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Merge pull request #1494 from hapifhir/2023-11-gg-misc1 

2023 11 gg misc1
This commit is contained in:
Grahame Grieve 2023-11-24 12:56:37 +11:00 committed by GitHub
parent 8fe88a320e 82f0fc953a
commit 7f42c7aa71
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GPG Key ID: 4AEE18F83AFDEB23
81 changed files with 6027 additions and 521 deletions
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15
RELEASE_NOTES.md
View File

@ -1,7 +1,18 @@
## Validator Changes
* no changes
* Rework bundle references validation for R4+ - this is a *significant* change - many existing bundles that were previously erroneously passing will now fail
* #1488 - don't fail on erroneously repeating elements
* Fix problem creating CDA type discriminators
* Fix problem with R3 expansion
* Add support for CCDA .hasTemplateIdOf(canonical)
* Add support for NZ IPS
## Other code changes
* no changes
* Start work on making IWorkerContext a versioned API
* Add fhirVersion to R5 Base and IWorkerContext methods
* move IContextResourceLoader, ValidationResult and CodingValidationRequest out of IWorkerContext to their own clasess
* Fix up VSAC import for large value sets
* fix FHIRPath cda tests for empty package cache
* Fix issue where markdown with multiple characters was being cut off sometimes when rendering profiles

114
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
View File

@ -2,11 +2,15 @@ package org.hl7.fhir.convertors.misc;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URISyntaxException;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import org.hl7.fhir.exceptions.FHIRException;
@ -24,6 +28,9 @@ import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.r4.terminologies.JurisdictionUtilities;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.model.JsonProperty;
public class VSACImporter extends OIDBasedValueSetImporter {
@ -45,54 +52,25 @@ public class VSACImporter extends OIDBasedValueSetImporter {
FHIRToolingClient fhirToolingClient = new FHIRToolingClient("https://cts.nlm.nih.gov/fhir", "fhir/vsac");
fhirToolingClient.setUsername("apikey");
fhirToolingClient.setPassword(apiKey);
fhirToolingClient.setTimeout(120000);
fhirToolingClient.setTimeoutNormal(6000);
CapabilityStatement cs = fhirToolingClient.getCapabilitiesStatement();
JsonParser json = new JsonParser();
json.setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "vsac-capability-statmenet.json")), cs);
int i = 0;
int j = 0;
System.out.println("Loading");
List<String> oids = new ArrayList<>();
while (csv.line()) {
String oid = csv.cell("OID");
oids.add(oid);
}
Collections.sort(oids);
System.out.println("Go: "+oids.size()+" oids");
int i = 0;
int j = 0;
for (String oid : oids) {
try {
if (!onlyNew || !(new File(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
ValueSet vs = fhirToolingClient.read(ValueSet.class, oid);
try {
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), null);
vs.setExpansion(vse.getExpansion());
j++;
} catch (Exception e) {
errs.put(oid, "Expansion: " +e.getMessage());
System.out.println(e.getMessage());
}
while (isIncomplete(vs.getExpansion())) {
Parameters p = new Parameters();
p.addParameter("offset", vs.getExpansion().getParameter("offset").getValueIntegerType().getValue() + vs.getExpansion().getParameter("count").getValueIntegerType().getValue());
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), p);
vs.getExpansion().getContains().addAll(vse.getExpansion().getContains());
vs.getExpansion().setParameter(vse.getExpansion().getParameter());
}
vs.getExpansion().setOffsetElement(null);
vs.getExpansion().getParameter().clear();
if (vs.hasTitle()) {
if (vs.getTitle().equals(vs.getDescription())) {
vs.setTitle(vs.getName());
} else {
// System.out.println(oid);
// System.out.println(" name: "+vs.getName());
// System.out.println(" title: "+vs.getTitle());
// System.out.println(" desc: "+vs.getDescription());
}
} else {
vs.setTitle(vs.getName());
}
vs.setName(makeValidName(vs.getName()));
JurisdictionUtilities.setJurisdictionCountry(vs.getJurisdiction(), "US");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
}
j = processOid(dest, onlyNew, errs, fhirToolingClient, j, oid.trim());
i++;
if (i % 100 == 0) {
System.out.println(":"+i+" ("+j+")");
@ -110,6 +88,62 @@ public class VSACImporter extends OIDBasedValueSetImporter {
System.out.println("Done. " + i + " ValueSets");
}
private int processOid(String dest, boolean onlyNew, Map<String, String> errs, FHIRToolingClient fhirToolingClient, int j, String oid)
throws IOException, InterruptedException, FileNotFoundException {
if (!onlyNew || !(new File(Utilities.path(dest, "ValueSet-" + oid + ".json")).exists())) {
ValueSet vs = null;
try {
vs = fhirToolingClient.read(ValueSet.class, oid);
} catch (Exception e) {
errs.put(oid, "Read: " +e.getMessage());
System.out.println("Read "+oid+" failed: "+e.getMessage());
}
if (vs != null) {
try {
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), null);
vs.setExpansion(vse.getExpansion());
j++;
} catch (Exception e) {
errs.put(oid, "Expansion: " +e.getMessage());
System.out.println("Expand "+oid+" failed: "+e.getMessage());
}
while (isIncomplete(vs.getExpansion())) {
Parameters p = new Parameters();
int offset = vs.getExpansion().getParameter("offset").getValueIntegerType().getValue() + vs.getExpansion().getParameter("count").getValueIntegerType().getValue();
p.addParameter("offset", offset);
try {
ValueSet vse = fhirToolingClient.expandValueset(vs.getUrl(), p);
vs.getExpansion().getContains().addAll(vse.getExpansion().getContains());
vs.getExpansion().setParameter(vse.getExpansion().getParameter());
} catch (Exception e2) {
errs.put(oid, "Expansion: " +e2.getMessage()+" @ "+offset);
System.out.println("Expand "+oid+" @ "+offset+" failed: "+e2.getMessage());
}
}
vs.getExpansion().setOffsetElement(null);
vs.getExpansion().getParameter().clear();
if (vs.hasTitle()) {
if (vs.getTitle().equals(vs.getDescription())) {
vs.setTitle(vs.getName());
} else {
// System.out.println(oid);
// System.out.println(" name: "+vs.getName());
// System.out.println(" title: "+vs.getTitle());
// System.out.println(" desc: "+vs.getDescription());
}
} else {
vs.setTitle(vs.getName());
}
vs.setName(makeValidName(vs.getName()));
JurisdictionUtilities.setJurisdictionCountry(vs.getJurisdiction(), "US");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
}
}
return j;
}
private boolean isIncomplete(ValueSetExpansionComponent expansion) {
IntegerType c = expansion.getParameter("count").getValueIntegerType();
IntegerType offset = expansion.getParameter("offset").getValueIntegerType();

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR2.java
View File

@ -125,8 +125,8 @@ public class TerminologyClientR2 implements ITerminologyClient {
}
@Override
public ITerminologyClient setTimeout(int i) {
client.setTimeout(i);
public ITerminologyClient setTimeoutFactor(int i) {
client.setTimeoutFactor(i);
return this;
}

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR3.java
View File

@ -123,8 +123,8 @@ public class TerminologyClientR3 implements ITerminologyClient {
}
@Override
public ITerminologyClient setTimeout(int i) {
client.setTimeout(i);
public ITerminologyClient setTimeoutFactor(int i) {
client.setTimeoutFactor(i);
return this;
}

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR4.java
View File

@ -133,8 +133,8 @@ public class TerminologyClientR4 implements ITerminologyClient {
}
@Override
public ITerminologyClient setTimeout(int i) {
client.setTimeout(i);
public ITerminologyClient setTimeoutFactor(int i) {
client.setTimeoutFactor(i);
return this;
}

4
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/txClient/TerminologyClientR5.java
View File

@ -117,8 +117,8 @@ public class TerminologyClientR5 implements ITerminologyClient {
}
@Override
public ITerminologyClient setTimeout(int i) {
client.setTimeout(i);
public ITerminologyClient setTimeoutFactor(int i) {
client.setTimeoutFactor(i);
return this;
}

2
org.hl7.fhir.convertors/src/test/resources/extension_r3_dt_base.json
View File

@ -21,7 +21,7 @@
"telecom": [
{
"system": "url",
"value": "http://hl7.org/special/committees/FHIR"
"value": "http://www.hl7.org/Special/committees/FHIR"
}
]
}

2
org.hl7.fhir.convertors/src/test/resources/extension_r3_dt_path.json
View File

@ -21,7 +21,7 @@
"telecom": [
{
"system": "url",
"value": "http://hl7.org/special/committees/FHIR"
"value": "http://www.hl7.org/Special/committees/FHIR"
}
]
}

2
org.hl7.fhir.convertors/src/test/resources/extension_r3_res_base.json
View File

@ -22,7 +22,7 @@
"telecom": [
{
"system": "url",
"value": "http://hl7.org/special/committees/fhir.htm"
"value": "http://www.hl7.org/Special/committees/fhir.htm"
}
]
}

2
org.hl7.fhir.convertors/src/test/resources/extension_r3_res_path.json
View File

@ -22,7 +22,7 @@
"telecom": [
{
"system": "url",
"value": "http://hl7.org/special/committees/fhir.htm"
"value": "http://www.hl7.org/Special/committees/fhir.htm"
}
]
}

41
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/client/FHIRToolingClient.java
View File

@ -48,6 +48,7 @@ import org.hl7.fhir.dstu2.model.PrimitiveType;
import org.hl7.fhir.dstu2.model.Resource;
import org.hl7.fhir.dstu2.model.StringType;
import org.hl7.fhir.dstu2.model.ValueSet;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
@ -81,15 +82,12 @@ import org.hl7.fhir.utilities.Utilities;
* @author Claude Nanjo
*
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient {
public static final String DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ssK";
public static final String DATE_FORMAT = "yyyy-MM-dd";
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1;
private static final int TIMEOUT_OPERATION = 2;
private static final int TIMEOUT_OPERATION_LONG = 3;
private String base;
private ResourceAddress resourceAddress;
@ -179,11 +177,11 @@ public class FHIRToolingClient {
try {
if (useOptionsVerb) {
conformance = (Conformance) utils
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), timeoutNormal)
.getReference();// TODO fix this
} else {
conformance = (Conformance) utils.issueGetResourceRequest(resourceAddress.resolveMetadataUri(false),
getPreferredResourceFormat(), TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), timeoutNormal).getReference();
}
} catch (Exception e) {
handleException("An error has occurred while trying to fetch the server's conformance statement", e);
@ -202,11 +200,11 @@ public class FHIRToolingClient {
try {
if (useOptionsVerb) {
conformance = (Conformance) utils
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), timeoutNormal)
.getReference();// TODO fix this
} else {
conformance = (Conformance) utils.issueGetResourceRequest(resourceAddress.resolveMetadataUri(true),
getPreferredResourceFormat(), TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), timeoutNormal).getReference();
}
} catch (Exception e) {
handleException("An error has occurred while trying to fetch the server's conformance statement", e);
@ -218,7 +216,7 @@ public class FHIRToolingClient {
ResourceRequest<T> result = null;
try {
result = utils.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addSuccessStatus(200);// Only one for now
@ -237,7 +235,7 @@ public class FHIRToolingClient {
try {
result = utils.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndIdAndVersion(resourceClass, id, version),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);// unknown
@ -260,7 +258,7 @@ public class FHIRToolingClient {
try {
result = utils.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndCanonical(resourceClass, canonicalURL),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);// unknown
@ -287,7 +285,7 @@ public class FHIRToolingClient {
result = utils.issuePutRequest(
resourceAddress.resolveGetUriFromResourceClassAndId(resource.getClass(), resource.getId()),
utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), headers, TIMEOUT_OPERATION);
getPreferredResourceFormat(), headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -322,7 +320,7 @@ public class FHIRToolingClient {
List<Header> headers = null;
result = utils.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), headers, TIMEOUT_OPERATION);
getPreferredResourceFormat(), headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -530,10 +528,10 @@ public class FHIRToolingClient {
if (complex)
result = utils.issuePostRequest(resourceAddress.resolveOperationURLFromClass(resourceClass, name, ps),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), TIMEOUT_OPERATION_LONG);
getPreferredResourceFormat(), timeoutLong);
else
result = utils.issueGetResourceRequest(resourceAddress.resolveOperationURLFromClass(resourceClass, name, ps),
getPreferredResourceFormat(), TIMEOUT_OPERATION_LONG);
getPreferredResourceFormat(), timeoutLong);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addSuccessStatus(200);// Only one for now
@ -554,7 +552,7 @@ public class FHIRToolingClient {
try {
transactionResult = utils.postBatchRequest(resourceAddress.getBaseServiceUri(),
utils.getFeedAsByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
TIMEOUT_NORMAL + batch.getEntry().size());
timeoutNormal + batch.getEntry().size());
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -721,7 +719,7 @@ public class FHIRToolingClient {
ResourceRequest<Resource> result = utils.issuePostRequest(
resourceAddress.resolveOperationUri(ValueSet.class, "expand"),
utils.getResourceAsByteArray(source, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
headers, TIMEOUT_OPERATION_LONG);
headers, timeoutLong);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -738,7 +736,7 @@ public class FHIRToolingClient {
public Parameters lookupCode(Map<String, String> params) {
ResourceRequest<Resource> result = utils.issueGetResourceRequest(
resourceAddress.resolveOperationUri(ValueSet.class, "lookup", params), getPreferredResourceFormat(),
TIMEOUT_NORMAL);
timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -802,7 +800,7 @@ public class FHIRToolingClient {
ResourceRequest<Resource> result = utils.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
headers, TIMEOUT_NORMAL);
headers, timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -824,7 +822,7 @@ public class FHIRToolingClient {
ResourceRequest<Resource> result = utils.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
headers, TIMEOUT_OPERATION);
headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -864,7 +862,7 @@ public class FHIRToolingClient {
public Parameters getTerminologyCapabilities() {
return (Parameters) utils
.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(), getPreferredResourceFormat(), timeoutNormal)
.getReference();
}
@ -899,4 +897,5 @@ public class FHIRToolingClient {
public void setLanguage(String lang) {
utils.setLanguage(lang);
}
}

38
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/client/FHIRToolingClient.java
View File

@ -49,6 +49,7 @@ import org.hl7.fhir.dstu2016may.model.PrimitiveType;
import org.hl7.fhir.dstu2016may.model.Resource;
import org.hl7.fhir.dstu2016may.model.StringType;
import org.hl7.fhir.dstu2016may.model.ValueSet;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
@ -82,15 +83,12 @@ import org.hl7.fhir.utilities.Utilities;
* @author Claude Nanjo
*
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient {
public static final String DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ssK";
public static final String DATE_FORMAT = "yyyy-MM-dd";
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1;
private static final int TIMEOUT_OPERATION = 2;
private static final int TIMEOUT_OPERATION_LONG = 3;
private String base;
private ResourceAddress resourceAddress;
@ -177,11 +175,11 @@ public class FHIRToolingClient {
try {
if (useOptionsVerb) {
conformance = (Conformance) utils
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), timeoutNormal)
.getReference();// TODO fix this
} else {
conformance = (Conformance) utils.issueGetResourceRequest(resourceAddress.resolveMetadataUri(false),
getPreferredResourceFormat(), TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), timeoutNormal).getReference();
}
} catch (Exception e) {
handleException("An error has occurred while trying to fetch the server's conformance statement", e);
@ -200,11 +198,11 @@ public class FHIRToolingClient {
try {
if (useOptionsVerb) {
conformance = (Conformance) utils
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueOptionsRequest(resourceAddress.getBaseServiceUri(), getPreferredResourceFormat(), timeoutNormal)
.getReference();// TODO fix this
} else {
conformance = (Conformance) utils.issueGetResourceRequest(resourceAddress.resolveMetadataUri(true),
getPreferredResourceFormat(), TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), timeoutNormal).getReference();
}
} catch (Exception e) {
handleException("An error has occurred while trying to fetch the server's conformance statement", e);
@ -216,7 +214,7 @@ public class FHIRToolingClient {
ResourceRequest<T> result = null;
try {
result = utils.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addSuccessStatus(200);// Only one for now
@ -235,7 +233,7 @@ public class FHIRToolingClient {
try {
result = utils.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndIdAndVersion(resourceClass, id, version),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);// unknown
@ -258,7 +256,7 @@ public class FHIRToolingClient {
try {
result = utils.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndCanonical(resourceClass, canonicalURL),
getPreferredResourceFormat(), TIMEOUT_NORMAL);
getPreferredResourceFormat(), timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);// unknown
@ -285,7 +283,7 @@ public class FHIRToolingClient {
result = utils.issuePutRequest(
resourceAddress.resolveGetUriFromResourceClassAndId(resource.getClass(), resource.getId()),
utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), headers, TIMEOUT_OPERATION);
getPreferredResourceFormat(), headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -320,7 +318,7 @@ public class FHIRToolingClient {
List<Header> headers = null;
result = utils.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), headers, TIMEOUT_OPERATION);
getPreferredResourceFormat(), headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -529,10 +527,10 @@ public class FHIRToolingClient {
if (complex)
result = utils.issuePostRequest(resourceAddress.resolveOperationURLFromClass(resourceClass, name, ps),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), TIMEOUT_OPERATION_LONG);
getPreferredResourceFormat(), timeoutLong);
else
result = utils.issueGetResourceRequest(resourceAddress.resolveOperationURLFromClass(resourceClass, name, ps),
getPreferredResourceFormat(), TIMEOUT_OPERATION_LONG);
getPreferredResourceFormat(), timeoutLong);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addSuccessStatus(200);// Only one for now
@ -558,7 +556,7 @@ public class FHIRToolingClient {
try {
transactionResult = utils.postBatchRequest(resourceAddress.getBaseServiceUri(),
utils.getFeedAsByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
TIMEOUT_NORMAL + batch.getEntry().size());
timeoutNormal + batch.getEntry().size());
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -745,7 +743,7 @@ public class FHIRToolingClient {
public Parameters lookupCode(Map<String, String> params) {
ResourceRequest<Resource> result = utils.issueGetResourceRequest(
resourceAddress.resolveOperationUri(CodeSystem.class, "lookup", params), getPreferredResourceFormat(),
TIMEOUT_NORMAL);
timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -809,7 +807,7 @@ public class FHIRToolingClient {
ResourceRequest<Resource> result = utils.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
headers, TIMEOUT_NORMAL);
headers, timeoutNormal);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -831,7 +829,7 @@ public class FHIRToolingClient {
ResourceRequest<Resource> result = utils.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
headers, TIMEOUT_OPERATION);
headers, timeoutOperation);
result.addErrorStatus(410);// gone
result.addErrorStatus(404);// unknown
result.addErrorStatus(405);
@ -871,7 +869,7 @@ public class FHIRToolingClient {
public Parameters getTerminologyCapabilities() {
return (Parameters) utils
.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(), getPreferredResourceFormat(), TIMEOUT_NORMAL)
.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(), getPreferredResourceFormat(), timeoutNormal)
.getReference();
}

12
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/model/codesystems/Hl7WorkGroup.java
View File

