaders(Request.Builder request) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
protected static void addDefaultHeaders(Request.Builder request, Headers headers) {
if (headers == null || !headers.names().contains("User-Agent")) {
request.addHeader("User-Agent", "hapi-fhir-tooling-client");
}
request.addHeader("Accept-Charset", DEFAULT_CHARSET);
}
@ -203,7 +205,7 @@ public class FhirRequestBuilder {
}
public <T extends Resource> ResourceRequest<T> execute() throws IOException {
formatHeaders(httpRequest, resourceFormat, null);
formatHeaders(httpRequest, resourceFormat, headers);
Response response = getHttpClient().newCall(httpRequest.build()).execute();
T resource = unmarshalReference(response, resourceFormat);
return new ResourceRequest<T>(resource, response.code(), getLocationHeader(response.headers()));

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/FHIRToolingClientTest.java
View File

@ -65,7 +65,7 @@ class FHIRToolingClientTest {
Mockito.when(mockClient.executeBundleRequest(Mockito.any(Request.Builder.class), Mockito.anyString(),
Mockito.any(Headers.class), Mockito.anyString(), Mockito.anyInt(), Mockito.anyLong()))
.thenReturn(generateBundle());
toolingClient = new FHIRToolingClient(TX_ADDR);
toolingClient = new FHIRToolingClient(TX_ADDR, "fhir/test-cases");
toolingClient.setClient(mockClient);
}

2
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/utils/client/network/FhirRequestBuilderTest.java
View File

@ -19,7 +19,7 @@ class FhirRequestBuilderTest {
@DisplayName("Test default headers are added correctly.")
void addDefaultHeaders() {
Request.Builder request = new Request.Builder().url("http://www.google.com");
FhirRequestBuilder.addDefaultHeaders(request);
FhirRequestBuilder.addDefaultHeaders(request, null);
Map<String, List<String>> headersMap = request.build().headers().toMultimap();
Assertions.assertNotNull(headersMap.get("User-Agent"), "User-Agent header null.");

30
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/ZipGenerator.java
View File

@ -121,19 +121,23 @@ public class ZipGenerator {
File f = new CSFile(actualDir);
String files[] = f.list();
for (int i = 0; i < files.length; i++) {
if ( new CSFile(actualDir + files[i]).isFile() && ((ext == null || files[i].endsWith(ext)) && (noExt == null || !files[i].endsWith(noExt)))) {
FileInputStream fi = new FileInputStream(actualDir + files[i]);
BufferedInputStream origin = new BufferedInputStream(fi, BUFFER);
ZipEntry entry = new ZipEntry(statedDir + files[i]);
names.add(statedDir + files[i]);
out.putNextEntry(entry);
int count;
while ((count = origin.read(data, 0, BUFFER)) != -1) {
out.write(data, 0, count);
}
origin.close();
}
if (files == null) {
System.out.println("no files found in "+f.getName());
} else {
for (int i = 0; i < files.length; i++) {
if ( new CSFile(actualDir + files[i]).isFile() && ((ext == null || files[i].endsWith(ext)) && (noExt == null || !files[i].endsWith(noExt)))) {
FileInputStream fi = new FileInputStream(actualDir + files[i]);
BufferedInputStream origin = new BufferedInputStream(fi, BUFFER);
ZipEntry entry = new ZipEntry(statedDir + files[i]);
names.add(statedDir + files[i]);
out.putNextEntry(entry);
int count;
while ((count = origin.read(data, 0, BUFFER)) != -1) {
out.write(data, 0, count);
}
origin.close();
}
}
}
}

