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Merge pull request #804 from hapifhir/gg-202205-pv 

Gg 202205 pv
This commit is contained in:
Grahame Grieve 2022-05-05 09:57:54 +10:00 committed by GitHub
parent 6df50d482b 3bc1f4bb38
commit 54494d699e
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 113 additions and 16 deletions
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4
RELEASE_NOTES.md
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@ -1,7 +1,7 @@
## Validator Changes
* no changes
* Handle invalid HTTP responses better when accessing packages
## Other code changes
* no changes
* Fix various rendering NPEs

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CodeSystemComparer.java
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@ -422,7 +422,7 @@ public class CodeSystemComparer extends CanonicalResourceComparer {
ConceptPropertyComponent cp = null;
if (cd != null) {
for (ConceptPropertyComponent t : cd.getProperty()) {
if (t.getCode().equals(c)) {
if (t.hasCode() && t.getCode().equals(c)) {
cp = t;
}
}

3
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
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@ -3800,6 +3800,9 @@ public class ProfileUtilities extends TranslatingUtilities {
if (contentReference.contains("#")) {
String url = contentReference.substring(0, contentReference.indexOf("#"));
contentReference = contentReference.substring(contentReference.indexOf("#"));
if (Utilities.noString(url)) {
url = source.getUrl();
}
if (!url.equals(source.getUrl())) {
source = context.fetchResource(StructureDefinition.class, url);
if (source == null) {

12
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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@ -490,11 +490,13 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
types = new String[] { "StructureDefinition", "ValueSet", "CodeSystem", "SearchParameter", "OperationDefinition", "Questionnaire", "ConceptMap", "StructureMap", "NamingSystem", "Measures" };
}
for (PackageResourceInformation pri : pi.listIndexedResources(types)) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version(), pi.dateAsDate()));
t++;
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
if (!pri.getFilename().contains("ig-r4")) {
try {
registerResourceFromPackage(new PackageResourceLoader(pri, loader), new PackageVersion(pi.id(), pi.version(), pi.dateAsDate()));
t++;
} catch (FHIRException e) {
throw new FHIRException(formatMessage(I18nConstants.ERROR_READING__FROM_PACKAGE__, pri.getFilename(), pi.name(), pi.version(), e.getMessage()), e);
}
}
}
}

8
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/SimpleHTTPClient.java
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@ -71,8 +71,12 @@ public class SimpleHTTPClient {
public void checkThrowException() throws IOException {
if (code >= 300) {
String filename = Utilities.path("[tmp]", "fhir-http-"+(++counter)+".log");
TextFile.bytesToFile(content, filename);
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (content in "+filename+")");
if (content.length == 0) {
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (no content)");
} else {
TextFile.bytesToFile(content, filename);
throw new IOException("Invalid HTTP response "+code+" from "+source+" ("+message+") (content in "+filename+")");
}
}
}
}

16
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/PackageHacker.java
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@ -27,7 +27,7 @@ public class PackageHacker {
private static boolean useSecureReferences = false;
public static void main(String[] args) throws FileNotFoundException, IOException {
new PackageHacker().edit("M:\\web\\hl7.org\\fhir\\5.0.0-snapshot1\\hl7.fhir.r5.examples.tgz");
new PackageHacker().edit("/Users/grahamegrieve/work/test-cases/validator/swiss.mednet.fhir#0.5.0.tgz");
}
private void edit(String name) throws FileNotFoundException, IOException {
@ -59,7 +59,7 @@ public class PackageHacker {
private void change(JsonObject npm, Map<String, byte[]> content) throws FileNotFoundException, IOException {
fixVersions(npm);
npm.remove("notForPublication");
// npm.remove("notForPublication");
// npm.addProperty("url", "http://hl7.org/fhir/us/carin-rtpbc/STU1");
// npm.remove("name");
// npm.addProperty("name", "hl7.fhir.uv.smart-app-launch");
@ -69,10 +69,14 @@ public class PackageHacker {
//// npm.addProperty("description", "Group Wrapper that includes all the R4 packages");
// npm.remove("url");
// npm.addProperty("url", "https://terminology.hl7.org/1.0.0/");
// npm.remove("dependencies");
// JsonObject dep = new JsonObject();
// npm.add("dependencies", dep);
// dep.addProperty("hl7.fhir.r3.core", "3.0.1");
npm.remove("dependencies");
JsonObject dep = new JsonObject();
npm.add("dependencies", dep);
dep.addProperty("hl7.fhir.r4.core", "4.0.1");
dep.addProperty("ch.fhir.ig.ch-core", "2.0.0");
dep.addProperty("ch.fhir.ig.ch-epr-term", "2.0.4");
dep.addProperty("ch.fhir.ig.ch-emed","2.0.0");
// dep.addProperty("hl7.fhir.r4.examples", "4.0.1");
// dep.addProperty("hl7.fhir.r4.expansions", "4.0.1");
// dep.addProperty("hl7.fhir.r4.elements", "4.0.1");

84
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ipa/IPAValidator.java Normal file
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@ -0,0 +1,84 @@
package org.hl7.fhir.validation.ipa;
import java.util.List;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.validation.instance.InstanceValidator;
/**
* You give this validator three parameters:
* URL of server
* access token for the server (most be already logged in)
* patient ID - the patient ID that was authorised by the log in
*
* @author grahamegrieve
*
*/
public class IPAValidator {
private String address;
private String token;
private String urn;
private InstanceValidator validator;
public IPAValidator(String address, String token, String urn, InstanceValidator validator) {
super();
this.address = address;
this.token = token;
this.urn = urn;
this.validator = validator;
}
public String getAddress() {
return address;
}
public void setAddress(String address) {
this.address = address;
}
public String getToken() {
return token;
}
public void setToken(String token) {
this.token = token;
}
public String getUrn() {
return urn;
}
public void setUrn(String urn) {
this.urn = urn;
}
public InstanceValidator getValidator() {
return validator;
}
public void setValidator(InstanceValidator validator) {
this.validator = validator;
}
public void validate() {
List<Patient> patients = searchPatients();
// check list of patients that have access to
// require that at least one of the patients matches the URL
// validate all resources and links
// validate search parameters
// check self links
// AllergyIntolerance patient patient+clinical-status
// Condition patient patient+category, patient+clinical-status, patient+code, patient+onset-date, patient+category+clinical_status
// DocumentReference _id, patient, patient+category, patient+type patient+category+date, patient+status, patient+type+period
// Immunization patient patient+date, patient+status
// MedicationRequest patient patient+intent, patient+intent+authoredon, patient+intent+status
// MedicationStatement subject subject+status
// Observation patient+category, patient+code, patient+category+date patient+category+status, patient+code+date
// Patient _id, identifier birthdate, family, gender, given, name, family+gender, birthdate+family, birthdate+name, gender+name
}
private List<Patient> searchPatients() {
return null;
}
}