@ -60,7 +60,7 @@ public enum Hl7WorkGroup {
*/
DEV,
/**
* Electronic Health Records (http://www.hl7.org/special/committees/ehr/index.cfm)
* Electronic Health Records (http://www.hl7.org/Special/committees/ehr/index.cfm)
*/
EHR,
/**
@ -80,11 +80,11 @@ public enum Hl7WorkGroup {
*/
II,
/**
* Infrastructure And Messaging (http://www.hl7.org/special/committees/inm/index.cfm)
* Infrastructure And Messaging (http://www.hl7.org/Special/committees/inm/index.cfm)
*/
INM,
/**
* Implementable Technology Specifications (http://www.hl7.org/special/committees/xml/index.cfm)
* Implementable Technology Specifications (http://www.hl7.org/Special/committees/xml/index.cfm)
*/
ITS,
/**
@ -225,13 +225,13 @@ public enum Hl7WorkGroup {
case CQI: return "Clinical Quality Information (http://www.hl7.org/Special/committees/cqi/index.cfm)";
case CG: return "Clinical Genomics (http://www.hl7.org/Special/committees/clingenomics/index.cfm)";
case DEV: return "Health Care Devices (http://www.hl7.org/Special/committees/healthcaredevices/index.cfm)";
case EHR: return "Electronic Health Records (http://www.hl7.org/special/committees/ehr/index.cfm)";
case EHR: return "Electronic Health Records (http://www.hl7.org/Special/committees/ehr/index.cfm)";
case FHIR: return "FHIR Infrastructure (http://www.hl7.org/Special/committees/fiwg/index.cfm)";
case FM: return "Financial Management (http://www.hl7.org/Special/committees/fm/index.cfm)";
case HSI: return "Health Standards Integration (http://www.hl7.org/Special/committees/hsi/index.cfm)";
case II: return "Imaging Integration (http://www.hl7.org/Special/committees/imagemgt/index.cfm)";
case INM: return "Infrastructure And Messaging (http://www.hl7.org/special/committees/inm/index.cfm)";
case ITS: return "Implementable Technology Specifications (http://www.hl7.org/special/committees/xml/index.cfm)";
case INM: return "Infrastructure And Messaging (http://www.hl7.org/Special/committees/inm/index.cfm)";
case ITS: return "Implementable Technology Specifications (http://www.hl7.org/Special/committees/xml/index.cfm)";
case OO: return "Orders and Observations (http://www.hl7.org/Special/committees/orders/index.cfm)";
case PA: return "Patient Administration (http://www.hl7.org/Special/committees/pafm/index.cfm)";
case PC: return "Patient Care (http://www.hl7.org/Special/committees/patientcare/index.cfm)";

45
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/client/FHIRToolingClient.java
View File

@ -26,6 +26,7 @@ import org.hl7.fhir.dstu3.utils.client.network.ByteUtils;
import org.hl7.fhir.dstu3.utils.client.network.Client;
import org.hl7.fhir.dstu3.utils.client.network.ResourceRequest;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
@ -58,19 +59,13 @@ import okhttp3.internal.http2.Header;
*
* @author Claude Nanjo
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient {
public static final String DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ssK";
public static final String DATE_FORMAT = "yyyy-MM-dd";
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1500;
private static final int TIMEOUT_OPERATION = 30000;
private static final int TIMEOUT_ENTRY = 500;
private static final int TIMEOUT_OPERATION_LONG = 60000;
private static final int TIMEOUT_OPERATION_EXPAND = 120000;
private String base;
private ResourceAddress resourceAddress;
private ResourceFormat preferredResourceFormat;
@ -155,7 +150,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"TerminologyCapabilities",
TIMEOUT_NORMAL).getReference();
timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's terminology capabilities", e);
}
@ -169,7 +164,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"CapabilitiesStatement",
TIMEOUT_NORMAL).getReference();
timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's conformance statement", e);
}
@ -183,7 +178,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"CapabilitiesStatement-Quick",
TIMEOUT_NORMAL).getReference();
timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's capability statement: "+e.getMessage(), e);
}
@ -197,7 +192,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Read " + resourceClass.getName() + "/" + id,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -214,7 +209,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -231,7 +226,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Read " + resourceClass.getName() + "?url=" + canonicalURL,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -254,7 +249,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Update " + resource.fhirType() + "/" + resource.getId(),
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -281,7 +276,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Update " + resource.fhirType() + "/" + id,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -318,12 +313,12 @@ public class FHIRToolingClient {
client.getLogger().logRequest("POST", url.toString(), null, body);
}
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + "/$" + name, timeoutLong);
} else {
if (client.getLogger() != null) {
client.getLogger().logRequest("GET", url.toString(), null, null);
}
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(), "GET " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(), "GET " + resourceClass.getName() + "/$" + name, timeoutLong);
}
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
@ -345,7 +340,7 @@ 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(), "transaction", timeoutOperation + (timeoutEntry * batch.getEntry().size()));
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -359,7 +354,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveValidateUri(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", timeoutLong);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -418,7 +413,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -436,7 +431,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"CodeSystem/$lookup",
TIMEOUT_NORMAL);
timeoutNormal);
} catch (IOException e) {
e.printStackTrace();
}
@ -459,7 +454,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -483,7 +478,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -507,7 +502,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Closure?name=" + name,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -528,7 +523,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"UpdateClosure?name=" + name,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}

431
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/ips/IPSBuilder.java Normal file
View File

@ -0,0 +1,431 @@
package org.hl7.fhir.r4.ips;
import java.util.Date;
import java.util.List;
import org.hl7.fhir.r4.ips.IPSBuilder.TypeAndId;
import org.hl7.fhir.r4.model.Age;
import org.hl7.fhir.r4.model.Annotation;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.Period;
import org.hl7.fhir.r4.model.Quantity;
import org.hl7.fhir.r4.model.Range;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.Type;
import org.hl7.fhir.r4.model.Composition.CompositionStatus;
import org.hl7.fhir.r4.model.Composition.SectionComponent;
import org.hl7.fhir.r4.model.Condition;
import org.hl7.fhir.r4.model.Device;
import org.hl7.fhir.r4.model.DomainResource;
import org.hl7.fhir.r4.model.Dosage;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Medication;
import org.hl7.fhir.r4.model.MedicationStatement;
import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
public class IPSBuilder {
public static class TypeAndId {
private String type;
private String id;
protected TypeAndId(String type, String id) {
super();
this.type = type;
this.id = id;
}
public String getType() {
return type;
}
public String getId() {
return id;
}
}
public static Bundle generateIPS(FHIRToolingClient server, String patientId) {
Patient pat = server.fetchResource(Patient.class, patientId);
Bundle bnd = initBundle();
Composition cmp = initComposition(bnd, server.getAddress(), pat);
pat = processPatient(bnd, server.getAddress(), pat);
// addMedications(bnd, cmp, server, patientId);
addConditions(bnd, cmp, server, patientId);
return bnd;
}
private static Bundle initBundle() {
Bundle bnd = new Bundle();
bnd.getIdentifier().setSystem("urn:ietf:rfc:3986");
bnd.getIdentifier().setValue(Utilities.makeUuidUrn());
bnd.setType(BundleType.DOCUMENT);
bnd.setTimestamp(new Date());
return bnd;
}
private static Composition initComposition(Bundle bnd, String url, Patient pat) {
Composition cmp = new Composition();
cmp.setIdBase(Utilities.makeUuidLC());
cmp.setStatus(CompositionStatus.FINAL);
cmp.getType().addCoding().setSystem("http://loinc.org").setCode("60591-5");
cmp.setDate(new Date());
cmp.setTitle("International Patient Summary");
cmp.getSubject().setReference("Patient/"+pat.getIdBase());
cmp.addAuthor().setReference("Device/java");
bnd.addEntry().setResource(cmp).setFullUrl(Utilities.pathURL(url, "Composition", cmp.getIdBase()));
Device dev = new Device();
dev.setId("java");
dev.addDeviceName().setName("Java Core Library");
dev.addVersion().setValue(VersionUtil.getVersion());
bnd.addEntry().setResource(dev).setFullUrl(Utilities.pathURL(url, "Device", dev.getIdBase()));
return cmp;
}
private static Patient processPatient(Bundle bnd, String url, Patient pat) {
bnd.addEntry().setResource(pat).setFullUrl(Utilities.pathURL(url, "Patient", pat.getIdBase()));
return pat;
}
private static void addMedications(Bundle bnd, Composition cmp, FHIRToolingClient server, String patientId) {
Bundle sb = server.search("MedicationStatement", "?patient="+patientId+"&_include=MedicationStatement:medication&_include=MedicationStatement:source");
SectionComponent sct = cmp.addSection();
sct.setTitle("Medications");
sct.getCode().addCoding().setSystem("http://loinc.org").setCode("10160-0");
sct.getText().setStatus(NarrativeStatus.GENERATED);
var x = sct.getText().getDiv();
var tbl = x.table("grid");
var tr = tbl.tr();
tr.th().tx("Medication");
tr.th().tx("Category");
tr.th().tx("Status");
tr.th().tx("When");
tr.th().tx("Dosage");
tr.th().tx("Reason");
tr.th().tx("Source");
tr.th().tx("Notes");
boolean ok = false;
for (BundleEntryComponent be : sb.getEntry()) {
if (be.hasResource() && be.getResource() instanceof MedicationStatement) {
MedicationStatement mdstmt = (MedicationStatement) be.getResource();
ok = true;
bnd.addEntry().setResource(mdstmt).setFullUrl(Utilities.pathURL(server.getAddress(), "MedicationStatement", mdstmt.getIdBase()));
sct.addEntry().setReference("MedicationStatement/"+mdstmt.getIdBase());
tr = tbl.tr();
if (mdstmt.hasMedicationReference()) {
Medication med = findMedication(sb, server, mdstmt, mdstmt.getMedicationReference());
if (med == null) {
tr.td().b().tx("Unknown?");
} else {
tr.td().tx(summarise(med));
bnd.addEntry().setResource(med).setFullUrl(Utilities.pathURL(server.getAddress(), "Medication", med.getIdBase()));
}
} else {
tr.td().tx(genCC(mdstmt.getMedicationCodeableConcept()));
}
tr.td().tx(genCC(mdstmt.getCategory()));
var td = tr.td();
td.tx(mdstmt.getStatus().getDisplay());
if (mdstmt.hasStatusReason()) {
td.tx(" (");
td.tx(genCC(mdstmt.getStatusReason()));
td.tx(")");
}
tr.td().tx(genDT(mdstmt.getEffective()));
genDosages(tr.td(), mdstmt.getDosage());
tr.td().tx(genReference(mdstmt, mdstmt.getInformationSource(), bnd, sb, server));
genNotes(tr.td(), mdstmt.getNote());
}
}
if (!ok) {
Condition cnd = new Condition();
cnd.setId(Utilities.makeUuidLC());
cnd.getText().setStatus(NarrativeStatus.GENERATED);
var rx = cnd.getText().getDiv();
rx.tx("No information is provided about the patient's medical problems");
tr = tbl.tr();
tr.td().colspan(7).tx("No information is provided about the patient's medical problems");
cnd.getClinicalStatus().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical").setCode("active").setDisplay("Active");
cnd.getCode().addCoding().setSystem("http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips").setCode("no-problem-info").setDisplay("No information about current problems");
cnd.getSubject().setReference("Patient/"+patientId);
}
}
private static void genDosages(XhtmlNode x, List<Dosage> dosages) {
if (dosages == null || dosages.size() == 0) {
} else if (dosages.size() == 1) {
genDosage(x, dosages.get(0));
} else {
var ul = x.ul();
for (Dosage d : dosages) {
genDosage(ul.li(), d);
}
}
}
private static void genDosage(XhtmlNode x, Dosage dosage) {
x.tx(dosage.getText());
if (dosage.hasAsNeeded()) {
x.nbsp();
if (dosage.hasAsNeededBooleanType()) {
if (dosage.getAsNeededBooleanType().booleanValue()) {
x.tx(" (as needed)");
}
} else {
x.tx(genDT(dosage.getAsNeeded()));
}
} else if (dosage.hasTiming()) {
x.nbsp();
x.tx(genDT(dosage.getTiming()));
}
if (dosage.hasSite()) {
x.tx(". ");
x.tx(genDT(dosage.getSite()));
}
if (dosage.hasRoute()) {
x.tx(". ");
x.tx(genDT(dosage.getRoute()));
}
}
private static Medication findMedication(Bundle sb, FHIRToolingClient server, MedicationStatement mdstmt, Reference ref) {
if (ref == null || !ref.hasReference()) {
return null;
}
if (ref.getReference().startsWith("#")) {
} else {
}
return null;
}
private static void addConditions(Bundle bnd, Composition cmp, FHIRToolingClient server, String patientId) {
Bundle sb = server.search("Condition", "?patient="+patientId+"&_include=Condition:asserter");
SectionComponent sct = cmp.addSection();
sct.setTitle("Problems");
sct.getCode().addCoding().setSystem("http://loinc.org").setCode("11450-4");
sct.getText().setStatus(NarrativeStatus.GENERATED);
var x = sct.getText().getDiv();
var tbl = x.table("grid");
var tr = tbl.tr();
tr.th().tx("Code");
tr.th().tx("Category");
tr.th().tx("Severity");
tr.th().tx("Status");
tr.th().tx("Onset");
tr.th().tx("Abatement");
tr.th().tx("Source");
tr.th().tx("Notes");
boolean ok = false;
for (BundleEntryComponent be : sb.getEntry()) {
if (be.hasResource() && be.getResource() instanceof Condition) {
Condition cnd = (Condition) be.getResource();
ok = true;
bnd.addEntry().setResource(cnd).setFullUrl(Utilities.pathURL(server.getAddress(), "Condition", cnd.getIdBase()));
sct.addEntry().setReference("Condition/"+cnd.getIdBase());
tr = tbl.tr();
tr.td().tx(genCC(cnd.getCode()));
tr.td().tx(genCC(cnd.getCategory()));
tr.td().tx(genCC(cnd.getSeverity()));
tr.td().tx(genStatus(cnd));
tr.td().tx(genDT(cnd.getOnset()));
tr.td().tx(genDT(cnd.getAbatement()));
tr.td().tx(genSource(cnd, bnd, sb, server));
genNotes(tr.td(), cnd.getNote());
}
}
if (!ok) {
Condition cnd = new Condition();
cnd.setId(Utilities.makeUuidLC());
cnd.getText().setStatus(NarrativeStatus.GENERATED);
var rx = cnd.getText().getDiv();
rx.tx("No information is provided about the patient's medical problems");
tr = tbl.tr();
tr.td().colspan(7).tx("No information is provided about the patient's medical problems");
cnd.getClinicalStatus().addCoding().setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical").setCode("active").setDisplay("Active");
cnd.getCode().addCoding().setSystem("http://hl7.org/fhir/uv/ips/CodeSystem/absent-unknown-uv-ips").setCode("no-problem-info").setDisplay("No information about current problems");
cnd.getSubject().setReference("Patient/"+patientId);
}
}
private static String genReference(DomainResource src, Reference ref, Bundle bnd, Bundle search, FHIRToolingClient server) {
if (ref == null || ref.isEmpty()) {
return null;
}
boolean contained = false;
DomainResource tgt = null;
if (ref.hasReference()) {
if (ref.getReference().startsWith("#")) {
tgt = (DomainResource) src.getContained(ref.getReference());
contained = true;
} else {
TypeAndId tid = getTypeAndId(server.getAddress(), ref.getReference());
if (tid != null) {
tgt = findInBundle(bnd, Utilities.pathURL(server.getAddress(), tid.getType(), tid.getId()));
if (tgt == null) {
tgt = findInBundle(search, Utilities.pathURL(server.getAddress(), tid.getType(), tid.getId()));
if (tgt == null) {
tgt = (DomainResource) server.read(tid.getType(), tid.getId());
}
} else {
contained = true;
}
}
}
}
if (tgt != null) {
if (!contained) {
bnd.addEntry().setResource(tgt).setFullUrl(Utilities.pathURL(server.getAddress(), tgt.fhirType(), tgt.getIdBase()));
}
return summarise(tgt);
} else if (ref.hasDisplay()) {
return ref.getDisplay();
} else if (ref.hasReference()) {
return ref.getReference();
} else if (ref.hasIdentifier()) {
return genIdentifier(ref.getIdentifier());
} else {
return "unknown";
}
}
private static TypeAndId getTypeAndId(String baseUrl, String url) {
if (Utilities.noString(url)) {
return null;
}
if (url.startsWith(baseUrl+"/")) {
url = url.substring(baseUrl.length()+1);
}
String[] p = url.split("\\/");
if (p.length > 1) {
if ("_history".equals(p[p.length-2]) && p.length > 3) {
return new TypeAndId(p[p.length-4], p[p.length-3]);
} else {
return new TypeAndId(p[p.length-2], p[p.length-1]);
}
}
return null;
}
private static DomainResource findInBundle(Bundle bnd, String url) {
for (BundleEntryComponent be : bnd.getEntry()) {
if (url.equals(be.getFullUrl()) && be.hasResource() && be.getResource() instanceof DomainResource) {
return (DomainResource) be.getResource();
}
}
return null;
}
private static String summarise(DomainResource tgt) {
// TODO Auto-generated method stub
return null;
}
private static String genIdentifier(Identifier id) {
return id.getValue();
}
private static void genNotes(XhtmlNode td, List<Annotation> notes) {
if (notes.size() > 0) {
if (notes.size() == 1) {
genNote(td, notes.get(0));
} else {
var ul = td.ul();
for (Annotation a : notes) {
genNote(ul.li(), a);
}
}
}
}
private static void genNote(XhtmlNode td, Annotation annotation) {
td.tx(annotation.getText());
}
private static String genSource(Condition cnd, Bundle bnd, Bundle sb, FHIRToolingClient server) {
if (cnd.hasAsserter()) {
return genReference(cnd, cnd.getAsserter(), bnd, sb, server);
} else if (cnd.hasRecorder()) {
return genReference(cnd, cnd.getRecorder(), bnd, sb, server);
} else {
return null;
}
}
private static String genDT(Type v) {
if (v == null) {
return null;
}
if (v.isPrimitive()) {
return v.primitiveValue();
}
if (v instanceof Age) {
return genQty((Age) v);
}
if (v instanceof Period) {
Period p = (Period) v;
return genDT(p.getStartElement())+" - "+genDT(p.getStartElement());
}
if (v instanceof Range) {
Range p = (Range) v;
return genDT(p.getLow())+" - "+genDT(p.getHigh());
}
return "not done: "+v.fhirType();
}
private static String genQty(Quantity v) {
return v.getValue().toPlainString()+v.getUnit();
}
private static String genStatus(Condition cnd) {
if (cnd.hasClinicalStatus() && cnd.hasVerificationStatus()) {
return genCC(cnd.getClinicalStatus()) +"/"+genCC(cnd.getVerificationStatus());
} else if (cnd.hasClinicalStatus()) {
return genCC(cnd.getClinicalStatus());
} else if (cnd.hasVerificationStatus()) {
return genCC(cnd.getVerificationStatus());
} else {
return null;
}
}
private static String genCC(List<CodeableConcept> list) {
if (list != null && list.size() == 1) {
return genCC(list.get(0));
} else {
return null;
}
}
private static String genCC(CodeableConcept code) {
if (code.hasText()) {
return code.getText();
} else if (code.hasCoding()) {
Coding c = code.getCodingFirstRep();
if (c.hasDisplay()) {
return c.getDisplay();
} else {
return c.getCode();
}
} else {
return null;
}
}
}

9
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/DomainResource.java
View File

@ -579,6 +579,15 @@ public abstract class DomainResource extends Resource
}
}
public Resource getContained(String reference) {
for (Resource c : getContained()) {
if (reference.equals("#"+c.getId())) {
return c;
}
}
return null;
}
// end addition
}

12
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/codesystems/Hl7WorkGroup.java
View File