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -510,7 +510,7 @@ public class I18nConstants {
public static final String TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE = "TYPE_SPECIFIC_CHECKS_DT_CANONICAL_TYPE";
public static final String TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE = "TYPE_SPECIFIC_CHECKS_DT_CANONICAL_RESOLVE";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_STRAT = "Type_Specific_Checks_DT_UUID_Strat";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_VAID = "Type_Specific_Checks_DT_UUID_Vaid";
public static final String TYPE_SPECIFIC_CHECKS_DT_UUID_VALID = "Type_Specific_Checks_DT_UUID_Valid";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER = "Unable_to_connect_to_terminology_server";
public static final String UNABLE_TO_CONNECT_TO_TERMINOLOGY_SERVER_USE_PARAMETER_TX_NA_TUN_RUN_WITHOUT_USING_TERMINOLOGY_SERVICES_TO_VALIDATE_LOINC_SNOMED_ICDX_ETC_ERROR__ = "Unable_to_connect_to_terminology_server_Use_parameter_tx_na_tun_run_without_using_terminology_services_to_validate_LOINC_SNOMED_ICDX_etc_Error__";
public static final String UNABLE_TO_FIND_BASE_DEFINITION_FOR_LOGICAL_MODEL__FROM_ = "Unable_to_find_base_definition_for_logical_model__from_";

11
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/json/JsonTrackingParser.java
View File

@ -38,6 +38,7 @@ import java.io.InputStream;
import java.math.BigDecimal;
import java.net.HttpURLConnection;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.Map;
import java.util.Stack;
@ -674,6 +675,16 @@ public class JsonTrackingParser {
return gson.toJson(json);
}
public static byte[] writeBytes(JsonObject json, boolean pretty) {
if (pretty) {
Gson gson = new GsonBuilder().setPrettyPrinting().create();
return gson.toJson(json).getBytes(StandardCharsets.UTF_8);
} else {
Gson gson = new GsonBuilder().create();
return gson.toJson(json).getBytes(StandardCharsets.UTF_8);
}
}
public static JsonObject fetchJson(String source) throws IOException {
URL url = new URL(source+"?nocache=" + System.currentTimeMillis());
HttpURLConnection c = (HttpURLConnection) url.openConnection();

19
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
View File

@ -64,6 +64,7 @@ import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JSONUtil;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.npm.NpmPackage.ITransformingLoader;
import org.hl7.fhir.utilities.npm.NpmPackage.PackageResourceInformationSorter;
import org.hl7.fhir.utilities.npm.PackageGenerator.PackageType;
@ -84,6 +85,12 @@ import com.google.gson.JsonObject;
*/
public class NpmPackage {
public interface ITransformingLoader {
byte[] load(File f);
}
public class PackageResourceInformationSorter implements Comparator<PackageResourceInformation> {
@Override
public int compare(PackageResourceInformation o1, PackageResourceInformation o2) {
@ -1054,6 +1061,18 @@ public class NpmPackage {
}
}
public void loadAllFiles(ITransformingLoader loader) throws IOException {
for (String folder : folders.keySet()) {
NpmPackageFolder pf = folders.get(folder);
String p = folder.contains("$") ? path : Utilities.path(path, folder);
for (File f : new File(p).listFiles()) {
if (!f.isDirectory() && !isInternalExemptFile(f)) {
pf.getContent().put(f.getName(), loader.load(f));
}
}
}
}
public boolean isChangedByLoader() {
return changedByLoader;
}

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/HierarchicalTableGenerator.java
View File

@ -598,7 +598,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
TableModel model = new TableModel(id, isActive);
model.setAlternating(alternating);
model.setDocoImg(prefix+"help16.png");
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Flags"), translate("sd.hint", "Information about the use of the element"), null, 0));
@ -615,7 +615,7 @@ public class HierarchicalTableGenerator extends TranslatingUtilities {
TableModel model = new TableModel(id, true);
model.setAlternating(true);
model.setDocoImg(prefix+"help16.png");
model.setDocoImg(Utilities.pathURL(prefix, "help16.png"));
model.setDocoRef(Utilities.pathURL(prefix, "formats.html#table"));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "Name"), translate("sd.hint", "The logical name of the element"), null, 0));
model.getTitles().add(new Title(null, model.getDocoRef(), translate("sd.head", "L Flags"), translate("sd.hint", "Information about the use of the element - Left Structure"), null, 0).setStyle("border-left: 1px grey solid"));

