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Merge pull request #1862 from hapifhir/2024-12-gg-r2-bye-bye
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2024 12 gg r2 bye bye
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@grahamegrieve
grahamegrieve authored Dec 17, 2024
2 parents 9cce17d + eb4981c commit eff515e
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Showing 11 changed files with 534 additions and 74 deletions.
48 changes: 48 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -905,6 +905,54 @@ public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean h
return expandVS(vs, cacheOk, heirarchical, false, p);
}

@Override
public ValueSetExpansionOutcome expandVS(String url, boolean cacheOk, boolean hierarchical, int count) {
if (expParameters == null)
throw new Error(formatMessage(I18nConstants.NO_EXPANSION_PARAMETERS_PROVIDED));
if (noTerminologyServer) {
return new ValueSetExpansionOutcome(formatMessage(I18nConstants.ERROR_EXPANDING_VALUESET_RUNNING_WITHOUT_TERMINOLOGY_SERVICES), TerminologyServiceErrorClass.NOSERVICE, null, false);
}

Parameters p = expParameters.copy();
p.addParameter("count", count);
p.addParameter("url", new UriType(url));
p.setParameter("_limit",new IntegerType("10000"));
p.setParameter("_incomplete", new BooleanType("true"));

CacheToken cacheToken = txCache.generateExpandToken(url, hierarchical);
ValueSetExpansionOutcome res;
if (cacheOk) {
res = txCache.getExpansion(cacheToken);
if (res != null) {
return res;
}
}
p.setParameter("excludeNested", !hierarchical);
List<String> allErrors = new ArrayList<>();

p.addParameter().setName("cache-id").setValue(new IdType(terminologyClientManager.getCacheId()));
TerminologyClientContext tc = terminologyClientManager.chooseServer(url, true);

txLog("$expand "+url+" on "+tc.getAddress());

try {
ValueSet result = tc.getClient().expandValueset(null, p);
if (result != null) {
if (!result.hasUrl()) {
result.setUrl(url);
}
if (!result.hasUrl()) {
throw new Error(formatMessage(I18nConstants.NO_URL_IN_EXPAND_VALUE_SET_2));
}
}
res = new ValueSetExpansionOutcome(result).setTxLink(txLog.getLastId());
} catch (Exception e) {
res = new ValueSetExpansionOutcome((e.getMessage() == null ? e.getClass().getName() : e.getMessage()), TerminologyServiceErrorClass.UNKNOWN, allErrors, true).setTxLink(txLog == null ? null : txLog.getLastId());
}
txCache.cacheExpansion(cacheToken, res, TerminologyCache.PERMANENT);
return res;
}

@Override
public ValueSetExpansionOutcome expandVS(ValueSet vs, boolean cacheOk, boolean heirarchical, boolean incompleteOk) {
if (expParameters == null)
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2 changes: 2 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/IWorkerContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -493,6 +493,8 @@ public String getUrl() {
*/
public ValueSetExpansionOutcome expandVS(ValueSet source, boolean cacheOk, boolean heiarchical, boolean incompleteOk);

public ValueSetExpansionOutcome expandVS(String uri, boolean cacheOk, boolean heiarchical, int count); // set to 0 to just check existence

/**
* ValueSet Expansion - see $expand, but resolves the binding first
*
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3 changes: 3 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/SimpleWorkerContext.java
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Expand Up @@ -244,6 +244,9 @@ public SimpleWorkerContext build() throws IOException {
}

private SimpleWorkerContext build(SimpleWorkerContext context) throws IOException {
if (VersionUtilities.isR2Ver(context.getVersion()) || VersionUtilities.isR2Ver(context.getVersion())) {
System.out.println("As of end 2024, FHIR R2 (version "+context.getVersion()+") is no longer officially supported.");
}
context.initTxCache(terminologyCachePath);
context.setUserAgent(userAgent);
context.setLogger(loggingService);
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52 changes: 33 additions & 19 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/renderers/NamingSystemRenderer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.List;

import org.hl7.fhir.exceptions.DefinitionException;
import org.hl7.fhir.exceptions.FHIRException;
Expand Down Expand Up @@ -70,16 +72,25 @@ public void render(RenderingStatus status, XhtmlNode x, NamingSystem ns) throws
if (ns.hasCopyright()) {
addMarkdown(row(tbl, (context.formatPhrase(RenderingContext.GENERAL_COPYRIGHT))), ns.getCopyright());
}
List<NamingSystem> nsl = new ArrayList<>();
nsl.add(ns);
renderList(x, nsl);
}