@ -62,7 +62,7 @@ public enum Hl7WorkGroup {
DEV,
/**
* Electronic Health Records
* (http://www.hl7.org/special/committees/ehr/index.cfm).
* (http://www.hl7.org/Special/committees/ehr/index.cfm).
*/
EHR,
/**
@ -85,12 +85,12 @@ public enum Hl7WorkGroup {
II,
/**
* Infrastructure And Messaging
* (http://www.hl7.org/special/committees/inm/index.cfm).
* (http://www.hl7.org/Special/committees/inm/index.cfm).
*/
INM,
/**
* Implementable Technology Specifications
* (http://www.hl7.org/special/committees/xml/index.cfm).
* (http://www.hl7.org/Special/committees/xml/index.cfm).
*/
ITS,
/**
@ -281,7 +281,7 @@ public enum Hl7WorkGroup {
case DEV:
return "Health Care Devices (http://www.hl7.org/Special/committees/healthcaredevices/index.cfm).";
case EHR:
return "Electronic Health Records (http://www.hl7.org/special/committees/ehr/index.cfm).";
return "Electronic Health Records (http://www.hl7.org/Special/committees/ehr/index.cfm).";
case FHIR:
return "FHIR Infrastructure (http://www.hl7.org/Special/committees/fiwg/index.cfm).";
case FM:
@ -291,9 +291,9 @@ public enum Hl7WorkGroup {
case II:
return "Imaging Integration (http://www.hl7.org/Special/committees/imagemgt/index.cfm).";
case INM:
return "Infrastructure And Messaging (http://www.hl7.org/special/committees/inm/index.cfm).";
return "Infrastructure And Messaging (http://www.hl7.org/Special/committees/inm/index.cfm).";
case ITS:
return "Implementable Technology Specifications (http://www.hl7.org/special/committees/xml/index.cfm).";
return "Implementable Technology Specifications (http://www.hl7.org/Special/committees/xml/index.cfm).";
case MNM:
return "Modeling and Methodology (http://www.hl7.org/Special/committees/mnm/index.cfm).";
case OO:

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/terminologies/TerminologyClientR4.java
View File

@ -87,7 +87,7 @@ public class TerminologyClientR4 implements TerminologyClient {
@Override
public void setTimeout(int i) {
client.setTimeout(i);
client.setTimeoutNormal(i); // #FIXME
}
@Override

21
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java
View File

@ -3338,9 +3338,11 @@ public class FHIRPathEngine {
}
case Iif: {
TypeDetails types = new TypeDetails(null);
types.update(paramTypes.get(0));
if (paramTypes.size() > 1) {
checkSingleton(focus, "iif", exp);
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean));
types.update(paramTypes.get(1));
if (paramTypes.size() > 2) {
types.update(paramTypes.get(2));
}
return types;
}
@ -3646,6 +3648,12 @@ public class FHIRPathEngine {
}
}
private void checkSingleton(TypeDetails focus, String name, ExpressionNode expr) throws PathEngineException {
if (focus.getCollectionStatus() != CollectionStatus.SINGLETON) {
// typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT, name, expr.toString()), I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT));
}
}
private void checkOrdered(TypeDetails focus, String name, ExpressionNode expr) throws PathEngineException {
if (focus.getCollectionStatus() == CollectionStatus.UNORDERED) {
throw makeException(expr, I18nConstants.FHIRPATH_ORDERED_ONLY, name);
@ -4806,9 +4814,12 @@ public class FHIRPathEngine {
}
private List<Base> funcIif(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> n1 = execute(context, focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (focus.size() > 1) {
throw makeException(exp, I18nConstants.FHIRPATH_NO_COLLECTION, "iif", focus.size());
}
List<Base> n1 = execute(focus.isEmpty() ? context : changeThis(context, focus.get(0)), focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (v == Equality.True) {
return execute(context, focus, exp.getParameters().get(1), true);
} else if (exp.getParameters().size() < 3) {
@ -4849,7 +4860,7 @@ public class FHIRPathEngine {
for (Base item : focus) {
result.add(item);
}
for (Base item : execute(context, focus, exp.getParameters().get(0), true)) {
for (Base item : execute(context, baseToList(context.thisItem), exp.getParameters().get(0), true)) {
result.add(item);
}
return result;

75
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/FHIRToolingClient.java
View File

@ -25,6 +25,7 @@ import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.utils.client.network.ByteUtils;
import org.hl7.fhir.r4.utils.client.network.Client;
import org.hl7.fhir.r4.utils.client.network.ResourceRequest;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
@ -60,19 +61,13 @@ import okhttp3.internal.http2.Header;
*
* @author Claude Nanjo
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient {
public static final String DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ssK";
public static final String DATE_FORMAT = "yyyy-MM-dd";
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1500;
private static final int TIMEOUT_OPERATION = 30000;
private static final int TIMEOUT_ENTRY = 500;
private static final int TIMEOUT_OPERATION_LONG = 60000;
private static final int TIMEOUT_OPERATION_EXPAND = 120000;
private String base;
private ResourceAddress resourceAddress;
private ResourceFormat preferredResourceFormat;
@ -134,7 +129,7 @@ public class FHIRToolingClient {
TerminologyCapabilities capabilities = null;
try {
capabilities = (TerminologyCapabilities) client.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(),
getPreferredResourceFormat(), generateHeaders(), "TerminologyCapabilities", TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), generateHeaders(), "TerminologyCapabilities", timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's terminology capabilities", e);
}
@ -145,7 +140,7 @@ public class FHIRToolingClient {
CapabilityStatement conformance = null;
try {
conformance = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(false),
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement", TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement", timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's conformance statement", e);
}
@ -157,7 +152,7 @@ public class FHIRToolingClient {
return capabilities;
try {
capabilities = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(true),
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement-Quick", TIMEOUT_NORMAL)
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement-Quick", timeoutNormal)
.getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's capability statement: " + e.getMessage(), e);
@ -165,12 +160,28 @@ public class FHIRToolingClient {
return capabilities;
}
public Resource read(String resourceClass, String id) {// TODO Change this to AddressableResource
ResourceRequest<Resource> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
getPreferredResourceFormat(), generateHeaders(), "Read " + resourceClass + "/" + id,
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
}
} catch (Exception e) {
throw new FHIRException(e);
}
return result.getPayload();
}
public <T extends Resource> T read(Class<T> resourceClass, String id) {// TODO Change this to AddressableResource
ResourceRequest<T> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
getPreferredResourceFormat(), generateHeaders(), "Read " + resourceClass.getName() + "/" + id,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -187,7 +198,7 @@ public class FHIRToolingClient {
result = client.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndIdAndVersion(resourceClass, id, version),
getPreferredResourceFormat(), generateHeaders(),
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version, TIMEOUT_NORMAL);
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version, timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -204,7 +215,7 @@ public class FHIRToolingClient {
result = client.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndCanonical(resourceClass, canonicalURL),
getPreferredResourceFormat(), generateHeaders(), "Read " + resourceClass.getName() + "?url=" + canonicalURL,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -227,7 +238,7 @@ public class FHIRToolingClient {
resourceAddress.resolveGetUriFromResourceClassAndId(resource.getClass(), resource.getId()),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Update " + resource.fhirType() + "/" + resource.getId(),
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -256,7 +267,7 @@ public class FHIRToolingClient {
result = client.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Update " + resource.fhirType() + "/" + id,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -293,10 +304,10 @@ public class FHIRToolingClient {
if (complex) {
byte[] body = ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat()));
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + "/$" + name, timeoutLong);
} else {
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(),
"GET " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"GET " + resourceClass.getName() + "/$" + name, timeoutLong);
}
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
@ -316,7 +327,7 @@ public class FHIRToolingClient {
try {
transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(),
ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), "transaction", TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
getPreferredResourceFormat(), "transaction", timeoutOperation + (timeoutEntry * batch.getEntry().size()));
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -330,7 +341,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveValidateUri(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", timeoutLong);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -373,7 +384,7 @@ public class FHIRToolingClient {
public Bundle fetchFeed(String url) {
Bundle feed = null;
try {
feed = client.issueGetFeedRequest(new URI(url), getPreferredResourceFormat());
feed = client.issueGetFeedRequest(new URI(url), getPreferredResourceFormat(), timeoutLong);
} catch (Exception e) {
handleException("An error has occurred while trying to retrieve history since last update", e);
}
@ -398,7 +409,7 @@ public class FHIRToolingClient {
org.hl7.fhir.r4.utils.client.network.ResourceRequest<Resource> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand", parameters),
getPreferredResourceFormat(), generateHeaders(), "ValueSet/$expand?url=" + vsUrl, TIMEOUT_OPERATION_EXPAND);
getPreferredResourceFormat(), generateHeaders(), "ValueSet/$expand?url=" + vsUrl, timeoutExpand);
} catch (IOException e) {
throw new FHIRException(e);
}
@ -416,7 +427,7 @@ public class FHIRToolingClient {
try {
result = client.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand"),
ByteUtils.resourceToByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), TIMEOUT_OPERATION_EXPAND);
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -431,7 +442,7 @@ public class FHIRToolingClient {
org.hl7.fhir.r4.utils.client.network.ResourceRequest<Resource> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveOperationUri(CodeSystem.class, "lookup", params),
getPreferredResourceFormat(), generateHeaders(), "CodeSystem/$lookup", TIMEOUT_NORMAL);
getPreferredResourceFormat(), generateHeaders(), "CodeSystem/$lookup", timeoutNormal);
} catch (IOException e) {
throw new FHIRException(e);
}
@ -455,7 +466,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand", params),
ByteUtils.resourceToByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(), source == null ? "ValueSet/$expand" : "ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -484,7 +495,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Closure?name=" + name, TIMEOUT_NORMAL);
getPreferredResourceFormat(), generateHeaders(), "Closure?name=" + name, timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -504,7 +515,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "UpdateClosure?name=" + name, TIMEOUT_OPERATION);
getPreferredResourceFormat(), generateHeaders(), "UpdateClosure?name=" + name, timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -531,14 +542,6 @@ public class FHIRToolingClient {
this.password = password;
}
public long getTimeout() {
return client.getTimeout();
}
public void setTimeout(long timeout) {
client.setTimeout(timeout);
}
public ToolingClientLogger getLogger() {
return client.getLogger();
}
@ -615,7 +618,7 @@ public class FHIRToolingClient {
org.hl7.fhir.r4.utils.client.network.ResourceRequest<Resource> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveGetResource(resourceClass, id),
getPreferredResourceFormat(), generateHeaders(), resourceClass.getName()+"/"+id, TIMEOUT_NORMAL);
getPreferredResourceFormat(), generateHeaders(), resourceClass.getName()+"/"+id, timeoutNormal);
} catch (IOException e) {
throw new FHIRException(e);
}
@ -625,4 +628,6 @@ public class FHIRToolingClient {
}
return (T) result.getPayload();
}
}

4
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/ResourceAddress.java
View File

@ -113,6 +113,10 @@ public class ResourceAddress {
return baseServiceUri.resolve(nameForClass(resourceClass) + "/" + id);
}
public URI resolveGetUriFromResourceClassAndId(String resourceClass, String id) {
return baseServiceUri.resolve(resourceClass + "/" + id);
}
public <T extends Resource> URI resolveGetUriFromResourceClassAndIdAndVersion(Class<T> resourceClass, String id,
String version) {
return baseServiceUri.resolve(nameForClass(resourceClass) + "/" + id + "/_history/" + version);

18
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/client/network/Client.java
View File

@ -17,12 +17,12 @@ import okhttp3.RequestBody;
public class Client {
public static final String DEFAULT_CHARSET = "UTF-8";
private static final long DEFAULT_TIMEOUT = 5000;
private ToolingClientLogger logger;
private FhirLoggingInterceptor fhirLoggingInterceptor;
private int retryCount;
private long timeout = DEFAULT_TIMEOUT;
private String base;
public String getBase() {
@ -51,14 +51,6 @@ public class Client {
this.retryCount = retryCount;
}
public long getTimeout() {
return timeout;
}
public void setTimeout(long timeout) {
this.timeout = timeout;
}
public <T extends Resource> ResourceRequest<T> issueOptionsRequest(URI optionsUri, String resourceFormat,
String message, long timeout) throws IOException {
Request.Builder request = new Request.Builder().method("OPTIONS", null).url(optionsUri.toURL());
@ -107,20 +99,20 @@ public class Client {
return executeFhirRequest(request, resourceFormat, headers, message, retryCount, timeout);
}
public boolean issueDeleteRequest(URI resourceUri) throws IOException {
public boolean issueDeleteRequest(URI resourceUri, int timeout) throws IOException {
Request.Builder request = new Request.Builder().url(resourceUri.toURL()).delete();
return executeFhirRequest(request, null, new Headers.Builder().build(), null, retryCount, timeout)
.isSuccessfulRequest();
}
public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat) throws IOException {
public Bundle issueGetFeedRequest(URI resourceUri, String resourceFormat, int timeout) throws IOException {
Request.Builder request = new Request.Builder().url(resourceUri.toURL());
return executeBundleRequest(request, resourceFormat, new Headers.Builder().build(), null, retryCount, timeout);
}
public Bundle issuePostFeedRequest(URI resourceUri, Map<String, String> parameters, String resourceName,
Resource resource, String resourceFormat) throws IOException {
Resource resource, String resourceFormat, int timeout) throws IOException {
String boundary = "----WebKitFormBoundarykbMUo6H8QaUnYtRy";
byte[] payload = ByteUtils.encodeFormSubmission(parameters, resourceName, resource, boundary);
RequestBody body = RequestBody.create(MediaType.parse(resourceFormat + ";charset=" + DEFAULT_CHARSET), payload);

30
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/ips/IpsBuilderTest.java Normal file
View File

@ -0,0 +1,30 @@
package org.hl7.fhir.r4.ips;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.net.URISyntaxException;
import org.hl7.fhir.r4.formats.IParser.OutputStyle;
import org.hl7.fhir.r4.formats.JsonParser;
import org.hl7.fhir.r4.model.Base64BinaryType;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.utils.client.FHIRToolingClient;
import org.hl7.fhir.utilities.Utilities;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;
public class IpsBuilderTest {
@Test
@DisplayName("Test IPS Generation")
void testIpsGeneration() throws URISyntaxException, FileNotFoundException, IOException {
FHIRToolingClient server = new FHIRToolingClient("https://hl7auconnectathon.salessbx.smiledigitalhealth.com/fhir-request", "FHIR-Validator");
server.setUsername("HL7AU");
server.setPassword("Connectathon123");
Bundle bnd = IPSBuilder.generateIPS(server, "wang-li");
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "ips-gen.json")), bnd);
}
}

21
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/FHIRPathEngine.java
View File

@ -3340,9 +3340,11 @@ public class FHIRPathEngine {
}
case Iif: {
TypeDetails types = new TypeDetails(null);
types.update(paramTypes.get(0));
if (paramTypes.size() > 1) {
checkSingleton(focus, "iif", exp);
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean));
types.update(paramTypes.get(1));
if (paramTypes.size() > 2) {
types.update(paramTypes.get(2));
}
return types;
}
@ -3648,6 +3650,12 @@ public class FHIRPathEngine {
}
}
private void checkSingleton(TypeDetails focus, String name, ExpressionNode expr) throws PathEngineException {
if (focus.getCollectionStatus() != CollectionStatus.SINGLETON) {
// typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT, name, expr.toString()), I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT));
}
}
private void checkOrdered(TypeDetails focus, String name, ExpressionNode expr) throws PathEngineException {
if (focus.getCollectionStatus() == CollectionStatus.UNORDERED) {
throw makeException(expr, I18nConstants.FHIRPATH_ORDERED_ONLY, name);
@ -4809,9 +4817,12 @@ public class FHIRPathEngine {
}
private List<Base> funcIif(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> n1 = execute(context, focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (focus.size() > 1) {
throw makeException(exp, I18nConstants.FHIRPATH_NO_COLLECTION, "iif", focus.size());
}
List<Base> n1 = execute(focus.isEmpty() ? context : changeThis(context, focus.get(0)), focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (v == Equality.True) {
return execute(context, focus, exp.getParameters().get(1), true);
} else if (exp.getParameters().size() < 3) {
@ -4852,7 +4863,7 @@ public class FHIRPathEngine {
for (Base item : focus) {
result.add(item);
}
for (Base item : execute(context, focus, exp.getParameters().get(0), true)) {
for (Base item : execute(context, baseToList(context.thisItem), exp.getParameters().get(0), true)) {
result.add(item);
}
return result;

43
org.hl7.fhir.r4b/src/main/java/org/hl7/fhir/r4b/utils/client/FHIRToolingClient.java
View File

@ -39,6 +39,7 @@ import org.hl7.fhir.r4b.utils.client.network.ByteUtils;
import org.hl7.fhir.r4b.utils.client.network.Client;
import org.hl7.fhir.r4b.utils.client.network.ClientHeaders;
import org.hl7.fhir.r4b.utils.client.network.ResourceRequest;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
@ -77,19 +78,13 @@ import java.util.*;
*
* @author Claude Nanjo
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient{
public static final String DATETIME_FORMAT = "yyyy-MM-dd'T'HH:mm:ssK";
public static final String DATE_FORMAT = "yyyy-MM-dd";
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1500;
private static final int TIMEOUT_OPERATION = 30000;
private static final int TIMEOUT_ENTRY = 500;
private static final int TIMEOUT_OPERATION_LONG = 60000;
private static final int TIMEOUT_OPERATION_EXPAND = 120000;
private String base;
private ResourceAddress resourceAddress;
private ResourceFormat preferredResourceFormat;
@ -151,7 +146,7 @@ public class FHIRToolingClient {
TerminologyCapabilities capabilities = null;
try {
capabilities = (TerminologyCapabilities) client.issueGetResourceRequest(resourceAddress.resolveMetadataTxCaps(),
getPreferredResourceFormat(), generateHeaders(), "TerminologyCapabilities", TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), generateHeaders(), "TerminologyCapabilities", timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's terminology capabilities", e);
}
@ -162,7 +157,7 @@ public class FHIRToolingClient {
CapabilityStatement conformance = null;
try {
conformance = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(false),
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement", TIMEOUT_NORMAL).getReference();
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement", timeoutNormal).getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's conformance statement", e);
}
@ -174,7 +169,7 @@ public class FHIRToolingClient {
return capabilities;
try {
capabilities = (CapabilityStatement) client.issueGetResourceRequest(resourceAddress.resolveMetadataUri(true),
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement-Quick", TIMEOUT_NORMAL)
getPreferredResourceFormat(), generateHeaders(), "CapabilitiesStatement-Quick", timeoutNormal)
.getReference();
} catch (Exception e) {
throw new FHIRException("Error fetching the server's capability statement: " + e.getMessage(), e);
@ -187,7 +182,7 @@ public class FHIRToolingClient {
try {
result = client.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
getPreferredResourceFormat(), generateHeaders(), "Read " + resourceClass.getName() + "/" + id,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -204,7 +199,7 @@ public class FHIRToolingClient {
result = client.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndIdAndVersion(resourceClass, id, version),
getPreferredResourceFormat(), generateHeaders(),
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version, TIMEOUT_NORMAL);
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version, timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -221,7 +216,7 @@ public class FHIRToolingClient {
result = client.issueGetResourceRequest(
resourceAddress.resolveGetUriFromResourceClassAndCanonical(resourceClass, canonicalURL),
getPreferredResourceFormat(), generateHeaders(), "Read " + resourceClass.getName() + "?url=" + canonicalURL,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -244,7 +239,7 @@ public class FHIRToolingClient {
resourceAddress.resolveGetUriFromResourceClassAndId(resource.getClass(), resource.getId()),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Update " + resource.fhirType() + "/" + resource.getId(),
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -273,7 +268,7 @@ public class FHIRToolingClient {
result = client.issuePutRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Update " + resource.fhirType() + "/" + id,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -311,10 +306,10 @@ public class FHIRToolingClient {
if (complex) {
byte[] body = ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat()));
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + "/$" + name, timeoutLong);
} else {
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(),
"GET " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"GET " + resourceClass.getName() + "/$" + name, timeoutLong);
}
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
@ -340,7 +335,7 @@ public class FHIRToolingClient {
transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(),
ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "transaction",
TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
timeoutOperation + (timeoutEntry * batch.getEntry().size()));
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -354,7 +349,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveValidateUri(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", timeoutLong);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -411,7 +406,7 @@ public class FHIRToolingClient {
try {
result = client.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand"),
ByteUtils.resourceToByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), TIMEOUT_OPERATION_EXPAND);
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -426,7 +421,7 @@ public class FHIRToolingClient {
org.hl7.fhir.r4b.utils.client.network.ResourceRequest<Resource> result = null;
try {
result = client.issueGetResourceRequest(resourceAddress.resolveOperationUri(CodeSystem.class, "lookup", params),
getPreferredResourceFormat(), generateHeaders(), "CodeSystem/$lookup", TIMEOUT_NORMAL);
getPreferredResourceFormat(), generateHeaders(), "CodeSystem/$lookup", timeoutNormal);
} catch (IOException e) {
e.printStackTrace();
}
@ -448,7 +443,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand", params),
ByteUtils.resourceToByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), TIMEOUT_OPERATION_EXPAND);
generateHeaders(), "ValueSet/$expand?url=" + source.getUrl(), timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -471,7 +466,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "Closure?name=" + name, TIMEOUT_NORMAL);
getPreferredResourceFormat(), generateHeaders(), "Closure?name=" + name, timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());
@ -491,7 +486,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(
resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(), "UpdateClosure?name=" + name, TIMEOUT_OPERATION);
getPreferredResourceFormat(), generateHeaders(), "UpdateClosure?name=" + name, timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(),
(OperationOutcome) result.getPayload());