2
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -208,7 +208,7 @@ Type_Specific_Checks_DT_URI_UUID = URI values cannot start with uuid:
Type_Specific_Checks_DT_URI_WS = URI values cannot have whitespace(''{0}'')
Type_Specific_Checks_DT_URL_Resolve = URL value ''{0}'' does not resolve
Type_Specific_Checks_DT_UUID_Strat = UUIDs must start with urn:uuid:
Type_Specific_Checks_DT_UUID_Vaid = UUIDs must be valid
Type_Specific_Checks_DT_UUID_Valid = UUIDs must be valid (and lowercase)
Validation_BUNDLE_Message = The first entry in a message must be a MessageHeader
Validation_VAL_Content_Unknown = Unrecognised Content {0}
Validation_VAL_NoType = Unknown type {0}

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -189,23 +189,26 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
igLoader = new IgLoader(getPcm(), getContext(), getVersion(), isDebug());
}
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, String vString) throws FHIRException, IOException, URISyntaxException {
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, boolean canRunWithoutTerminologyServer, String vString, String userAgent) throws FHIRException, IOException, URISyntaxException {
loadCoreDefinitions(src, false, null);
getContext().setUserAgent(userAgent);
getContext().setCanRunWithoutTerminology(canRunWithoutTerminologyServer);
setTerminologyServer(txsrvr, txLog, version);
setVersion(vString);
igLoader = new IgLoader(getPcm(), getContext(), getVersion(), isDebug());
}
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, String vString) throws FHIRException, IOException, URISyntaxException {
public ValidationEngine(String src, String txsrvr, String txLog, FhirPublication version, String vString, String userAgent) throws FHIRException, IOException, URISyntaxException {
loadCoreDefinitions(src, false, null);
getContext().setUserAgent(userAgent);
setTerminologyServer(txsrvr, txLog, version);
setVersion(vString);
igLoader = new IgLoader(getPcm(), getContext(), getVersion(), isDebug());
}
public ValidationEngine(String src, String vString, TimeTracker tt) throws FHIRException, IOException, URISyntaxException {
public ValidationEngine(String src, String vString, TimeTracker tt, String userAgent) throws FHIRException, IOException, URISyntaxException {
loadCoreDefinitions(src, false, tt);
getContext().setUserAgent(userAgent);
setVersion(vString);
igLoader = new IgLoader(getPcm(), getContext(), getVersion(), isDebug());
}
@ -271,7 +274,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IPackageInst
return "n/a: No Terminology Server";
} else {
try {
return context.connectToTSServer(TerminologyClientFactory.makeClient(url, version), log);
return context.connectToTSServer(TerminologyClientFactory.makeClient(url, context.getUserAgent(), version), log);
} catch (Exception e) {
if (context.isCanRunWithoutTerminology()) {
return "n/a: Running without Terminology Server (error: " + e.getMessage() + ")";

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcher.java
View File

@ -231,7 +231,7 @@ public class StandAloneValidatorFetcher implements IValidatorResourceFetcher, IC
String root = getRoot(p, url);
if (root != null) {
TerminologyClient c;
c = TerminologyClientFactory.makeClient(root, context.getVersion());
c = TerminologyClientFactory.makeClient(root, "fhir/validator", context.getVersion());
return c.read(p[p.length - 2], p[p.length - 1]);
} else {
throw new FHIRException("The URL '" + url + "' is not known to the FHIR validator, and has not been provided as part of the setup / parameters");

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/services/ValidationService.java
View File