public void renderList(XhtmlNode x, List<NamingSystem> nsl) {

boolean hasPreferred = false;
boolean hasPeriod = false;
boolean hasComment = false;
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
hasPreferred = hasPreferred || id.hasPreferred();
hasPeriod = hasPeriod || id.hasPeriod();
hasComment = hasComment || id.hasComment();
for (NamingSystem ns : nsl) {
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
hasPreferred = hasPreferred || id.hasPreferred();
hasPeriod = hasPeriod || id.hasPeriod();
hasComment = hasComment || id.hasComment();
}
}
x.h3().tx(context.formatPhrase(RenderingContext.NAME_SYS_IDEN));
tbl = x.table("grid");
XhtmlNode tbl = x.table("grid");
XhtmlNode tr = tbl.tr();
tr.td().b().tx((context.formatPhrase(RenderingContext.GENERAL_TYPE)));
tr.td().b().tx((context.formatPhrase(RenderingContext.GENERAL_VALUE)));
Expand All @@ -92,21 +103,24 @@ public void render(RenderingStatus status, XhtmlNode x, NamingSystem ns) throws
if (hasComment) {
tr.td().b().tx((context.formatPhrase(RenderingContext.GENERAL_COMMENT)));
}
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
tr = tbl.tr();
tr.td().tx(id.getType().getDisplay());
tr.td().tx(id.getValue());
if (hasPreferred) {
tr.td().tx(id.getPreferredElement().primitiveValue());
}
if (hasPeriod) {
tr.td().tx(displayDataType(id.getPeriod()));
}
if (hasComment) {
tr.td().tx(id.getComment());
}
}
for (NamingSystem ns : nsl) {
for (NamingSystemUniqueIdComponent id : ns.getUniqueId()) {
tr = tbl.tr();
tr.td().tx(id.getType().getDisplay());
tr.td().tx(id.getValue());
if (hasPreferred) {
tr.td().tx(id.getPreferredElement().primitiveValue());
}
if (hasPeriod) {
tr.td().tx(displayDataType(id.getPeriod()));
}
if (hasComment) {
tr.td().tx(id.getComment());
}
}
}
}


private XhtmlNode row(XhtmlNode tbl, String name) {
XhtmlNode tr = tbl.tr();
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6 changes: 4 additions & 2 deletions ....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientContext.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,10 @@ public ITerminologyClient getClient() {
}

public void seeUse(Set<String> systems, TerminologyClientContextUseType useType) {
for (String s : systems) {
seeUse(s, useType);
if (systems != null) {
for (String s : systems) {
seeUse(s, useType);
}
}
}

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33 changes: 32 additions & 1 deletion ....fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/client/TerminologyClientManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -291,6 +291,37 @@ public TerminologyClientContext chooseServer(ValueSet vs, Set<String> systems, b
}
}

public TerminologyClientContext chooseServer(String vs, boolean expand) throws TerminologyServiceException {
if (serverList.isEmpty()) {
return null;
}
if (IGNORE_TX_REGISTRY || !useEcosystem) {
return findClient(getMasterClient().getAddress(), null, expand);
}
String request = Utilities.pathURL(monitorServiceURL, "resolve?fhirVersion="+factory.getVersion()+"&valueSet="+Utilities.URLEncode(vs));
if (usage != null) {
request = request + "&usage="+usage;
}
try {
JsonObject json = JsonParser.parseObjectFromUrl(request);
for (JsonObject item : json.getJsonObjects("authoritative")) {
return findClient(item.asString("url"), null, expand);
}
for (JsonObject item : json.getJsonObjects("candidates")) {
return findClient(item.asString("url"), null, expand);
}
} catch (Exception e) {
String msg = "Error resolving valueSet "+vs+": "+e.getMessage();
if (!hasMessage(msg)) {
internalLog.add(new InternalLogEvent(msg, vs, request));
}
if (logger.isDebugLogging()) {
e.printStackTrace();
}
}
return null;
}

private void log(ValueSet vs, String server, Set<String> systems, List<ServerOptionList> choices, String message) {
String svs = (vs == null ? "null" : vs.getVersionedUrl());
String sys = systems.isEmpty() ? "--" : systems.size() == 1 ? systems.iterator().next() : systems.toString();
Expand Down Expand Up @@ -550,7 +581,7 @@ public SourcedValueSet findValueSetOnServer(String canonical) {
}
}
if (server == null) {
return null;
server = getMasterClient().getAddress();
}
if (server.contains("://tx.fhir.org")) {
try {
Expand Down
7 changes: 7 additions & 0 deletions org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/utilities/TerminologyCache.java
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Original file line number Diff line number Diff line change
Expand Up @@ -528,6 +528,13 @@ public CacheToken generateExpandToken(ValueSet vs, boolean hierarchical) {
ct.key = String.valueOf(hashJson(ct.request));
return ct;
}

public CacheToken generateExpandToken(String url, boolean hierarchical) {
CacheToken ct = new CacheToken();
ct.request = "{\"hierarchical\" : "+(hierarchical ? "true" : "false")+", \"url\": \""+Utilities.escapeJson(url)+"\"}\r\n";
ct.key = String.valueOf(hashJson(ct.request));
return ct;
}

public void nameCacheToken(ValueSet vs, CacheToken ct) {
if (vs != null) {
Expand Down
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