18
org.hl7.fhir.r4b/src/test/java/org/hl7/fhir/r4b/test/XmlParserTests.java
View File

@ -44,22 +44,4 @@ public class XmlParserTests {
}
}
@Test
/**
* Deserializes a simplified CDA example into the logical model and checks that
* xml deserialization works for the xsi:type
*
* @throws IOException
*/
public void testXsiDeserialiserXmlParser() throws IOException {
Element cda = Manager.parseSingle(context,
TestingUtilities.loadTestResourceStream("validator", "cda", "example-xsi.xml"), FhirFormat.XML);
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(context, cda, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
String cdaSerialised = baosXml.toString();
Assertions.assertTrue(cdaSerialised.indexOf("xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"") > 0);
Assertions.assertTrue(cdaSerialised.indexOf("xsi:type=\"CD\"") > 0);
}
}

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

@ -177,6 +177,8 @@ public abstract class CanonicalResourceComparer extends ResourceComparer {
s = s + refCell(left);
s = s + refCell(right);
s = s + "<td><a href=\""+getId()+".html\">Comparison</a></td>";
s = s + "<td><a href=\""+getId()+"-union.html\">Union</a></td>";
s = s + "<td><a href=\""+getId()+"-intersection.html\">Intersection</a></td>";
s = s + "<td>"+outcomeSummary()+"</td>";
return "<tr style=\"background-color: "+color()+"\">"+s+"</tr>\r\n";
}

32
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/CapabilityStatementComparer.java
View File

@ -183,6 +183,7 @@ public class CapabilityStatementComparer extends CanonicalResourceComparer {
private void compareRestSecurityService(CapabilityStatementRestSecurityComponent left, CapabilityStatementRestSecurityComponent right, StructuralMatch<Element> combined, CapabilityStatementRestSecurityComponent union, CapabilityStatementRestSecurityComponent intersection, CapabilityStatement csU, CapabilityStatement csI, CapabilityStatementComparison res, String path) {
List<CodeableConcept> matchR = new ArrayList<>();
if (left != null) {
for (CodeableConcept l : left.getService()) {
CodeableConcept r = findInList(right.getService(), l);
if (r == null) {
@ -199,6 +200,7 @@ public class CapabilityStatementComparer extends CanonicalResourceComparer {
combined.getChildren().add(sm);
}
}
}
if (right != null) {
for (CodeableConcept r : right.getService()) {
if (!matchR.contains(r)) {
@ -257,23 +259,23 @@ public class CapabilityStatementComparer extends CanonicalResourceComparer {
}
private void compareExpectations(StructuralMatch<Element> combined, Element left, Element right, String path, CapabilityStatementComparison res, Element union, Element intersection) {
Extension l = left.getExtensionByUrl(ToolingExtensions.EXT_CAP_STMT_EXPECT);
Extension r = right.getExtensionByUrl(ToolingExtensions.EXT_CAP_STMT_EXPECT);
if (l != null || r != null) {
if (l == null) {
union.addExtension(r.copy());
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this expectation", path), r));
} else if (r == null) {
union.addExtension(l.copy());
combined.getChildren().add(new StructuralMatch<Element>(l, vmI(IssueSeverity.INFORMATION, "Removed this expectation", path)));
} else {
StructuralMatch<Element> sm = new StructuralMatch<Element>(l, r);
List<Extension> l = left.getExtensionsByUrl(ToolingExtensions.EXT_CAP_STMT_EXPECT);
List<Extension> r = right.getExtensionsByUrl(ToolingExtensions.EXT_CAP_STMT_EXPECT);
if (l.size() == 1 || r.size() == 1) {
if (l.size() == 0) {
union.addExtension(r.get(0).copy());
combined.getChildren().add(new StructuralMatch<Element>(vmI(IssueSeverity.INFORMATION, "Added this expectation", path), r.get(0)));
} else if (r.size() == 0) {
union.addExtension(l.get(0).copy());
combined.getChildren().add(new StructuralMatch<Element>(l.get(0), vmI(IssueSeverity.INFORMATION, "Removed this expectation", path)));
} else if (l.size() == 1 && r.size() == 1) {
StructuralMatch<Element> sm = new StructuralMatch<Element>(l.get(0), r.get(0));
combined.getChildren().add(sm);
String ls = l.getValue().primitiveValue();
String rs = r.getValue().primitiveValue();
String ls = l.get(0).getValue().primitiveValue();
String rs = r.get(0).getValue().primitiveValue();
if (ls.equals(rs)) {
union.addExtension(l.copy());
intersection.addExtension(l.copy());
union.addExtension(l.get(0).copy());
intersection.addExtension(l.get(0).copy());
} else {
sm.getMessages().add(new ValidationMessage(Source.ProfileComparer, IssueType.INFORMATIONAL, path+".extension('http://hl7.org/fhir/StructureDefinition/capabilitystatement-expectation')", "Changed value for expectation: '"+ls+"' vs '"+rs+"'", IssueSeverity.WARNING));
String lowest = lower(ls, rs) ? ls : rs;

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/ComparisonRenderer.java
View File

@ -79,6 +79,8 @@ public class ComparisonRenderer implements IEvaluationContext {
b.append(" <td width=\"260\"><b>"+Utilities.escapeXml(leftName)+"</b></td>\r\n");
b.append(" <td width=\"260\"><b>"+Utilities.escapeXml(rightName)+"</b></td>\r\n");
b.append(" <td width=\"100\"><b>Difference</b></td>\r\n");
b.append(" <td width=\"100\"><b>Union</b></td>\r\n");
b.append(" <td width=\"100\"><b>Intersection</b></td>\r\n");
b.append(" <td width=\"260\"><b>Notes</b></td>\r\n");
b.append(" </tr>\r\n");
@ -225,8 +227,22 @@ public class ComparisonRenderer implements IEvaluationContext {
vars.put("errors", new StringType(new XhtmlComposer(true).compose(cs.renderErrors(comp))));
vars.put("metadata", new StringType(new XhtmlComposer(true).compose(cs.renderMetadata(comp, "", ""))));
vars.put("structure", new StringType(new XhtmlComposer(true).compose(cs.renderStructure(comp, "", "", "http://hl7.org/fhir"))));
String cnt = processTemplate(template, "CodeSystem", vars);
String union = new XhtmlComposer(true).compose(cs.renderUnion(comp, "", folder, "http://hl7.org/fhir"));
String intersection = new XhtmlComposer(true).compose(cs.renderIntersection(comp, "", folder, "http://hl7.org/fhir"));
vars.put("union", new StringType(union));
vars.put("intersection", new StringType(intersection));
String cnt = processTemplate(template, "Profile", vars);
TextFile.stringToFile(cnt, file(comp.getId()+".html"));
template = templates.get("Profile-Union");
cnt = processTemplate(template, "Profile-Union", vars);
TextFile.stringToFile(cnt, file(comp.getId()+"-union.html"));
template = templates.get("Profile-Intersection");
cnt = processTemplate(template, "Profile-Intersection", vars);
TextFile.stringToFile(cnt, file(comp.getId()+"-intersection.html"));
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-union.json")), comp.getUnion());
new org.hl7.fhir.r5.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(folder, comp.getId() + "-intersection.json")), comp.getIntersection());
}

15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/comparison/StructureDefinitionComparer.java
View File

@ -5,6 +5,7 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
@ -46,6 +47,7 @@ import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableGenerationMode;
import org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.TableModel;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -1252,10 +1254,21 @@ public class StructureDefinitionComparer extends CanonicalResourceComparer imple
HierarchicalTableGenerator gen = new HierarchicalTableGenerator(Utilities.path("[tmp]", "compare"), false, true);
gen.setTranslator(session.getContextRight().translator());
TableModel model = gen.initComparisonTable(corePath, id);
genElementComp(null /* oome back to this later */, gen, model.getRows(), comp.combined, corePath, prefix, null, true);
genElementComp(null /* come back to this later */, gen, model.getRows(), comp.combined, corePath, prefix, null, true);
return gen.generate(model, prefix, 0, null);
}
public XhtmlNode renderUnion(ProfileComparison comp, String id, String prefix, String corePath) throws FHIRException, IOException {
StructureDefinitionRenderer sdr = new StructureDefinitionRenderer(new RenderingContext(utilsLeft.getContext(), null, utilsLeft.getTerminologyServiceOptions(), corePath, prefix, null, ResourceRendererMode.TECHNICAL, GenerationRules.IG_PUBLISHER).setPkp(this));
return sdr.generateTable(corePath, comp.union, false, prefix, false, id, true, corePath, prefix, false, true, null, false, sdr.getContext(), "u");
}
public XhtmlNode renderIntersection(ProfileComparison comp, String id, String prefix, String corePath) throws FHIRException, IOException {
StructureDefinitionRenderer sdr = new StructureDefinitionRenderer(new RenderingContext(utilsLeft.getContext(), null, utilsLeft.getTerminologyServiceOptions(), corePath, prefix, null, ResourceRendererMode.TECHNICAL, GenerationRules.IG_PUBLISHER).setPkp(this));
return sdr.generateTable(corePath, comp.intersection, false, prefix, false, id, true, corePath, prefix, false, true, null, false, sdr.getContext(), "i");
}
private void genElementComp(String defPath, HierarchicalTableGenerator gen, List<Row> rows, StructuralMatch<ElementDefinitionNode> combined, String corePath, String prefix, Row slicingRow, boolean root) throws IOException {
Row originalRow = slicingRow;
Row typesRow = null;

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/XmlSchemaGenerator.java
View File

@ -239,8 +239,8 @@ public class XmlSchemaGenerator {
private String getNs(StructureDefinition sd) {
String ns = "http://hl7.org/fhir";
if (sd.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE))
ns = ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_XML_NAMESPACE);
if (sd.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED))
ns = ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
return ns;
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/profile/ProfileUtilities.java
View File

@ -262,7 +262,7 @@ public class ProfileUtilities extends TranslatingUtilities {
"http://hl7.org/fhir/tools/StructureDefinition/json-property-key",
"http://hl7.org/fhir/tools/StructureDefinition/type-specifier",
"http://hl7.org/fhir/tools/StructureDefinition/xml-choice-group",
"http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace",
ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED,
"http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype"
);

28
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
View File

@ -60,7 +60,7 @@ import org.hl7.fhir.exceptions.NoTerminologyServiceException;
import org.hl7.fhir.exceptions.TerminologyServiceException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.context.ILoggingService.LogCategory;
import org.hl7.fhir.r5.model.ActorDefinition;
import org.hl7.fhir.r5.model.BooleanType;
import org.hl7.fhir.r5.model.Bundle;
@ -3024,4 +3024,30 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
}
public void unload() {
codeSystems.unload();
valueSets.unload();
maps.unload();
transforms.unload();
structures.unload();
typeManager.unload();
measures.unload();
libraries.unload();
guides.unload();
capstmts.unload();
searchParameters.unload();
questionnaires.unload();
operations.unload();
plans.unload();
actors.unload();
requirements.unload();
systems.unload();
binaries.clear();
validationCache.clear();
txCache.clear();
}
}

13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/CanonicalResourceManager.java
View File

@ -197,6 +197,11 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
}
}
public void unload() {
if (proxy != null) {
resource = null;
}
}
}
public class MetadataResourceVersionComparator<T1 extends CachedCanonicalResource<T>> implements Comparator<T1> {
@ -659,4 +664,12 @@ public class CanonicalResourceManager<T extends CanonicalResource> {
}
public void unload() {
for (CachedCanonicalResource<T> t : list) {
t.unload();
}
}
}

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ContextUtilities.java
View File

@ -362,8 +362,8 @@ public class ContextUtilities implements ProfileKnowledgeProvider {
public StructureDefinition fetchByJsonName(String key) {
for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
ElementDefinition ed = sd.getSnapshot().getElementFirstRep();
if (sd.getKind() == StructureDefinitionKind.LOGICAL && ed != null && ed.hasExtension(ToolingExtensions.EXT_JSON_NAME) &&
key.equals(ToolingExtensions.readStringExtension(ed, ToolingExtensions.EXT_JSON_NAME))) {
if (sd.getKind() == StructureDefinitionKind.LOGICAL && ed != null && ed.hasExtension(ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED) &&
key.equals(ToolingExtensions.readStringExtension(ed, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED))) {
return sd;
}
}

15
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/ILoggingService.java Normal file
View File

@ -0,0 +1,15 @@
package org.hl7.fhir.r5.context;
public interface ILoggingService {
public enum LogCategory {
INIT,
PROGRESS,
TX,
CONTEXT,
GENERATE,
HTML
}
public void logMessage(String message); // status messages, always display
public void logDebugMessage(ILoggingService.LogCategory category, String message); // verbose; only when debugging
public boolean isDebugLogging(); // whether to log debug information
}

13
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
View File

@ -499,19 +499,6 @@ public interface IWorkerContext {
public Map<String, NamingSystem> getNSUrlMap();
public TranslationServices translator();
public interface ILoggingService {
public enum LogCategory {
INIT,
PROGRESS,
TX,
CONTEXT,
GENERATE,
HTML
}
public void logMessage(String message); // status messages, always display
public void logDebugMessage(LogCategory category, String message); // verbose; only when debugging
public boolean isDebugLogging(); // whether to log debug information
}
public void setLogger(@Nonnull ILoggingService logger);
public ILoggingService getLogger();

5
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
View File

@ -53,7 +53,7 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.context.CanonicalResourceManager.CanonicalResourceProxy;
import org.hl7.fhir.r5.context.IWorkerContext.ILoggingService.LogCategory;
import org.hl7.fhir.r5.context.ILoggingService.LogCategory;
import org.hl7.fhir.r5.formats.IParser;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.formats.XmlParser;
@ -211,7 +211,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
private final boolean allowLoadingDuplicates;
@With
private final IWorkerContext.ILoggingService loggingService;
private final ILoggingService loggingService;
public SimpleWorkerContextBuilder() {
cacheTerminologyClientErrors = false;
@ -809,5 +809,6 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
}

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SystemOutLoggingService.java
View File

@ -3,7 +3,7 @@ package org.hl7.fhir.r5.context;
import lombok.RequiredArgsConstructor;
@RequiredArgsConstructor
public class SystemOutLoggingService implements IWorkerContext.ILoggingService {
public class SystemOutLoggingService implements ILoggingService {
private final boolean debug;

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/TypeManager.java
View File

@ -127,4 +127,13 @@ public class TypeManager {
}
}
public void unload() {
structures.unload();
typeDefinitions.clear();
fhirTypeDefinitions.clear();
primitiveNames.clear();
dataTypeNames.clear();
}
}

21
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -59,6 +59,7 @@ import org.hl7.fhir.r5.formats.JsonCreator;
import org.hl7.fhir.r5.formats.JsonCreatorCanonical;
import org.hl7.fhir.r5.formats.JsonCreatorDirect;
import org.hl7.fhir.r5.model.ElementDefinition.TypeRefComponent;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
@ -104,18 +105,34 @@ public class JsonParser extends ParserBase {
}
public Element parse(String source, String type) throws Exception {
return parse(source, type, false);
}
public Element parse(String source, String type, boolean inner) throws Exception {
ValidatedFragment focusFragment = new ValidatedFragment(ValidatedFragment.FOCUS_NAME, "json", source.getBytes(StandardCharsets.UTF_8), false);
JsonObject obj = org.hl7.fhir.utilities.json.parser.JsonParser.parseObject(source, true, true);
String path = "/"+type;
StructureDefinition sd = getDefinition(focusFragment.getErrors(), -1, -1, type);
if (sd == null)
if (sd == null) {
return null;
}
if (inner) {
// we have an anonymous wrapper that has an arbitrarily named property with the specified type. We're going to invent a snapshot for that
sd = new StructureDefinition();
sd.setType("Wrapper");
ElementDefinition bEd = sd.getSnapshot().addElement();
ElementDefinition nEd = sd.getSnapshot().addElement();
bEd.setPath("Wrapper");
nEd.setPath("Wrapper."+obj.getProperties().get(0).getName());
nEd.addType().setCode(type);
nEd.setMax(obj.getProperties().get(0).getValue().isJsonArray() ? "*" : "1");
}
Element result = new Element(type, new Property(context, sd.getSnapshot().getElement().get(0), sd, this.profileUtilities)).setFormat(FhirFormat.JSON);
result.setPath(type);
checkObject(focusFragment.getErrors(), obj, result, path);
result.setType(type);
parseChildren(focusFragment.getErrors(), path, obj, result, true, new ArrayList<>());
parseChildren(focusFragment.getErrors(), path, obj, result, true, null);
result.numberChildren();
return result;
}

6
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/ParserBase.java
View File

@ -152,7 +152,7 @@ public abstract class ParserBase {
expectedName = expectedName.substring(expectedName.lastIndexOf("/")+1);
}
}
String expectedNamespace = ToolingExtensions.readStringExtension(logical, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
String expectedNamespace = ToolingExtensions.readStringExtension(logical, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
if (matchesNamespace(expectedNamespace, ns) && matchesName(expectedName, name)) {
return logical;
} else {
@ -175,9 +175,9 @@ public abstract class ParserBase {
for (StructureDefinition sd : context.fetchResourcesByType(StructureDefinition.class)) {
if (sd.getDerivation() == TypeDerivationRule.SPECIALIZATION && !sd.getUrl().startsWith("http://hl7.org/fhir/StructureDefinition/de-")) {
String type = urlTail(sd.getType());
if(name.equals(type) && (ns == null || ns.equals(FormatUtilities.FHIR_NS)) && !ToolingExtensions.hasExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))
if(name.equals(type) && (ns == null || ns.equals(FormatUtilities.FHIR_NS)) && !ToolingExtensions.hasAnyOfExtensions(sd, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED))
return sd;
String sns = ToolingExtensions.readStringExtension(sd, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
String sns = ToolingExtensions.readStringExtension(sd, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
if ((name.equals(type) || name.equals(sd.getName())) && ns != null && ns.equals(sns))
return sd;
}