@ -265,7 +265,7 @@ public class ValidationService {
System.out.println("No such cached session exists for session id " + sessionId + ", re-instantiating validator.");
}
System.out.print(" Load FHIR v" + cliContext.getSv() + " from " + definitions);
ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt);
ValidationEngine validator = new ValidationEngine(definitions, cliContext.getSv(), tt, "fhir/validator");
sessionId = sessionCache.cacheSession(validator);
FhirPublication ver = FhirPublication.fromCode(cliContext.getSv());

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Common.java
View File

@ -87,7 +87,7 @@ public class Common {
public static ValidationEngine getValidationEngine(String version, String txServer, String definitions, String txLog, TimeTracker tt) throws Exception {
System.out.println("Loading (v = " + version + ", tx server -> " + txServer + ")");
ValidationEngine ve = new ValidationEngine(definitions, version, tt);
ValidationEngine ve = new ValidationEngine(definitions, version, tt, "fhir/validator");
ve.connectToTSServer(txServer, txLog, FhirPublication.fromCode(version));
return ve;
}

2
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2035,7 +2035,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
if (url != null && url.startsWith("urn:uuid:")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isValidUUID(url.substring(9)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_UUID_VAID);
rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isValidUUID(url.substring(9)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_UUID_VALID);
}
if (url != null && url.startsWith("urn:oid:")) {
rule(errors, IssueType.INVALID, e.line(), e.col(), path, Utilities.isOid(url.substring(8)), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_OID_VALID);

20
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationEngineTests.java
View File

@ -17,8 +17,8 @@ import org.junit.jupiter.api.Test;
public class ValidationEngineTests {
private static final String DEF_TX = "http://tx.fhir.org";
private static final String DBG_TX = "http://local.fhir.org:960";
public static final String DEF_TX = "http://tx.fhir.org";
// public static final String DEF_TX = "http://local.fhir.org:960";
public static boolean inbuild;
@ -26,7 +26,7 @@ public class ValidationEngineTests {
public void testCurrentXml() throws Exception {
if (!TestUtilities.silent)
System.out.println("TestCurrentXml: Validate patient-example.xml in Current version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4, "4.0.1");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4, "4.0.1", "fhir/test-cases");
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient-example.xml"), null);
int e = errors(op);
int w = warnings(op);
@ -46,7 +46,7 @@ public class ValidationEngineTests {
public void testCurrentJson() throws Exception {
if (!TestUtilities.silent)
System.out.println("TestCurrentJson: Validate patient-example.json in Current version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4, "4.0.1");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, null, FhirPublication.R4, "4.0.1", "fhir/test-cases");
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "patient-example.json"), null);
int e = errors(op);
int w = warnings(op);
@ -66,8 +66,8 @@ public class ValidationEngineTests {
}
if (!TestUtilities.silent)
System.out.println("Test140: Validate patient-example.xml in v1.4.0 version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, null, FhirPublication.DSTU2016May, "1.4.0");
ve.setNoInvariantChecks(true);
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, null, FhirPublication.DSTU2016May, "1.4.0", "fhir/test-cases");
ve.getContext().setUserAgent("fhir/test-cases");
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient140.xml"), null);
if (!TestUtilities.silent)
for (OperationOutcomeIssueComponent iss : op.getIssue()) {
@ -91,7 +91,7 @@ public class ValidationEngineTests {
}
if (!org.hl7.fhir.validation.tests.utilities.TestUtilities.silent)
System.out.println("Test102: Validate patient-example.xml in v1.0.2 version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2", "fhir/test-cases");
ve.setNoInvariantChecks(true);
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "patient102.xml"), null);
if (!TestUtilities.silent)
@ -116,7 +116,7 @@ public class ValidationEngineTests {
}
if (!TestUtilities.silent)
System.out.println("TestObs102: Validate patient-example.xml in v1.0.2 version");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, null, FhirPublication.DSTU2, "1.0.2", "fhir/test-cases");
ve.setNoInvariantChecks(true);
OperationOutcome op = ve.validate(FhirFormat.JSON, TestingUtilities.loadTestResourceStream("validator", "observation102.json"), null);
if (!TestUtilities.silent)
@ -138,7 +138,7 @@ public class ValidationEngineTests {
public void test301() throws Exception {
if (!TestUtilities.silent)
System.out.println("Test301: Validate observation301.xml against Core");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3, "3.0.2");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3, "3.0.2", "fhir/test-cases");
if (!TestUtilities.silent)
System.out.println(" .. load USCore");
OperationOutcome op = ve.validate(FhirFormat.XML, TestingUtilities.loadTestResourceStream("validator", "observation301.xml"), null);
@ -157,7 +157,7 @@ public class ValidationEngineTests {
public void test301USCore() throws Exception {
if (!TestUtilities.silent)
System.out.println("Test301USCore: Validate patient300.xml against US-Core");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3, "3.0.2");
ValidationEngine ve = new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, null, FhirPublication.STU3, "3.0.2", "fhir/test-cases");
IgLoader igLoader = new IgLoader(ve.getPcm(), ve.getContext(), ve.getVersion(), true);
if (!TestUtilities.silent)
System.out.println(" .. load USCore");