16
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/Property.java
View File

@ -90,8 +90,8 @@ public class Property {
}
public String getJsonName() {
if (definition.hasExtension(ToolingExtensions.EXT_JSON_NAME)) {
return ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_JSON_NAME);
if (definition.hasExtension(ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED)) {
return ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED);
} else {
return getName();
}
@ -100,16 +100,18 @@ public class Property {
public String getXmlName() {
if (definition.hasExtension(ToolingExtensions.EXT_XML_NAME)) {
return ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_XML_NAME);
} else if (definition.hasExtension(ToolingExtensions.EXT_XML_NAME_DEPRECATED)) {
return ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_XML_NAME_DEPRECATED);
} else {
return getName();
}
}
public String getXmlNamespace() {
if (ToolingExtensions.hasExtension(definition, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")) {
return ToolingExtensions.readStringExtension(definition, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
} else if (ToolingExtensions.hasExtension(structure, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")) {
return ToolingExtensions.readStringExtension(structure, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace");
if (ToolingExtensions.hasAnyOfExtensions(definition, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED)) {
return ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
} else if (ToolingExtensions.hasAnyOfExtensions(structure, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED)) {
return ToolingExtensions.readStringExtension(structure, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
} else {
return FormatUtilities.FHIR_NS;
}
@ -596,7 +598,7 @@ public class Property {
public boolean hasJsonName() {
return definition.hasExtension(ToolingExtensions.EXT_JSON_NAME);
return definition.hasExtension(ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED);
}

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/Element.java
View File

@ -482,6 +482,15 @@ public abstract class Element extends Base implements IBaseHasExtensions, IBaseE
return ext.get(0).getValue().primitiveValue();
}
public String getExtensionString(String... theUrls) throws FHIRException {
for (String url : theUrls) {
if (hasExtension(url)) {
return getExtensionString(url);
}
}
return null;
}
public StandardsStatus getStandardsStatus() {
return ToolingExtensions.getStandardsStatus(this);

9
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/TypeDetails.java
View File

@ -44,6 +44,7 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.ExpressionNode.CollectionStatus;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.TypeDetails.ProfiledTypeSorter;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.Utilities;
@ -253,6 +254,14 @@ public class TypeDetails {
return true;
}
}
t = ProfiledType.ns(n);
StructureDefinition sd = context.fetchTypeDefinition(t);
if (sd != null && sd.getKind() != StructureDefinitionKind.LOGICAL && Utilities.existsInList(sd.getType(), "boolean", "string", "integer", "decimal", "Quantity", "dateTime", "time")) {
t = FP_NS+"System."+Utilities.capitalize(sd.getType());
if (typesContains(t)) {
return true;
}
}
}
for (String n: tn) {
String id = n.contains("#") ? n.substring(0, n.indexOf("#")) : n;

77
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/DataRenderer.java
View File

@ -67,6 +67,7 @@ import org.hl7.fhir.r5.model.Timing;
import org.hl7.fhir.r5.model.Timing.EventTiming;
import org.hl7.fhir.r5.model.Timing.TimingRepeatComponent;
import org.hl7.fhir.r5.model.Timing.UnitsOfTime;
import org.hl7.fhir.r5.model.TriggerDefinition;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.model.ValueSet;
@ -1202,12 +1203,8 @@ public class DataRenderer extends Renderer implements CodeResolver {
String s = Utilities.noString(ii.getValue()) ? "?ngen-9?" : ii.getValue();
NamingSystem ns = context.getContext().getNSUrlMap().get(ii.getSystem());
if (ns != null) {
if (ns.hasWebPath()) {
s = "<a href=\""+Utilities.escapeXml(ns.getWebPath())+"\">"+ns.present()+"</a>#"+s;
} else {
s = ns.present()+"#"+s;
}
}
if (ii.hasType()) {
if (ii.getType().hasText())
s = ii.getType().getText()+":\u00A0"+s;
@ -1236,7 +1233,47 @@ public class DataRenderer extends Renderer implements CodeResolver {
}
protected void renderIdentifier(XhtmlNode x, Identifier ii) {
x.addText(displayIdentifier(ii));
if (ii.hasType()) {
if (ii.getType().hasText())
x.tx(ii.getType().getText()+":");
else if (ii.getType().hasCoding() && ii.getType().getCoding().get(0).hasDisplay())
x.tx(ii.getType().getCoding().get(0).getDisplay()+":");
else if (ii.getType().hasCoding() && ii.getType().getCoding().get(0).hasCode())
x.tx(lookupCode(ii.getType().getCoding().get(0).getSystem(), ii.getType().getCoding().get(0).getVersion(), ii.getType().getCoding().get(0).getCode())+":");
} else {
x.tx("id:");
}
x.nbsp();
NamingSystem ns = context.getContext().getNSUrlMap().get(ii.getSystem());
if (ns != null) {
if (ns.hasWebPath()) {
x.ah(ns.getWebPath()).tx("#");
} else {
x.tx(ns.present()+"#");
}
}
x.tx(Utilities.noString(ii.getValue()) ? "?ngen-9?" : ii.getValue());
if (ii.hasUse() || ii.hasPeriod()) {
x.nbsp();
x.tx("(");
if (ii.hasUse()) {
x.tx("use:");
x.nbsp();
x.tx(ii.getUse().toString());
}
if (ii.hasUse() && ii.hasPeriod()) {
x.tx(",");
x.nbsp();
}
if (ii.hasPeriod()) {
x.tx("period:");
x.nbsp();
x.tx(displayPeriod(ii.getPeriod()));
}
x.tx(")");
}
}
public static String displayHumanName(HumanName name) {
@ -1541,6 +1578,36 @@ public class DataRenderer extends Renderer implements CodeResolver {
render(x, u.getValue());
}
public void renderTriggerDefinition(XhtmlNode x, TriggerDefinition td) throws FHIRFormatError, DefinitionException, IOException {
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().b().tx("Type");
tr.td().tx(td.getType().getDisplay());
if (td.hasName()) {
tr = tbl.tr();
tr.td().b().tx("Name");
tr.td().tx(td.getType().getDisplay());
}
if (td.hasCode()) {
tr = tbl.tr();
tr.td().b().tx("Code");
renderCodeableConcept(tr.td(), td.getCode());
}
if (td.hasTiming()) {
tr = tbl.tr();
tr.td().b().tx("Timing");
render(tr.td(), td.getTiming());
}
if (td.hasCondition()) {
tr = tbl.tr();
tr.td().b().tx("Condition");
renderExpression(tr.td(), td.getCondition());
}
}
public void renderDataRequirement(XhtmlNode x, DataRequirement dr) throws FHIRFormatError, DefinitionException, IOException {
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ProfileDrivenRenderer.java
View File

@ -61,6 +61,7 @@ import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r5.model.Timing;
import org.hl7.fhir.r5.model.TriggerDefinition;
import org.hl7.fhir.r5.model.UriType;
import org.hl7.fhir.r5.model.UsageContext;
import org.hl7.fhir.r5.renderers.utils.BaseWrappers.BaseWrapper;
@ -512,6 +513,9 @@ public class ProfileDrivenRenderer extends ResourceRenderer {
} else if (e instanceof DataRequirement) {
DataRequirement p = (DataRequirement) e;
renderDataRequirement(x, p);
} else if (e instanceof TriggerDefinition) {
TriggerDefinition p = (TriggerDefinition) e;
renderTriggerDefinition(x, p);
} else if (e instanceof UsageContext) {
UsageContext p = (UsageContext) e;
renderUsageContext(x, p);

53
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/StructureDefinitionRenderer.java
View File

@ -537,6 +537,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
}
public XhtmlNode generateTable(String defFile, StructureDefinition profile, boolean diff, String imageFolder, boolean inlineGraphics, String profileBaseFileName, boolean snapshot, String corePath, String imagePath,
boolean logicalModel, boolean allInvariants, Set<String> outputTracker, boolean mustSupport, RenderingContext rc, String anchorPrefix) throws IOException, FHIRException {
assert(diff != snapshot);// check it's ok to get rid of one of these
@ -1256,14 +1257,14 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
row.getCells().add(c);
if (used) {
if (logicalModel && ToolingExtensions.hasExtension(profile, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")) {
if (logicalModel && ToolingExtensions.hasAnyOfExtensions(profile, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED)) {
if (root) {
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Namespace")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, ToolingExtensions.readStringExtension(profile, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"), null));
} else if (!root && ToolingExtensions.hasExtension(definition, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace") &&
!ToolingExtensions.readStringExtension(definition, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").equals(ToolingExtensions.readStringExtension(profile, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"))) {
c.getPieces().add(gen.new Piece(null, ToolingExtensions.readStringExtension(profile, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED), null));
} else if (!root && ToolingExtensions.hasAnyOfExtensions(definition, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED) &&
!ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED).equals(ToolingExtensions.readStringExtension(profile, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED))) {
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Namespace")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, ToolingExtensions.readStringExtension(definition, "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace"), null));
c.getPieces().add(gen.new Piece(null, ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED), null));
}
}
if (root) {
@ -1416,27 +1417,22 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
c.getPieces().add(gen.new Piece(null, translate("sd.table", "Choice Group")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, "This is a repeating choice group that does not appear directly in the instance", null));
}
if (definition.hasExtension(ToolingExtensions.EXT_XML_NAME)) {
if (definition.hasExtension(ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED)) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
if (definition.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE)) {
if (definition.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED)) {
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAME), null));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED), null));
c.getPieces().add(gen.new Piece(null, " (", null));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAMESPACE), null));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED), null));
c.getPieces().add(gen.new Piece(null, ")", null));
} else {
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Element Name")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAME), null));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED), null));
}
} else if (definition.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE)) {
} else if (definition.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED)) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Namespace")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAMESPACE), null));
}
if (root && ToolingExtensions.readBoolExtension(profile, ToolingExtensions.EXT_XML_NO_ORDER)) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
c.getPieces().add(gen.new Piece(null, translate("sd.table", "XML Order")+": ", null).addStyle("font-weight:bold"));
c.getPieces().add(gen.new Piece(null, "The properties of this type can appear in any order in the XML", null));
c.getPieces().add(gen.new Piece(null, definition.getExtensionString(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED), null));
}
if (definition.hasExtension(ToolingExtensions.EXT_JSON_EMPTY)) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
@ -1447,7 +1443,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
c.getPieces().add(gen.new Piece(null, "JSON: This element may be present as a JSON Array even when there are no items in the instance", null));
}
}
String jn = ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_JSON_NAME);
String jn = ToolingExtensions.readStringExtension(definition, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED);
if (!Utilities.noString(jn)) {
if (!c.getPieces().isEmpty()) { c.addPiece(gen.new Piece("br")); }
if (definition.getPath().contains(".")) {
@ -3642,11 +3638,12 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
// tooling extensions for formats
if (ToolingExtensions.hasExtensions(d, ToolingExtensions.EXT_JSON_EMPTY, ToolingExtensions.EXT_JSON_PROP_KEY, ToolingExtensions.EXT_JSON_NULLABLE,
ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_PRIMITIVE_CHOICE)) {
if (ToolingExtensions.hasAnyOfExtensions(d, ToolingExtensions.EXT_JSON_EMPTY, ToolingExtensions.EXT_JSON_PROP_KEY, ToolingExtensions.EXT_JSON_NULLABLE,
ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED, ToolingExtensions.EXT_JSON_PRIMITIVE_CHOICE)) {
tableRow(tbl, "JSON Format", null, strikethrough, describeJson(d));
}
if (d.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE) || sd.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE) || d.hasExtension(ToolingExtensions.EXT_XML_NAME) || (root && sd.hasExtension(ToolingExtensions.EXT_XML_NO_ORDER)) ||
if (d.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED) || sd.hasExtension(ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED) ||
d.hasExtension(ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED) || sd.hasExtension(ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED) ||
d.hasRepresentation()) {
tableRow(tbl, "XML Format", null, strikethrough, describeXml(sd, d, root));
}
@ -3733,28 +3730,24 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
}
}
}
String name = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_XML_NAMESPACE);
String name = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
if (name == null && root) {
name = ToolingExtensions.readStringExtension(profile, ToolingExtensions.EXT_XML_NAMESPACE);
name = ToolingExtensions.readStringExtension(profile, ToolingExtensions.EXT_XML_NAMESPACE, ToolingExtensions.EXT_XML_NAMESPACE_DEPRECATED);
}
if (name != null) {
ret.codeWithText("In the XML format, this property has the namespace ", name, ".");
}
name = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_XML_NAME);
name = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_XML_NAME, ToolingExtensions.EXT_XML_NAME_DEPRECATED);
if (name != null) {
ret.codeWithText("In the XML format, this property has the actual name", name, ".");
}
boolean no = root && ToolingExtensions.readBoolExtension(profile, ToolingExtensions.EXT_XML_NO_ORDER);
if (no) {
ret.tx("The children of this type can appear in any order in the XML.");
}
return ret;
}
private XhtmlNode describeJson(ElementDefinition d) {
XhtmlNode ret = new XhtmlNode(NodeType.Element, "div");
var ul = ret.ul();
boolean list = ToolingExtensions.countExtensions(d, ToolingExtensions.EXT_JSON_EMPTY, ToolingExtensions.EXT_JSON_PROP_KEY, ToolingExtensions.EXT_JSON_NULLABLE, ToolingExtensions.EXT_JSON_NAME) > 1;
boolean list = ToolingExtensions.countExtensions(d, ToolingExtensions.EXT_JSON_EMPTY, ToolingExtensions.EXT_JSON_PROP_KEY, ToolingExtensions.EXT_JSON_NULLABLE, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED) > 1;
String code = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_JSON_EMPTY);
if (code != null) {
@ -3770,7 +3763,7 @@ public class StructureDefinitionRenderer extends ResourceRenderer {
break;
}
}
String jn = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_JSON_NAME);
String jn = ToolingExtensions.readStringExtension(d, ToolingExtensions.EXT_JSON_NAME, ToolingExtensions.EXT_JSON_NAME_DEPRECATED);
if (jn != null) {
if (d.getPath().contains(".")) {
ul.li().codeWithText("This property appears in JSON with the property name ", jn, null);

17
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/ValueSetRenderer.java
View File

@ -187,6 +187,9 @@ public class ValueSetRenderer extends TerminologyRenderer {
if (vs.hasCopyright())
generateCopyright(x, vs);
}
boolean hasFragment = generateContentModeNotices(x, vs.getExpansion(), vs);
generateVersionNotice(x, vs.getExpansion(), vs);
if (ToolingExtensions.hasExtension(vs.getExpansion(), ToolingExtensions.EXT_EXP_TOOCOSTLY)) {
List<Extension> exl = vs.getExpansion().getExtensionsByUrl(ToolingExtensions.EXT_EXP_TOOCOSTLY);
boolean other = false;
@ -203,11 +206,9 @@ public class ValueSetRenderer extends TerminologyRenderer {
if (count == null)
x.para().tx("This value set does not contain a fixed number of concepts");
else
x.para().tx("This value set contains "+count.toString()+" concepts");
x.para().tx("This value set contains "+(hasFragment ? "at least " : "")+count.toString()+" concepts");
}
generateContentModeNotices(x, vs.getExpansion(), vs);
generateVersionNotice(x, vs.getExpansion(), vs);
boolean doLevel = false;
for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
@ -319,12 +320,13 @@ public class ValueSetRenderer extends TerminologyRenderer {
return false;
}
private void generateContentModeNotices(XhtmlNode x, ValueSetExpansionComponent expansion, Resource vs) {
private boolean generateContentModeNotices(XhtmlNode x, ValueSetExpansionComponent expansion, Resource vs) {
generateContentModeNotice(x, expansion, "example", "Expansion based on example code system", vs);
generateContentModeNotice(x, expansion, "fragment", "Expansion based on code system fragment", vs);
return generateContentModeNotice(x, expansion, "fragment", "Expansion based on code system fragment", vs);
}
private void generateContentModeNotice(XhtmlNode x, ValueSetExpansionComponent expansion, String mode, String text, Resource vs) {
private boolean generateContentModeNotice(XhtmlNode x, ValueSetExpansionComponent expansion, String mode, String text, Resource vs) {
boolean res = false;
Multimap<String, String> versions = HashMultimap.create();
for (ValueSetExpansionParameterComponent p : expansion.getParameter()) {
if (p.getName().equals(mode)) {
@ -343,6 +345,7 @@ public class ValueSetRenderer extends TerminologyRenderer {
XhtmlNode p = x.para().style("border: black 1px dotted; background-color: #ffcccc; padding: 8px; margin-bottom: 8px");
p.tx(text+" ");
expRef(p, s, v, vs);
res = true;
}
} else {
for (String v : versions.get(s)) {
@ -351,12 +354,14 @@ public class ValueSetRenderer extends TerminologyRenderer {
div.para().tx(text+"s: ");
ul = div.ul();
first = false;
res = true;
}
expRef(ul.li(), s, v, vs);
}
}
}
}
return res;
}
private boolean checkDoSystem(ValueSet vs, ValueSet src) {

10
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/utils/DirectWrappers.java
View File

@ -219,8 +219,14 @@ public class DirectWrappers {
Property family = b.getChildByName("family");
Property given = wrapped.getChildByName("given");
String s = given != null && given.hasValues() ? given.getValues().get(0).primitiveValue() : "";
if (family != null && family.hasValues())
s = s + " " + family.getValues().get(0).primitiveValue().toUpperCase();
if (family != null && family.hasValues()) {
String v = family.getValues().get(0).primitiveValue();
if (v == null) {
s = s + " " + "??";
} else {
s = s + " " + v.toUpperCase();
}
}
return s;
} else {
Property p = b.getChildByName("name");

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/ITerminologyClient.java
View File

@ -54,7 +54,7 @@ public interface ITerminologyClient {
ValueSet expandValueset(ValueSet vs, Parameters p, Map<String, String> params) throws FHIRException;
Parameters validateCS(Parameters pin) throws FHIRException;
Parameters validateVS(Parameters pin) throws FHIRException;
ITerminologyClient setTimeout(int i) throws FHIRException;
ITerminologyClient setTimeoutFactor(int i) throws FHIRException;
ITerminologyClient setLogger(ToolingClientLogger txLog) throws FHIRException;
int getRetryCount() throws FHIRException;
ITerminologyClient setRetryCount(int retryCount) throws FHIRException;

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/ValueSetExpander.java
View File

@ -668,8 +668,6 @@ public class ValueSetExpander extends ValueSetProcessBase {
}
if (langs == null && focus.hasLanguage()) {
langs = new AcceptLanguageHeader(focus.getLanguage(), true);
} else if (langs != null && langs.hasChosen()) {
focus.setLanguage(langs.getChosen());
}
try {

26
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -3272,6 +3272,7 @@ public class FHIRPathEngine {
case Count :
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Integer);
case Where :
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean));
// special case: where the focus is Reference, and the parameter to where is resolve() "is", we will suck up the target types
if (focus.hasType("Reference")) {
boolean canRestrictTargets = !exp.getParameters().isEmpty();
@ -3298,6 +3299,7 @@ public class FHIRPathEngine {
case Select :
return paramTypes.get(0);
case All :
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean));
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean);
case Repeat :
return paramTypes.get(0);
@ -3383,9 +3385,11 @@ public class FHIRPathEngine {
}
case Iif : {
TypeDetails types = new TypeDetails(null);
types.update(paramTypes.get(0));
if (paramTypes.size() > 1) {
checkSingleton(focus, "iif", exp);
checkParamTypes(exp, exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_Boolean));
types.update(paramTypes.get(1));
if (paramTypes.size() > 2) {
types.update(paramTypes.get(2));
}
return types;
}
@ -3679,7 +3683,7 @@ public class FHIRPathEngine {
}
private void checkParamTypes(ExpressionNode expr, String funcName, List<TypeDetails> paramTypes, TypeDetails... typeSet) throws PathEngineException {
private void checkParamTypes(ExpressionNode expr, String funcName,List<TypeDetails> paramTypes, TypeDetails... typeSet) throws PathEngineException {
int i = 0;
for (TypeDetails pt : typeSet) {
if (i == paramTypes.size()) {
@ -3692,6 +3696,15 @@ public class FHIRPathEngine {
throw makeException(expr, I18nConstants.FHIRPATH_WRONG_PARAM_TYPE, funcName, i, a, pt.toString());
}
}
if (actual.getCollectionStatus() != CollectionStatus.SINGLETON && pt.getCollectionStatus() == CollectionStatus.SINGLETON) {
typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_COLLECTION_STATUS_PARAMETER, funcName, i, expr.toString()), I18nConstants.FHIRPATH_COLLECTION_STATUS_PARAMETER));
}
}
}
private void checkSingleton(TypeDetails focus, String name, ExpressionNode expr) throws PathEngineException {
if (focus.getCollectionStatus() != CollectionStatus.SINGLETON) {
typeWarnings.add(new IssueMessage(worker.formatMessage(I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT, name, expr.toString()), I18nConstants.FHIRPATH_COLLECTION_STATUS_CONTEXT));
}
}
@ -4811,9 +4824,12 @@ public class FHIRPathEngine {
private List<Base> funcIif(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> n1 = execute(context, focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (focus.size() > 1) {
throw makeException(exp, I18nConstants.FHIRPATH_NO_COLLECTION, "iif", focus.size());
}
List<Base> n1 = execute(focus.isEmpty() ? context : changeThis(context, focus.get(0)), focus, exp.getParameters().get(0), true);
Equality v = asBool(n1, exp);
if (v == Equality.True) {
return execute(context, focus, exp.getParameters().get(1), true);
} else if (exp.getParameters().size() < 3) {

43
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/ToolingExtensions.java
View File

@ -117,8 +117,9 @@ public class ToolingExtensions {
public static final String EXT_ISSUE_COL = "http://hl7.org/fhir/StructureDefinition/operationoutcome-issue-col";
public static final String EXT_OO_FILE = "http://hl7.org/fhir/StructureDefinition/operationoutcome-file";
public static final String EXT_RESOURCE_IMPLEMENTS = "http://hl7.org/fhir/StructureDefinition/structuredefinition-implements";
public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type";
public static final String EXT_XML_NAME = "http://hl7.org/fhir/StructureDefinition/elementdefinition-xml-name";
public static final String EXT_XML_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-type"; // r2 - r3
public static final String EXT_XML_NAME_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/elementdefinition-xml-name";
public static final String EXT_XML_NAME = "http://hl7.org/fhir/tools/StructureDefinition/xml-name";
public static final String EXT_EXPLICIT_TYPE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name";
public static final String EXT_IGP_RESOURCES = "http://hl7.org/fhir/StructureDefinition/igpublisher-folder-resource";
@ -137,7 +138,8 @@ public class ToolingExtensions {
public static final String EXT_IGP_RESOURCE_INFO = "http://hl7.org/fhir/tools/StructureDefinition/resource-information";
public static final String EXT_IGP_LOADVERSION = "http://hl7.org/fhir/StructureDefinition/igpublisher-loadversion";
public static final String EXT_LIST_PACKAGE = "http://hl7.org/fhir/StructureDefinition/list-packageId";
public static final String EXT_JSON_NAME = "http://hl7.org/fhir/tools/StructureDefinition/elementdefinition-json-name";
public static final String EXT_JSON_NAME_DEPRECATED = "http://hl7.org/fhir/tools/StructureDefinition/elementdefinition-json-name";
public static final String EXT_JSON_NAME = "http://hl7.org/fhir/tools/StructureDefinition/json-name";
public static final String EXT_BINDING_STYLE = "http://hl7.org/fhir/tools/StructureDefinition/elementdefinition-binding-style";
public static final String EXT_EXTENSION_STYLE = "http://hl7.org/fhir/tools/StructureDefinition/elementdefinition-extension-style";
public static final String EXT_LOGICAL_TARGET = "http://hl7.org/fhir/tools/StructureDefinition/logical-target";
@ -151,10 +153,6 @@ public class ToolingExtensions {
public static final String EXT_OT = "http://hl7.org/fhir/StructureDefinition/originalText";
public static final String EXT_CQF_EXP = "http://hl7.org/fhir/StructureDefinition/cqf-expression";
// validated
// private static final String EXT_OID = "http://hl7.org/fhir/StructureDefinition/valueset-oid";
// public static final String EXT_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/codesystem-deprecated";
public static final String EXT_PATTERN = "http://hl7.org/fhir/StructureDefinition/elementdefinition-pattern";
public static final String EXT_ALLOWEDRESOURCE = "http://hl7.org/fhir/StructureDefinition/questionnaire-referenceResource";
private static final String EXT_ALLOWABLE_UNITS = "http://hl7.org/fhir/StructureDefinition/elementdefinition-allowedUnits";
@ -208,7 +206,8 @@ public class ToolingExtensions {
public static final String EXT_VS_COMMENT = "http://hl7.org/fhir/StructureDefinition/valueset-concept-comments";
public static final String EXT_VS_KEYWORD = "http://hl7.org/fhir/StructureDefinition/valueset-keyWord";
public static final String EXT_WORKGROUP = "http://hl7.org/fhir/StructureDefinition/structuredefinition-wg";
public static final String EXT_XML_NAMESPACE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace";
public static final String EXT_XML_NAMESPACE_DEPRECATED = "http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace";
public static final String EXT_XML_NAMESPACE = "http://hl7.org/fhir/tools/StructureDefinition/xml-namespace";
public static final String EXT_OLD_CONCEPTMAP_EQUIVALENCE = "http://hl7.org/fhir/1.0/StructureDefinition/extension-ConceptMap.element.target.equivalence";
public static final String EXT_Q_IS_SUBJ = "http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire-isSubject";
public static final String EXT_Q_HIDDEN = "http://hl7.org/fhir/StructureDefinition/questionnaire-hidden";
@ -221,7 +220,6 @@ public class ToolingExtensions {
public static final String EXT_ED_HEIRARCHY = "http://hl7.org/fhir/StructureDefinition/elementdefinition-heirarchy";
public static final String EXT_SD_IMPOSE_PROFILE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-imposeProfile";
public static final String EXT_SD_COMPLIES_WITH_PROFILE = "http://hl7.org/fhir/StructureDefinition/structuredefinition-compliesWithProfile";
public static final String EXT_XML_NO_ORDER = "http://hl7.org/fhir/StructureDefinition/structuredefinition-xml-no-order";
public static final String EXT_DEF_TYPE = "http://hl7.org/fhir/StructureDefinition/elementdefinition-defaulttype";
public static final String EXT_TYPE_SPEC = "http://hl7.org/fhir/tools/StructureDefinition/type-specifier";
public static final String EXT_TYPE_CHARACTERISTICS = "http://hl7.org/fhir/StructureDefinition/structuredefinition-type-characteristics";
@ -413,6 +411,14 @@ public class ToolingExtensions {
return readStringExtension(def, EXT_DISPLAY_HINT);
}
public static String readStringExtension(Element c, String... uris) {
for (String uri : uris) {
if (hasExtension(c, uri)) {
return readStringExtension(c, uri);
}
}
return null;
}
public static String readStringExtension(Element c, String uri) {
Extension ex = ExtensionHelper.getExtension(c, uri);
if (ex == null)
@ -438,6 +444,14 @@ public class ToolingExtensions {
return ((StringType) ex.getValue()).getValue();
}
public static String readStringExtension(DomainResource c, String... uris) {
for (String uri : uris) {
if (hasExtension(c, uri)) {
return readStringExtension(c, uri);
}
}
return null;
}
public static String readStringExtension(DomainResource c, String uri) {
Extension ex = getExtension(c, uri);
if (ex == null)
@ -1099,7 +1113,7 @@ public class ToolingExtensions {
return cachedConsts;
}
public static boolean hasExtensions(ElementDefinition d, String... urls) {
public static boolean hasAnyOfExtensions(Element d, String... urls) {
for (String url : urls) {
if (d.hasExtension(url)) {
return true;
@ -1108,6 +1122,15 @@ public class ToolingExtensions {
return false;
}
public static boolean hasAnyOfExtensions(DomainResource dr, String... urls) {
for (String url : urls) {
if (dr.hasExtension(url)) {
return true;
}
}
return false;
}
public static int countExtensions(ElementDefinition d, String... urls) {
int res = 0;
for (String url : urls) {

39
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/client/FHIRToolingClient.java
View File

@ -38,6 +38,7 @@ import org.hl7.fhir.r5.model.Parameters.ParametersParameterComponent;
import org.hl7.fhir.r5.utils.client.network.ByteUtils;
import org.hl7.fhir.r5.utils.client.network.Client;
import org.hl7.fhir.r5.utils.client.network.ResourceRequest;
import org.hl7.fhir.utilities.FHIRBaseToolingClient;
import org.hl7.fhir.utilities.ToolingClientLogger;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
@ -76,7 +77,7 @@ import java.util.stream.Stream;
*
* @author Claude Nanjo
*/
public class FHIRToolingClient {
public class FHIRToolingClient extends FHIRBaseToolingClient {
private static final Logger logger = LoggerFactory.getLogger(FHIRToolingClient.class);
@ -86,12 +87,6 @@ public class FHIRToolingClient {
public static final String hostKey = "http.proxyHost";
public static final String portKey = "http.proxyPort";
private static final int TIMEOUT_NORMAL = 1500;
private static final int TIMEOUT_OPERATION = 30000;
private static final int TIMEOUT_ENTRY = 500;
private static final int TIMEOUT_OPERATION_LONG = 60000;
private static final int TIMEOUT_OPERATION_EXPAND = 120000;
private String base;
private ResourceAddress resourceAddress;
private ResourceFormat preferredResourceFormat;
@ -160,7 +155,7 @@ public class FHIRToolingClient {
preferredResourceFormat.getHeader(),
generateHeaders(),
message,
TIMEOUT_NORMAL).getReference();
timeoutNormal).getReference();
if (attemptedResourceFormat != preferredResourceFormat) {
setPreferredResourceFormat(attemptedResourceFormat);
}
@ -212,7 +207,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Read " + resourceClass.getName() + "/" + id,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -229,7 +224,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"VRead " + resourceClass.getName() + "/" + id + "/?_history/" + version,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -246,7 +241,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Read " + resourceClass.getName() + "?url=" + canonicalURL,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -269,7 +264,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Update " + resource.fhirType() + "/" + resource.getId(),
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -296,7 +291,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Update " + resource.fhirType() + "/" + id,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -330,9 +325,9 @@ public class FHIRToolingClient {
if (complex) {
byte[] body = ByteUtils.resourceToByteArray(params, false, isJson(getPreferredResourceFormat()));
result = client.issuePostRequest(url, body, getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + "/$" + name, timeoutLong);
} else {
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(), "GET " + resourceClass.getName() + "/$" + name, TIMEOUT_OPERATION_LONG);
result = client.issueGetResourceRequest(url, getPreferredResourceFormat(), generateHeaders(), "GET " + resourceClass.getName() + "/$" + name, timeoutLong);
}
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
@ -355,7 +350,7 @@ public class FHIRToolingClient {
try {
transactionResult = client.postBatchRequest(resourceAddress.getBaseServiceUri(), ByteUtils.resourceToByteArray(batch, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(),
generateHeaders(),
"transaction", TIMEOUT_OPERATION + (TIMEOUT_ENTRY * batch.getEntry().size()));
"transaction", timeoutOperation + (timeoutEntry * batch.getEntry().size()));
} catch (Exception e) {
handleException("An error occurred trying to process this transaction request", e);
}
@ -369,7 +364,7 @@ public class FHIRToolingClient {
result = client.issuePostRequest(resourceAddress.resolveValidateUri(resourceClass, id),
ByteUtils.resourceToByteArray(resource, false, isJson(getPreferredResourceFormat())),
getPreferredResourceFormat(), generateHeaders(),
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", TIMEOUT_OPERATION_LONG);
"POST " + resourceClass.getName() + (id != null ? "/" + id : "") + "/$validate", timeoutLong);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -428,7 +423,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
} catch (IOException e) {
throw new FHIRException(e);
}
@ -446,7 +441,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"CodeSystem/$lookup",
TIMEOUT_NORMAL);
timeoutNormal);
} catch (IOException e) {
e.printStackTrace();
}
@ -475,7 +470,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
source == null ? "ValueSet/$expand" : "ValueSet/$expand?url=" + source.getUrl(),
TIMEOUT_OPERATION_EXPAND);
timeoutExpand);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -499,7 +494,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"Closure?name=" + name,
TIMEOUT_NORMAL);
timeoutNormal);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}
@ -520,7 +515,7 @@ public class FHIRToolingClient {
getPreferredResourceFormat(),
generateHeaders(),
"UpdateClosure?name=" + name,
TIMEOUT_OPERATION);
timeoutOperation);
if (result.isUnsuccessfulRequest()) {
throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome) result.getPayload());
}

68
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/FHIRBaseToolingClient.java Normal file
View File

@ -0,0 +1,68 @@
package org.hl7.fhir.utilities;
public class FHIRBaseToolingClient {
private static final int DEFAULT_TIMEOUT_NORMAL = 1500;
private static final int DEFAULT_TIMEOUT_OPERATION = 30000;
private static final int DEFAULT_TIMEOUT_ENTRY = 500;
private static final int DEFAULT_TIMEOUT_OPERATION_LONG = 60000;
private static final int DEFAULT_TIMEOUT_OPERATION_EXPAND = 120000;
protected int timeoutNormal = DEFAULT_TIMEOUT_NORMAL;
protected int timeoutOperation = DEFAULT_TIMEOUT_OPERATION;
protected int timeoutEntry = DEFAULT_TIMEOUT_ENTRY;
protected int timeoutLong = DEFAULT_TIMEOUT_OPERATION_LONG;
protected int timeoutExpand = DEFAULT_TIMEOUT_OPERATION_EXPAND;
public long getTimeoutNormal() {
return timeoutNormal;
}
public void setTimeoutNormal(int timeoutNormal) {
this.timeoutNormal = timeoutNormal;
}
public long getTimeoutOperation() {
return timeoutOperation;
}
public void setTimeoutOperation(int timeoutOperation) {
this.timeoutOperation = timeoutOperation;
}
public long getTimeoutEntry() {
return timeoutEntry;
}
public void setTimeoutEntry(int timeoutEntry) {
this.timeoutEntry = timeoutEntry;
}
public long getTimeoutLong() {
return timeoutLong;
}
public void setTimeoutLong(int timeoutLong) {
this.timeoutLong = timeoutLong;
}
public long getTimeoutExpand() {
return timeoutExpand;
}
public void setTimeoutExpand(int timeoutExpand) {
this.timeoutExpand = timeoutExpand;
}
public void setTimeoutFactor(int i) {
timeoutNormal = i * DEFAULT_TIMEOUT_NORMAL;
timeoutOperation = i * DEFAULT_TIMEOUT_OPERATION;
timeoutEntry = i * DEFAULT_TIMEOUT_ENTRY;
timeoutLong = i * DEFAULT_TIMEOUT_OPERATION_LONG;
timeoutExpand = i * DEFAULT_TIMEOUT_OPERATION_EXPAND;
}
}

6
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/HL7WorkGroups.java
View File

@ -52,7 +52,7 @@ public class HL7WorkGroups {
case "claims": return "http://www.hl7.org/Special/committees/claims";
case "cqi": return "http://www.hl7.org/Special/committees/cqi";
case "dev": return "http://www.hl7.org/Special/committees/healthcaredevices";
case "ehr": return "http://www.hl7.org/special/committees/ehr";
case "ehr": return "http://www.hl7.org/Special/committees/ehr";
case "ec": return "http://www.hl7.org/Special/committees/emergencycare";
case "fhir": return "http://www.hl7.org/Special/committees/fiwg";
case "fmg": return "http://www.hl7.org/Special/committees/fhirmg";
@ -62,8 +62,8 @@ public class HL7WorkGroups {
case "hta": return "http://www.hl7.org/Special/committees/termauth";
case "ictc": return "http://www.hl7.org/Special/committees/ictc";
case "ii": return "http://www.hl7.org/Special/committees/imagemgt";
case "inm": return "http://www.hl7.org/special/committees/inm";
case "its": return "http://www.hl7.org/special/committees/xml";
case "inm": return "http://www.hl7.org/Special/committees/inm";
case "its": return "http://www.hl7.org/Special/committees/xml";
case "lhs": return "http://www.hl7.org/Special/committees/lhs";
case "mnm": return "http://www.hl7.org/Special/committees/mnm";
case "mobile": return "http://www.hl7.org/Special/committees/mobile";

12
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/VersionUtil.java → org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/VersionUtil.java
View File

@ -1,4 +1,4 @@
package org.hl7.fhir.validation.cli.utils;
package org.hl7.fhir.utilities;
import static org.apache.commons.lang3.StringUtils.defaultIfBlank;
import static org.apache.commons.lang3.StringUtils.left;
@ -34,11 +34,11 @@ import static org.apache.commons.lang3.StringUtils.left;
import java.io.InputStream;
import java.text.SimpleDateFormat;
import java.time.Duration;
import java.util.Date;
import java.util.Properties;
import org.hl7.fhir.r5.model.InstantType;
import org.hl7.fhir.utilities.Utilities;
/**
@ -93,12 +93,12 @@ public class VersionUtil {
private static String getDurationSinceBuild() {
try {
InstantType dt = new InstantType(ourBuildTime);
return Utilities.describeDuration(Duration.ofMillis(new Date().getTime() - dt.getValue().getTime()))+" old";
// InstantType dt = new InstantType(ourBuildTime);
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
Date dt = sdf.parse(ourBuildTime.substring(0, 19));
return Utilities.describeDuration(Duration.ofMillis(new Date().getTime() - dt.getTime()))+" old";
} catch (Exception e) {
return "??";
}
}
}

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nBase.java
View File

@ -63,11 +63,13 @@ public abstract class I18nBase {
private boolean messageExistsForLocale(String message, boolean hasArgs) {
checkResourceBundleIsLoaded();
if (!messageKeyExistsForLocale(message)) {
if (!message.contains(" ")) {
if (warnAboutMissingMessages && (hasArgs || !message.contains(" "))) {
System.out.println("Attempting to localize message " + message + ", but no such equivalent message exists for" +
" the locale " + getLocale());
}
}
}
return messageKeyExistsForLocale(message);
}

3
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/i18n/I18nConstants.java
View File

@ -1027,6 +1027,9 @@ public class I18nConstants {
public static final String BUNDLE_ENTRY_URL_MATCHES_NO_ID = "BUNDLE_ENTRY_URL_MATCHES_NO_ID";
public static final String BUNDLE_ENTRY_URL_ABSOLUTE = "BUNDLE_ENTRY_URL_ABSOLUTE";
public static final String BUNDLE_BUNDLE_ENTRY_FOUND_MULTIPLE = "BUNDLE_BUNDLE_ENTRY_FOUND_MULTIPLE";
public static final String FHIRPATH_COLLECTION_STATUS_PARAMETER = "FHIRPATH_COLLECTION_STATUS_PARAMETER";
public static final String FHIRPATH_COLLECTION_STATUS_CONTEXT = "FHIRPATH_COLLECTION_STATUS_CONTEXT";
public static final String SEARCHPARAMETER_MISSING_COMPONENTS = "SEARCHPARAMETER_MISSING_COMPONENTS";
}