13
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -110,8 +110,6 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
private String version;
private String name;
private static final String DEF_TX = "http://tx.fhir.org";
// private static final String DEF_TX = "http://local.fhir.org:960";
private static Map<String, ValidationEngine> ve = new HashMap<>();
private static ValidationEngine vCurr;
private static IgLoader igLoader;
@ -142,19 +140,20 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
version = VersionUtilities.getMajMin(version);
if (!ve.containsKey(version)) {
if (version.startsWith("5.0"))
ve.put(version, new ValidationEngine("hl7.fhir.r5.core#4.5.0", DEF_TX, txLog, FhirPublication.R5, true, "4.5.0"));
ve.put(version, new ValidationEngine("hl7.fhir.r5.core#4.5.0", ValidationEngineTests.DEF_TX, txLog, FhirPublication.R5, true, "4.5.0", "fhir/test-cases"));
else if (version.startsWith("3.0"))
ve.put(version, new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, txLog, FhirPublication.STU3, true, "3.0.2"));
ve.put(version, new ValidationEngine("hl7.fhir.r3.core#3.0.2", ValidationEngineTests.DEF_TX, txLog, FhirPublication.STU3, true, "3.0.2", "fhir/test-cases"));
else if (version.startsWith("4.0"))
ve.put(version, new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, txLog, FhirPublication.R4, true, "4.0.1"));
ve.put(version, new ValidationEngine("hl7.fhir.r4.core#4.0.1", ValidationEngineTests.DEF_TX, txLog, FhirPublication.R4, true, "4.0.1", "fhir/test-cases"));
else if (version.startsWith("1.0"))
ve.put(version, new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, txLog, FhirPublication.DSTU2, true, "1.0.2"));
ve.put(version, new ValidationEngine("hl7.fhir.r2.core#1.0.2", ValidationEngineTests.DEF_TX, txLog, FhirPublication.DSTU2, true, "1.0.2", "fhir/test-cases"));
else if (version.startsWith("1.4"))
ve.put(version, new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, txLog, FhirPublication.DSTU2016May, true, "1.4.0"));
ve.put(version, new ValidationEngine("hl7.fhir.r2b.core#1.4.0", ValidationEngineTests.DEF_TX, txLog, FhirPublication.DSTU2016May, true, "1.4.0", "fhir/test-cases"));
else
throw new Exception("unknown version " + version);
}
vCurr = ve.get(version);
vCurr.getContext().setUserAgent("fhir/test-cases");
igLoader = new IgLoader(vCurr.getPcm(), vCurr.getContext(), vCurr.getVersion(), true);
if (TestingUtilities.fcontexts == null) {
TestingUtilities.fcontexts = new HashMap<>();