47
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlComposer.java
View File

@ -48,6 +48,7 @@ public class XhtmlComposer {
public static final String XHTML_NS = "http://www.w3.org/1999/xhtml";
private boolean pretty;
private boolean xml;
private boolean autoLinks;
public static final boolean XML = true;
public static final boolean HTML = false;
@ -99,11 +100,11 @@ public class XhtmlComposer {
private void composeDoc(XhtmlDocument doc) throws IOException {
// headers....
// dst.append("<html>" + (pretty ? "\r\n" : ""));
// dst.append("<html>" + (pretty ? "\r\n" : ""));
for (XhtmlNode c : doc.getChildNodes()) {
writeNode(" ", c, false);
}
// dst.append("</html>" + (pretty ? "\r\n" : ""));
// dst.append("</html>" + (pretty ? "\r\n" : ""));
}
private void writeNode(String indent, XhtmlNode node, boolean noPrettyOverride) throws IOException {
@ -126,9 +127,31 @@ public class XhtmlComposer {
}
}
private boolean isValidUrlChar(char c) {
return Character.isAlphabetic(c) || Character.isDigit(c) || Utilities.existsInList(c, ';', ',', '/', '?', ':', '@', '&', '=', '+', '$', '-', '_', '.', '!', '~', '*', '\'', '(', ')');
}
private void writeText(XhtmlNode node) throws IOException {
for (char c : node.getContent().toCharArray())
{
String src = node.getContent();
int i = 0;
while (i < src.length()) {
char c = src.charAt(i);
if (autoLinks && c == 'h' && Utilities.startsWithInList(src.substring(i), "http://", "https://")) {
int j = i;
while (i < src.length() && isValidUrlChar(src.charAt(i))) {
i++;
}
String url = src.substring(j, i);
if (url.endsWith(".") || url.endsWith(",")) {
i--;
url = url.substring(0, url.length()-1);
}
url = Utilities.escapeXml(url);
dst.append("<a href=\""+url+"\">"+ url +"</a>");
} else {
i++;
if (c == '&') {
dst.append("&amp;");
} else if (c == '<') {
@ -158,18 +181,19 @@ public class XhtmlComposer {
}
}
}
}
private void writeComment(String indent, XhtmlNode node, boolean noPrettyOverride) throws IOException {
dst.append(indent + "<!-- " + node.getContent().trim() + " -->" + (pretty && !noPrettyOverride ? "\r\n" : ""));
}
}
private void writeDocType(XhtmlNode node) throws IOException {
dst.append("<!" + node.getContent() + ">\r\n");
}
}
private void writeInstruction(XhtmlNode node) throws IOException {
dst.append("<?" + node.getContent() + "?>\r\n");
}
}
private String escapeHtml(String s) {
if (s == null || s.equals(""))
@ -380,4 +404,13 @@ public class XhtmlComposer {
return sdst.toString();
}
public boolean isAutoLinks() {
return autoLinks;
}
public XhtmlComposer setAutoLinks(boolean autoLinks) {
this.autoLinks = autoLinks;
return this;
}
}

9
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/xhtml/XhtmlParser.java
View File

@ -1290,6 +1290,15 @@ public class XhtmlParser {
return div.getChildNodes();
}
public List<XhtmlNode> parseMDFragmentStripParas(String source) throws IOException, FHIRException {
XhtmlNode div = parseFragment( "<div>"+source+"</div>");
List<XhtmlNode> res = new ArrayList<>();
for (XhtmlNode x : div.getChildNodes()) {
res.addAll(x.getChildNodes());
}
return res;
}
public XhtmlNode parseFragment(String source) throws IOException, FHIRException {
rdr = new StringReader(source);
try {

51
org.hl7.fhir.utilities/src/main/resources/Messages.properties
View File

@ -53,7 +53,7 @@ Extension_EXT_SubExtension_Invalid = Sub-extension url ''{0}'' is not defined by
Extension_EXT_Type = The Extension ''{0}'' definition allows for the types {1} but found type {2}
Extension_EXT_URL_Absolute = Extension.url must be an absolute URL
Extension_EXT_Unknown = Unknown extension {0}
Extension_EXT_Unknown_NotHere = The extension {0} is unknown, and not allowed here
Extension_EXT_Unknown_NotHere = The extension {0} could not be found so is not allowed here
Extension_EXT_Url_NotFound = Extension.url is required
Extension_EXT_Version_Internal = Extension url ''{0}'' evaluation state invalid
Extension_EXT_Version_Invalid = Extension url ''{0}'' is not valid (invalid Version ''{1}'')
@ -78,7 +78,7 @@ Profile_VAL_NotAllowed = The element {0} is present in the instance but not allo
Measure_MR_M_None = No Measure is identified, so no validation can be performed against the Measure
Measure_MR_M_NotFound = The Measure ''{0}'' could not be resolved, so no validation can be performed against the Measure
Questionnaire_QR_Item_BadOption = The code provided {1} in the system {0}) is not in the options value set ({2}) in the questionnaire: {3}
QUESTIONNAIRE_QR_ITEM_BADOPTION_CS = The code provided {1} cannot be validated in the options value set ({2}) in the questionnaire because the system {0} is unknown
QUESTIONNAIRE_QR_ITEM_BADOPTION_CS = The code provided {1} cannot be validated in the options value set ({2}) in the questionnaire because the system {0} could not be found
Questionnaire_QR_Item_Coding = Error {0} validating Coding against Questionnaire Options
Questionnaire_QR_Item_CodingNoOptions = Cannot validate Coding option because no option list is provided
Questionnaire_QR_Item_DateNoOptions = Cannot validate date answer option because no option list is provided
@ -157,7 +157,7 @@ Terminology_TX_Coding_Count = Expected {0} but found {1} coding elements
Terminology_TX_Confirm_1_CC = Could not confirm that the codings provided are in the value set {0} and a coding from this value set is required (class = {1})
Terminology_TX_Confirm_2_CC = Could not confirm that the codings provided are in the value set {0} and a coding should come from this value set unless it has no suitable code (the validator cannot judge what is suitable) (class = {1})
Terminology_TX_Confirm_3_CC = Could not confirm that the codings provided are in the value set {0} and a coding is recommended to come from this value set (class = {1})
Terminology_TX_Confirm_4a = The code provided ({2}) is not in the value set {0}, and a code from this value set is required: {1}
Terminology_TX_Confirm_4a = The code provided ({2}) was not found in the value set {0}, and a code from this value set is required: {1}
Terminology_TX_Confirm_4b = The codes provided ({2}) are not in the value set {0}, and a code from this value set is required: {1}
Terminology_TX_Confirm_5 = Could not confirm that the codes provided are in the value set {0}, and a code should come from this value set unless it has no suitable code (the validator cannot judge what is suitable)
Terminology_TX_Confirm_6 = Could not confirm that the codes provided are in the value set {0}, and a code is recommended to come from this value set
@ -169,24 +169,24 @@ Terminology_TX_Error_Coding2 = Error {0} validating Coding: {1}
Terminology_TX_NoValid_1_CC = None of the codings provided are in the value set {0}, and a coding from this value set is required) (codes = {1})
Terminology_TX_NoValid_10 = The code provided is not in the maximum value set {0}, and a code from this value set is required) (code = {1}#{2})
Terminology_TX_NoValid_11 = The code provided is not in the maximum value set {0}, and a code from this value set is required) (code = {1}#{2}), error = {3})
Terminology_TX_NoValid_12 = The Coding provided ({2}) is not in the value set {0}, and a code is required from this value set. {1}
Terminology_TX_NoValid_13 = The Coding provided ({2}) is not in the value set {0}, and a code should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable). {1}
Terminology_TX_NoValid_14 = The Coding provided ({2}) is not in the value set {0}, and a code is recommended to come from this value set. {1}
Terminology_TX_NoValid_12 = The Coding provided ({2}) was not found in the value set {0}, and a code is required from this value set. {1}
Terminology_TX_NoValid_13 = The Coding provided ({2}) was not found in the value set {0}, and a code should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable). {1}
Terminology_TX_NoValid_14 = The Coding provided ({2}) was not found in the value set {0}, and a code is recommended to come from this value set. {1}
Terminology_TX_NoValid_15 = The value provided (''{0}'') could not be validated in the absence of a terminology server
Terminology_TX_NoValid_15A = The value provided (''{0}'') could not be validated because the code system {1} is not known
Terminology_TX_NoValid_16 = The value provided (''{0}'') is not in the value set {1}, and a code is required from this value set {2}
Terminology_TX_NoValid_17 = The value provided (''{0}'') is not in the value set {1}, and a code should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) {2}
Terminology_TX_NoValid_18 = The value provided (''{0}'') is not in the value set {1}, and a code is recommended to come from this value set){2}
Terminology_TX_NoValid_16 = The value provided (''{0}'') was not found in the value set {1}, and a code is required from this value set {2}
Terminology_TX_NoValid_17 = The value provided (''{0}'') was not found in the value set {1}, and a code should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) {2}
Terminology_TX_NoValid_18 = The value provided (''{0}'') was not found in the value set {1}, and a code is recommended to come from this value set){2}
Terminology_TX_NoValid_2_CC = None of the codings provided are in the value set {0}, and a coding should come from this value set unless it has no suitable code (note that the validator cannot judge what is suitable) (codes = {1})
Terminology_TX_NoValid_3_CC = None of the codings provided are in the value set {0}, and a coding is recommended to come from this value set) (codes = {1})
Terminology_TX_NoValid_4 = The Coding provided ({2}) is not in the value set {0}, and a code is required from this value set {1}
Terminology_TX_NoValid_5 = The Coding provided ({2}) is not in the value set {0}, and a code should come from this value set unless it has no suitable code (the validator cannot judge what is suitable) {1}
Terminology_TX_NoValid_6 = The Coding provided ({2}) is not in the value set {0}, and a code is recommended to come from this value set {1}
Terminology_TX_NoValid_4 = The Coding provided ({2}) was not found in the value set {0}, and a code is required from this value set {1}
Terminology_TX_NoValid_5 = The Coding provided ({2}) was not found in the value set {0}, and a code should come from this value set unless it has no suitable code (the validator cannot judge what is suitable) {1}
Terminology_TX_NoValid_6 = The Coding provided ({2}) was not found in the value set {0}, and a code is recommended to come from this value set {1}
Terminology_TX_NoValid_7 = None of the codes provided could be validated against the maximum value set {0}, (error = {2})
Terminology_TX_NoValid_8 = None of the codes provided are in the maximum value set {0}, and a code from this value set is required) (codes = {1})
Terminology_TX_NoValid_9 = The code provided ({2}) could not be validated against the maximum value set {0}, (error = {1})
Terminology_TX_System_Invalid = Invalid System URI: {0}
Terminology_TX_System_NotKnown = Code System URI ''{0}'' is unknown so the code cannot be validated
Terminology_TX_System_NotKnown = Code System URI ''{0}'' could not be found so the code cannot be validated
TERMINOLOGY_TX_SYSTEM_NOT_USABLE = The definition for the Code System with URI ''{0}'' doesn't provide any codes so the code cannot be validated
Terminology_TX_System_Relative = Coding.system must be an absolute reference, not a local reference
Terminology_TX_System_Unknown = Unknown Code System ''{0}''
@ -257,10 +257,10 @@ Validation_VAL_Profile_NotAllowed = This element is not allowed by the profile {
Validation_VAL_Profile_NotSlice = This element does not match any known slice {0} and slicing is CLOSED: {1}
Validation_VAL_Profile_OutOfOrder = As specified by profile {0}, Element ''{1}'' is out of order (found after {2})
Validation_VAL_Profile_SliceOrder = As specified by profile {0}, Element ''{1}'' is out of order in ordered slice
Validation_VAL_Profile_Unknown = Profile reference ''{0}'' has not been checked because it is unknown
VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY = Profile reference ''{0}'' has not been checked because it is unknown, and the validator is set to not fetch unknown profiles
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR = Profile reference ''{0}'' has not been checked because it is unknown, and fetching it resulted in the error {1}
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR_NETWORK = Profile reference ''{0}'' has not been checked because it is unknown, and the host {1} cannot be found
Validation_VAL_Profile_Unknown = Profile reference ''{0}'' has not been checked because it could not be found
VALIDATION_VAL_PROFILE_UNKNOWN_NOT_POLICY = Profile reference ''{0}'' has not been checked because it could not be found, and the validator is set to not fetch unknown profiles
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR = Profile reference ''{0}'' has not been checked because it could not be found, and fetching it resulted in the error {1}
VALIDATION_VAL_PROFILE_UNKNOWN_ERROR_NETWORK = Profile reference ''{0}'' has not been checked because it could not be found, and the host {1} cannot be found
Validation_VAL_Unknown_Profile = Unknown profile {0}
VALIDATION_VAL_PROFILE_DEPENDS_NOT_RESOLVED = Profile {1} identifies {2} as a dependency (using the extension http://hl7.org/fhir/StructureDefinition/structuredefinition-dependencies), but this profile could not be found
XHTML_XHTML_Attribute_Illegal = Invalid attribute name in the XHTML (''{0}'' on ''{1}'')
@ -476,7 +476,7 @@ Display_Name_WS_for__should_be_one_of__instead_of_other = Wrong whitespace in Di
Unknown_Code__in_ = Unknown Code ''{0}'' in the system ''{1}''
UNKNOWN_CODE__IN_FRAGMENT = Unknown Code ''{0}'' in the system ''{1}'' - note that the code system is labeled as a fragment, so the code may be valid in some other fragment
Code_found_in_expansion_however_ = Code found in expansion, however: {0}
None_of_the_provided_codes_are_in_the_value_set_one = The provided code {2} is not in the value set ''{1}''
None_of_the_provided_codes_are_in_the_value_set_one = The provided code {2} was not found in the value set ''{1}''
None_of_the_provided_codes_are_in_the_value_set_other = None of the provided codes [{2}] are in the value set ''{1}''
Coding_has_no_system__cannot_validate = Coding has no system - cannot validate
Unable_to_handle_system__concept_filter_with_op__ = Unable to handle system {0} concept filter with op = {1}
@ -484,7 +484,7 @@ UNABLE_TO_HANDLE_SYSTEM__PROPERTY_FILTER_WITH_OP__ = Unable to handle system {0}
Unable_to_handle_system__filter_with_property__ = Unable to handle system {0} filter with property = {1}, op = {2}
Unable_to_resolve_system__value_set_has_include_with_no_system = Unable to resolve system - value set {0} include #{1} has no system
UNABLE_TO_RESOLVE_SYSTEM_SYSTEM_IS_INDETERMINATE = The code system {1} referred to from value set {0} has a grammar, and the code might be valid in it
Unable_to_resolve_system__value_set_has_include_with_unknown_system = Unable to resolve system - value set {0} include #{1} has system {2} which is unknown, and the server return error {3}
Unable_to_resolve_system__value_set_has_include_with_unknown_system = Unable to resolve system - value set {0} include #{1} has system {2} which icould not be found, and the server returned error {3}
Unable_to_resolve_system__value_set_has_include_with_filter = Unable to resolve system - value set {0} include #{1} has a filter on system {2}
Unable_to_resolve_system__value_set_has_imports = Unable to resolve system - value set has imports
Unable_to_resolve_system__value_set_has_multiple_matches = Unable to resolve system - value set expansion has multiple matches: {0}
@ -568,6 +568,7 @@ SEARCHPARAMETER_NOTFOUND = Unable to find the base Search Parameter {0} so can''
SEARCHPARAMETER_BASE_WRONG = The resource type {1} is not listed as a base in the SearchParameter this is derived from ({0})
SEARCHPARAMETER_TYPE_WRONG = The type {1} is different to the type {0} in the derivedFrom SearchParameter
SEARCHPARAMETER_EXP_WRONG = The expression ''{2}'' is not compatible with the expression ''{1}'' in the derivedFrom SearchParameter {0}, and this likely indicates that the derivation relationship is not valid
SEARCHPARAMETER_MISSING_COMPONENTS = When the SearchParameter has a type of 'composite', then the SearchParameter must define two or more components
VALUESET_NO_SYSTEM_WARNING = No System specified, so Concepts and Filters can't be checked
VALUESET_INCLUDE_INVALID_CONCEPT_CODE = The code ''{1}'' is not valid in the system {0}
VALUESET_INCLUDE_INVALID_CONCEPT_CODE_VER = The code ''{2}'' is not valid in the system {0} version {1}
@ -728,7 +729,7 @@ SD_VALUE_TYPE_IILEGAL = The element {0} has a {1} of type {2}, which is not in t
SD_VALUE_TYPE_REPEAT_HINT = The repeating element has a {1}. The {1} will apply to all the repeats (this has not been clear to all users)
SD_VALUE_TYPE_REPEAT_WARNING_DOTNET = The repeating element has a {1} value for a primitive type. The DotNet validator will not apply this to all the repeats - this is an error
SD_NO_TYPES_OR_CONTENTREF = The element {0} has no assigned types, and no content reference
CODESYSTEM_CS_UNK_EXPANSION = The code provided ({2}) is not in the expansion in the value set {0}, and a code is required from this value set. The system {1} is unknown.
CODESYSTEM_CS_UNK_EXPANSION = The code provided ({2}) is not in the expansion in the value set {0}, and a code is required from this value set. The system {1} could not be found.
BUNDLE_SEARCH_NOSELF = SearchSet Bundles should have a self link that specifies what the search was
BUNDLE_SEARCH_SELF_NOT_UNDERSTOOD = No types could be determined from the search string, so the types can''t be checked
BUNDLE_SEARCH_ENTRY_NO_RESOURCE = SearchSet Bundle Entries must have resources
@ -917,13 +918,13 @@ CONCEPTMAP_GROUP_TARGET_PROPERTY_INVALID = The property code ''{0}'' is not know
CONCEPTMAP_GROUP_TARGET_PROPERTY_TYPE_MISMATCH = The type of this property should be {1} not {0}
CONCEPTMAP_GROUP_TARGET_PROPERTY_TYPE_NO_SYSTEM = Since no system has been provided, a plain code cannot be used
CONCEPTMAP_GROUP_TARGET_PROPERTY_CODE_INVALID = The code {0} is invalid in the system {1}
CONCEPTMAP_GROUP_TARGET_PROPERTY_TYPE_UNKNOWN_SYSTEM = The system {0} is unknown, so code values can''t be checked
CONCEPTMAP_GROUP_TARGET_PROPERTY_TYPE_UNKNOWN_SYSTEM = The code system {0} could not be found, so code values can''t be checked
SM_DEPENDENT_PARAM_TYPE_MISMATCH_DUPLICATE = The group {0} has already been used with different parameters, so the type checking may be incorrect (other = [{1}]; this = [{2}])
CONCEPTMAP_GROUP_SOURCE_INCOMPLETE = Source Code System {0} doesn''t have all content (content = {1}), so the source codes cannot be checked
CONCEPTMAP_GROUP_TARGET_INCOMPLETE = Target Code System {0} doesn''t have all content (content = {1}), so the target codes cannot be checked
SD_NO_TYPE_CODE_ON_CODE = Snapshot for {1} element {0} has type.code without a value
UNKNOWN_CODESYSTEM = The CodeSystem {0} is unknown
UNKNOWN_CODESYSTEM_VERSION = The CodeSystem {0} version {1} is unknown. Valid versions: {2}
UNKNOWN_CODESYSTEM = The code system {0} could not be found
UNKNOWN_CODESYSTEM_VERSION = The code system {0} version {1} could not be found. Valid versions: {2}
UNABLE_TO_INFER_CODESYSTEM = The System URI could not be determined for the code {0} in the ValueSet {1}
VALUESET_TOO_COSTLY = The value set {0} has too many codes to display ({1})
VALUESET_TOO_COSTLY_TIME = The value set {0} took too long to process (>{1}sec)
@ -1046,7 +1047,7 @@ VALUESET_CIRCULAR_REFERENCE = Found a circularity pointing to {0} processing Val
VALUESET_SUPPLEMENT_MISSING_one = Required supplement not found: {1}
VALUESET_SUPPLEMENT_MISSING_other = Required supplements not found: {1}
CONCEPTMAP_VS_TOO_MANY_CODES = The concept map has too many codes to validate ({0})
CONCEPTMAP_VS_CONCEPT_CODE_UNKNOWN_SYSTEM = The code ''{1}'' comes from the system {0} which is unknown, so it''s not known whether it''s valid in the value set ''{2}''
CONCEPTMAP_VS_CONCEPT_CODE_UNKNOWN_SYSTEM = The code ''{1}'' comes from the system {0} which could not be found, so it''s not known whether it''s valid in the value set ''{2}''
CONCEPTMAP_VS_INVALID_CONCEPT_CODE = The code ''{1}'' in the system {0} is not valid in the value set ''{2}''
CONCEPTMAP_VS_INVALID_CONCEPT_CODE_VER = The code ''{2}'' in the system {0} version {1} is not valid in the value set ''{3}''
VALUESET_INC_TOO_MANY_CODES = The value set include has too many codes to validate ({0})
@ -1085,3 +1086,5 @@ FHIRPATH_ARITHMETIC_MINUS = Error in date arithmetic: Unable to subtract type {0
BUNDLE_ENTRY_URL_MATCHES_NO_ID = The fullUrl ''{0}'' looks like a RESTful server URL, but the resource has no id
BUNDLE_ENTRY_URL_MATCHES_TYPE_ID = The fullUrl ''{0}'' looks like a RESTful server URL, so it must end with the correct type and id (/{1}/{2})
BUNDLE_ENTRY_URL_ABSOLUTE = The fullUrl must be an absolute URL (not ''{0}'')
FHIRPATH_COLLECTION_STATUS_PARAMETER = Parameter {1} is inherently a collection, and so the expression ''{0}'' may fail, create an error, or return false if there is more than one item in the parameter value ({2})
FHIRPATH_COLLECTION_STATUS_CONTEXT = The context is inherently a collection, and so the expression ''{0}'' may fail, create an error, or return false if there is more than one item in the context ({2})

7
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/ValidationEngine.java
View File

@ -28,6 +28,7 @@ import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.profile.ProfileUtilities;
import org.hl7.fhir.r5.context.ContextUtilities;
import org.hl7.fhir.r5.context.ILoggingService;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.context.IWorkerContextManager;
import org.hl7.fhir.r5.context.SimpleWorkerContext;
@ -324,7 +325,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
private final boolean canRunWithoutTerminologyServer;
@With
private final IWorkerContext.ILoggingService loggingService;
private final ILoggingService loggingService;
@With
private boolean THO = true;
@ -342,7 +343,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
loggingService = new SystemOutLoggingService();
}
public ValidationEngineBuilder(String terminologyCachePath, String userAgent, String version, String txServer, String txLog, FhirPublication txVersion, TimeTracker timeTracker, boolean canRunWithoutTerminologyServer, IWorkerContext.ILoggingService loggingService, boolean THO) {
public ValidationEngineBuilder(String terminologyCachePath, String userAgent, String version, String txServer, String txLog, FhirPublication txVersion, TimeTracker timeTracker, boolean canRunWithoutTerminologyServer, ILoggingService loggingService, boolean THO) {
this.terminologyCachePath = terminologyCachePath;
this.userAgent = userAgent;
this.version = version;
@ -431,7 +432,7 @@ public class ValidationEngine implements IValidatorResourceFetcher, IValidationP
*
* @see IgLoader#loadIgSource(String, boolean, boolean) loadIgSource for detailed description of the src parameter
*/
private void loadCoreDefinitions(String src, boolean recursive, String terminologyCachePath, String userAgent, TimeTracker tt, IWorkerContext.ILoggingService loggingService) throws FHIRException, IOException {
private void loadCoreDefinitions(String src, boolean recursive, String terminologyCachePath, String userAgent, TimeTracker tt, ILoggingService loggingService) throws FHIRException, IOException {
NpmPackage npm = getPcm().loadPackage(src, null);
if (npm != null) {
version = npm.fhirVersion();

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

@ -5,10 +5,10 @@ import java.util.Date;
import java.util.List;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.hl7.fhir.validation.ValidationRecord;
import org.hl7.fhir.validation.cli.utils.VersionUtil;
public class HTMLOutputGenerator {

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Common.java
View File

@ -2,6 +2,7 @@ package org.hl7.fhir.validation.cli.utils;
import org.hl7.fhir.utilities.FhirPublication;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.validation.ValidationEngine;

1
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/cli/utils/Display.java
View File

@ -5,6 +5,7 @@ import java.io.InputStream;
import java.io.PrintStream;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
/**

13
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/InstanceValidator.java
View File

@ -2219,7 +2219,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
ok = true;
} else if (en.equals("Resource") && container.isResource()) {
ok = true;
} else if (en.equals("CanonicalResource") && VersionUtilities.getExtendedCanonicalResourceNames(context.getVersion()).contains(stack.getLiteralPath())) {
} else if (en.equals("CanonicalResource") && containsAny(VersionUtilities.getExtendedCanonicalResourceNames(context.getVersion()), plist)) {
ok = true;
} else if (hasElementName(plist, en) && pu == null) {
ok = true;
@ -2310,6 +2310,15 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
private boolean containsAny(Set<String> set, List<String> list) {
for (String p : list) {
if (set.contains(p)) {
return true;
}
}
return false;
}
private boolean hasElementName(List<String> plist, String en) {
String[] ep = en.split("\\.");
for (String s : plist) {
@ -2726,7 +2735,7 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
if (dok) {
try {
DateTimeType dt = new DateTimeType(e.primitiveValue());
if (isCoreDefinition(profile) || (context.hasExtension(ToolingExtensions.EXT_DATE_RULES) && ToolingExtensions.readStringExtension(context, ToolingExtensions.EXT_DATE_RULES).contains("year-valid"))) {
if (isCoreDefinition(profile) || !context.hasExtension(ToolingExtensions.EXT_DATE_RULES) || ToolingExtensions.readStringExtension(context, ToolingExtensions.EXT_DATE_RULES).contains("year-valid")) {
warning(errors, NO_RULE_DATE, IssueType.INVALID, e.line(), e.col(), path, yearIsValid(e.primitiveValue()), I18nConstants.TYPE_SPECIFIC_CHECKS_DT_DATETIME_REASONABLE, e.primitiveValue());
}
} catch (Exception ex) {

10
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/SpecialExtensions.java
View File

File diff suppressed because one or more lines are too long

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

@ -633,7 +633,7 @@ public class BundleValidator extends BaseValidator {
for (EntrySummary e : entryList) {
List<StringWithSource> references = findReferences(e.getEntry());
for (StringWithSource ref : references) {
Element tgt = resolveInBundle(bundle, entries, ref.getReference(), e.getEntry().getChildValue(FULL_URL), e.getResource().fhirType(), e.getResource().getIdBase(), stack, errors, ref.getSource().getPath(), ref.getSource(), ref.isWarning());
Element tgt = resolveInBundle(bundle, entries, ref.getReference(), e.getEntry().getChildValue(FULL_URL), e.getResource().fhirType(), e.getResource().getIdBase(), stack, errors, ref.getSource().getPath(), ref.getSource(), ref.isWarning() || true);
if (tgt != null) {
EntrySummary t = entryForTarget(entryList, tgt);
if (t != null ) {

11
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/validation/instance/type/SearchParameterValidator.java
View File

@ -68,10 +68,17 @@ public class SearchParameterValidator extends BaseValidator {
String expOther = canonicalise(sp.getExpression(), bases);
warning(errors, NO_RULE_DATE, IssueType.BUSINESSRULE,stack.getLiteralPath(), expThis.equals(expOther), I18nConstants.SEARCHPARAMETER_EXP_WRONG, master, sp.getExpression(), cs.getNamedChildValue("expression", false));
}
// todo: check compositions
}
}
if ("composite".equals(cs.getNamedChildValue("type", false))) {
List<Element> components = cs.getChildren("component");
if (rule(errors, NO_RULE_DATE, IssueType.BUSINESSRULE, stack.getLiteralPath(), components.size() > 1, I18nConstants.SEARCHPARAMETER_MISSING_COMPONENTS)) {
// todo: check compositions
} else {
ok = false;
}
}
return ok;
}

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/terminology/tests/LocalTerminologyServiceTests.java
View File

@ -50,7 +50,7 @@ public class LocalTerminologyServiceTests implements ITxTesterLoader {
private static boolean localTxRunning() {
return new File("/Users/grahamegrieve/work/server/serverx").exists();
return new File("/Users/grahamegrieve/work/server/server").exists();
}

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/services/StandAloneValidatorFetcherTests.java
View File

@ -2,8 +2,8 @@ package org.hl7.fhir.validation.cli.services;
import org.hl7.fhir.r5.context.IWorkerContext;
import org.hl7.fhir.r5.terminologies.client.ITerminologyClient;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.validation.cli.utils.VersionUtil;
import org.junit.Test;
import java.net.URISyntaxException;

2
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/cli/services/ValidationServiceTest.java
View File

@ -30,12 +30,12 @@ import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.utilities.TimeTracker;
import org.hl7.fhir.utilities.VersionUtil;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.cli.model.CliContext;
import org.hl7.fhir.validation.cli.model.FileInfo;
import org.hl7.fhir.validation.cli.model.ValidationRequest;
import org.hl7.fhir.validation.cli.utils.VersionUtil;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Test;

33
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTests.java
View File

@ -22,6 +22,7 @@ import org.hl7.fhir.convertors.factory.VersionConvertorFactory_10_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_14_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_30_50;
import org.hl7.fhir.convertors.factory.VersionConvertorFactory_40_50;
import org.hl7.fhir.convertors.loaders.loaderR5.R4ToR5Loader;
import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
@ -73,6 +74,7 @@ import org.hl7.fhir.utilities.VersionUtilities;
import org.hl7.fhir.utilities.json.JsonException;
import org.hl7.fhir.utilities.json.JsonTrackingParser;
import org.hl7.fhir.utilities.json.JsonUtilities;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.npm.NpmPackage;
import org.hl7.fhir.utilities.settings.FhirSettings;
import org.hl7.fhir.utilities.tests.CacheVerificationLogger;
@ -80,6 +82,7 @@ import org.hl7.fhir.utilities.validation.IDigitalSignatureServices;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.validation.IgLoader;
import org.hl7.fhir.validation.ValidationEngine;
import org.hl7.fhir.validation.ValidatorUtils;
import org.hl7.fhir.validation.cli.model.HtmlInMarkdownCheck;
import org.hl7.fhir.validation.cli.services.StandAloneValidatorFetcher;
import org.hl7.fhir.validation.instance.InstanceValidator;
@ -304,6 +307,28 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
} else {
val.setDebug(false);
}
StructureDefinition sd = null;
if (content.has("ips")) {
val.setCheckIPSCodes(true);
val.getContext().loadFromPackage(loadPackage("hl7.fhir.uv.ips#1.1.0"), ValidatorUtils.loaderForVersion("4.0.1"));
if (content.get("ips").getAsString().equals("uv")) {
sd = val.getContext().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/uv/ips/StructureDefinition/Bundle-uv-ips");
val.getBundleValidationRules().add(new BundleValidationRule().setRule("Composition:0").setProfile("http://hl7.org/fhir/uv/ips/StructureDefinition/Composition-uv-ips"));
} else if (content.get("ips").getAsString().equals("au")) {
val.getContext().loadFromPackage(loadPackage("hl7.fhir.au.base#current"), ValidatorUtils.loaderForVersion("4.0.1"));
val.getContext().loadFromPackage(loadPackage("hl7.fhir.au.core#current"), ValidatorUtils.loaderForVersion("4.0.1"));
val.getContext().loadFromPackage(loadPackage("hl7.fhir.au.ips#current"), ValidatorUtils.loaderForVersion("4.0.1"));
sd = val.getContext().fetchResource(StructureDefinition.class, "http://hl7.org.au/fhir/ips/StructureDefinition/Bundle-au-ips");
val.getBundleValidationRules().add(new BundleValidationRule().setRule("Composition:0").setProfile("http://hl7.org/fhir/uv/ips/StructureDefinition/Composition-uv-ips"));
} else if (content.get("ips").getAsString().equals("nz")) {
val.getContext().loadFromPackage(loadPackage("tewhatuora.fhir.nzps#current"), ValidatorUtils.loaderForVersion("4.0.1"));
sd = val.getContext().fetchResource(StructureDefinition.class, "https://standards.digital.health.nz/fhir/StructureDefinition/nzps-bundle");
val.getBundleValidationRules().add(new BundleValidationRule().setRule("Composition:0").setProfile("http://hl7.org/fhir/uv/ips/StructureDefinition/Composition-uv-ips"));
} else {
throw new Error("Unknown IPS "+content.get("ips").getAsString());
}
}
if (content.has("best-practice")) {
val.setBestPracticeWarningLevel(BestPracticeWarningLevel.valueOf(content.get("best-practice").getAsString()));
}
@ -356,7 +381,6 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
}
}
}
StructureDefinition sd = null;
String filename = profile.get("source").getAsString();
if (Utilities.isAbsoluteUrl(filename)) {
sd = val.getContext().fetchResource(StructureDefinition.class, filename);
@ -398,7 +422,7 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
}
List<StructureDefinition> profiles = new ArrayList<>();
if (logical.has("format")) {
StructureDefinition sd = val.getContext().fetchResource(StructureDefinition.class, JsonUtilities.str(logical, "format"));
sd = val.getContext().fetchResource(StructureDefinition.class, JsonUtilities.str(logical, "format"));
if (sd != null) {
profiles.add(sd);
} else {
@ -420,6 +444,11 @@ public class ValidationTests implements IEvaluationContext, IValidatorResourceFe
}
private NpmPackage loadPackage(String idAndVer) throws IOException {
var pcm = new FilesystemPackageCacheManager(true);
return pcm.loadPackage(idAndVer);
}
private ValidationEngine buildVersionEngine(String ver, String txLog) throws Exception {
String server = FhirSettings.getTxFhirDevelopment();
switch (ver) {

661
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/all-systems.cache
View File

@ -1509,7 +1509,6 @@ v: {
"code" : "276885007",
"system" : "http://snomed.info/sct",
"version" : "http://snomed.info/sct/900000000000207008/version/20230731",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
@ -1530,6 +1529,666 @@ v: {
"code" : "Cel",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "en-NZ"
}, "url": "http://hl7.org/fhir/ValueSet/languages", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "en-NZ",
"system" : "urn:ietf:bcp:47",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "d"
}, "url": "http://hl7.org/fhir/ValueSet/units-of-time", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "d",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "Cel"
}, "url": "http://hl7.org/fhir/ValueSet/ucum-bodytemp", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "Cel",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "cm"
}, "url": "http://hl7.org/fhir/ValueSet/ucum-bodylength", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "cm",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "kg"
}, "url": "http://hl7.org/fhir/ValueSet/ucum-bodyweight", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "kg",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"code" : "NZ"
}, "url": "http://hl7.org/fhir/ValueSet/iso3166-1-2", "version": "4.0.1", "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"true", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "New Zealand",
"code" : "NZ",
"system" : "urn:iso:std:iso:3166",
"version" : "2018",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "26643006"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"severity" : "error",
"error" : "The provided code 'http://snomed.info/sct#26643006' is not in the value set 'http://terminology.hl7.org/ValueSet/snomed-intl-ips|20211027' (from Tx-Server)",
"class" : "UNKNOWN",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "767525000"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"severity" : "error",
"error" : "The provided code 'http://snomed.info/sct#767525000' is not in the value set 'http://terminology.hl7.org/ValueSet/snomed-intl-ips|20211027' (from Tx-Server)",
"class" : "UNKNOWN",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "237599002"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "237599002",
"system" : "http://snomed.info/sct",
"version" : "http://snomed.info/sct/900000000000207008/version/20230131",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "1201005"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "1201005",
"system" : "http://snomed.info/sct",
"version" : "http://snomed.info/sct/900000000000207008/version/20230131",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "109081006"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"severity" : "error",
"error" : "The provided code 'http://snomed.info/sct#109081006' is not in the value set 'http://terminology.hl7.org/ValueSet/snomed-intl-ips|20211027' (from Tx-Server)",
"class" : "UNKNOWN",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://snomed.info/sct",
"code" : "5913000"
}, "valueSet" :http://terminology.hl7.org/ValueSet/snomed-intl-ips, "langs":"en, en-US", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"true", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "5913000",
"system" : "http://snomed.info/sct",
"version" : "http://snomed.info/sct/900000000000207008/version/20230131",
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220
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/cvx.cache
View File

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}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://hl7.org/fhir/sid/cvx",
"code" : "208",
"display" : "SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 30 mcg/0.3mL dose"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "SARS-COV-2 (COVID-19) vaccine, mRNA, spike protein, LNP, preservative free, 30 mcg/0.3mL dose",
"code" : "208",
"system" : "http://hl7.org/fhir/sid/cvx",
"version" : "20210406",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://hl7.org/fhir/sid/cvx",
"code" : "141",
"display" : "Influenza, seasonal, injectable"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "Influenza, seasonal, injectable",
"code" : "141",
"system" : "http://hl7.org/fhir/sid/cvx",
"version" : "20210406",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://hl7.org/fhir/sid/cvx",
"code" : "20",
"display" : "diphtheria, tetanus toxoids and acellular pertussis vaccine"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "diphtheria, tetanus toxoids and acellular pertussis vaccine",
"code" : "20",
"system" : "http://hl7.org/fhir/sid/cvx",
"version" : "20210406",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://hl7.org/fhir/sid/cvx",
"code" : "138",
"display" : "tetanus and diphtheria toxoids, not adsorbed, for adult use"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "tetanus and diphtheria toxoids, not adsorbed, for adult use",
"code" : "138",
"system" : "http://hl7.org/fhir/sid/cvx",
"version" : "20210406",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://hl7.org/fhir/sid/cvx",
"code" : "133",
"display" : "pneumococcal conjugate vaccine, 13 valent"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "pneumococcal conjugate vaccine, 13 valent",
"code" : "133",
"system" : "http://hl7.org/fhir/sid/cvx",
"version" : "20210406",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"

1115
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/loinc.cache
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2454
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/snomed.cache
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181
org.hl7.fhir.validation/src/test/resources/txCache/org.hl7.fhir.validation/4.0.1/ucum.cache
View File

@ -618,6 +618,187 @@ v: {
"severity" : "error",
"error" : "The provided code 'http://unitsofmeasure.org#mm[Hg]{hg}' is not in the value set 'http://hl7.org/fhir/ValueSet/ucum-vitals-common--0|4.0.1' (from Tx-Server)",
"class" : "UNKNOWN",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "mmol/L"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "mmol/L",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "mmol/mol"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "mmol/mol",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "Cel"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "Cel",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "/min"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "/min",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "mm[Hg]"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "mm[Hg]",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "mm[Hg]"
}, "url": "http://hl7.org/fhir/ValueSet/ucum-vitals-common--0", "version": "4.0.1", "langs":"en-NZ", "useServer":"true", "useClient":"false", "guessSystem":"false", "valueSetMode":"CHECK_MEMERSHIP_ONLY", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "mm[Hg]",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "cm"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "cm",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "kg"
}, "valueSet" :null, "langs":"en-NZ", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"code" : "kg",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"issues" : {
"resourceType" : "OperationOutcome"
}
}
-------------------------------------------------------------------------------------
{"code" : {
"system" : "http://unitsofmeasure.org",
"code" : "mmol/mol"
}, "valueSet" :null, "langs":"", "useServer":"true", "useClient":"true", "guessSystem":"false", "valueSetMode":"ALL_CHECKS", "displayWarningMode":"false", "versionFlexible":"false", "profile": {
"resourceType" : "Parameters",
"parameter" : [{
"name" : "profile-url",
"valueString" : "http://hl7.org/fhir/ExpansionProfile/dc8fd4bc-091a-424a-8a3b-6198ef146891"
}]
}}####
v: {
"display" : "mmol/mol",
"code" : "mmol/mol",
"system" : "http://unitsofmeasure.org",
"version" : "2.0.1",
"unknown-systems" : "",
"issues" : {
"resourceType" : "OperationOutcome"

2
pom.xml
View File

@ -20,7 +20,7 @@
<properties>
<guava_version>32.0.1-jre</guava_version>
<hapi_fhir_version>6.4.1</hapi_fhir_version>
<validator_test_case_version>1.4.17</validator_test_case_version>
<validator_test_case_version>1.4.18-SNAPSHOT</validator_test_case_version>
<jackson_version>2.15.2</jackson_version>
<junit_jupiter_version>5.9.2</junit_jupiter_version>
<junit_platform_launcher_version>1.8.2</junit_platform_launcher_version>