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Send supplements to tx server

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This commit is contained in:
Grahame Grieve 2024-04-20 23:35:01 +10:00
parent dd3981c090
commit 213363fc1e
1 changed files with 66 additions and 50 deletions
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116
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/context/BaseWorkerContext.java
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@ -76,6 +76,7 @@ import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.ElementDefinition.ElementDefinitionBindingComponent;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.r5.model.Extension;
import org.hl7.fhir.r5.model.IdType;
import org.hl7.fhir.r5.model.Identifier;
import org.hl7.fhir.r5.model.IntegerType;
@ -157,9 +158,11 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
class OIDSource {
private String folder;
private Connection db;
protected OIDSource(String folder) {
private String pid;
protected OIDSource(String folder, String pid) {
super();
this.folder = folder;
this.pid = pid;
}
}
@ -261,7 +264,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
private UcumService ucumService;
protected Map<String, byte[]> binaries = new HashMap<String, byte[]>();
protected Map<String, Set<String>> oidCacheManual = new HashMap<>();
protected Map<String, Set<OIDDefinition>> oidCacheManual = new HashMap<>();
protected List<OIDSource> oidSources = new ArrayList<>();
protected Map<String, Map<String, ValidationResult>> validationCache = new HashMap<String, Map<String,ValidationResult>>();
@ -495,7 +498,7 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if (!oidCacheManual.containsKey(s)) {
oidCacheManual.put(s, new HashSet<>());
}
oidCacheManual.get(s).add(url);
oidCacheManual.get(s).add(new OIDDefinition(r.fhirType(), s, url, ((CanonicalResource) r).getVersion(), null));
}
}
}
@ -1778,15 +1781,24 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
if (vs != null && !hasCanonicalResource(pin, "tx-resource", vs.getVUrl())) {
cache = checkAddToParams(tc, pin, vs) || cache;
addDependentResources(tc, pin, vs);
for (Extension ext : vs.getExtensionsByUrl(ToolingExtensions.EXT_VS_CS_SUPPL_NEEDED)) {
if (ext.hasValueCanonicalType()) {
String url = ext.getValueCanonicalType().asStringValue();
CodeSystem supp = fetchResource(CodeSystem.class, url);
if (supp != null) {
cache = checkAddToParams(tc, pin, supp) || cache;
}
}
}
}
}
CodeSystem cs = fetchResource(CodeSystem.class, inc.getSystem(), src);
if (cs != null && !hasCanonicalResource(pin, "tx-resource", cs.getVUrl()) && (cs.getContent() == CodeSystemContentMode.COMPLETE || cs.getContent() == CodeSystemContentMode.FRAGMENT)) {
cache = checkAddToParams(tc, pin, cs) || cache;
for (CodeSystem supp : fetchResourcesByType(CodeSystem.class)) {
if (supp.getContent() == CodeSystemContentMode.SUPPLEMENT && supp.getSupplements().equals(cs.getUrl())) {
cache = checkAddToParams(tc, pin, supp) || cache;
}
}
for (CodeSystem supp : fetchResourcesByType(CodeSystem.class)) {
if (supp.getContent() == CodeSystemContentMode.SUPPLEMENT && supp.getSupplements().equals(inc.getSystem())) {
cache = checkAddToParams(tc, pin, supp) || cache;
}
}
return cache;
@ -3101,62 +3113,66 @@ public abstract class BaseWorkerContext extends I18nBase implements IWorkerConte
}
@Override
public Set<String> urlsForOid(boolean codeSystem, String oid) {
Set<String> set = urlsForOid(codeSystem, oid, true);
if (set.size() > 1) {
set = urlsForOid(codeSystem, oid, false);
public OIDSummary urlsForOid(String oid, String resourceType) {
OIDSummary set = urlsForOid(oid, resourceType, true);
if (set.getDefinitions().size() > 1) {
set = urlsForOid(oid, resourceType, false);
}
return set;
}
public Set<String> urlsForOid(boolean codeSystem, String oid, boolean retired) {
if (oid == null) {
return null;
}
Set<String> urls = new HashSet<>();
if (oidCacheManual.containsKey(oid)) {
urls.addAll(oidCacheManual.get(oid));
}
for (OIDSource os : oidSources) {
if (os.db == null) {
os.db = connectToOidSource(os.folder);
public OIDSummary urlsForOid(String oid, String resourceType, boolean retired) {
Set<OIDDefinition> urls = new HashSet<>();
if (oid != null) {
if (oidCacheManual.containsKey(oid)) {
urls.addAll(oidCacheManual.get(oid));
}
if (os.db != null) {
try {
PreparedStatement psql = os.db.prepareStatement("Select URL, Status from OIDMap where OID = ?");
psql.setString(1, oid);
ResultSet rs = psql.executeQuery();
while (rs.next()) {
if (retired || !"retired".equals(rs.getString(2))) {
urls.add(rs.getString(1));
}
}
} catch (Exception e) {
// nothing, there would alreagy have been an error
// e.printStackTrace();
for (OIDSource os : oidSources) {
if (os.db == null) {
os.db = connectToOidSource(os.folder);
}
if (os.db != null) {
try {
PreparedStatement psql = resourceType == null ?
os.db.prepareStatement("Select TYPE, URL, VERSION, Status from OIDMap where OID = ?") :
os.db.prepareStatement("Select TYPE, URL, VERSION, Status from OIDMap where TYPE = '"+resourceType+"' and OID = ?");
psql.setString(1, oid);
ResultSet rs = psql.executeQuery();
while (rs.next()) {
if (retired || !"retired".equals(rs.getString(4))) {
String rt = rs.getString(1);
String url = rs.getString(2);
String version = rs.getString(3);
urls.add(new OIDDefinition(rt, oid, url, version, os.pid));
}
}
} catch (Exception e) {
// nothing, there would alreagy have been an error
// e.printStackTrace();
}
}
}
switch (oid) {
case "2.16.840.1.113883.6.1" :
urls.add(new OIDDefinition("CodeSystem", "2.16.840.1.113883.6.1", "http://loinc.org", null, null));
break;
case "2.16.840.1.113883.6.8" :
urls.add(new OIDDefinition("CodeSystem", "2.16.840.1.113883.6.8", "http://unitsofmeasure.org", null, null));
break;
case "2.16.840.1.113883.6.96" :
urls.add(new OIDDefinition("CodeSystem", "2.16.840.1.113883.6.96", "http://snomed.info/sct", null, null));
break;
default:
}
}
switch (oid) {
case "2.16.840.1.113883.6.1" :
urls.add("http://loinc.org");
break;
case "2.16.840.1.113883.6.8" :
urls.add("http://unitsofmeasure.org");
break;
case "2.16.840.1.113883.6.96" :
urls.add("http://snomed.info/sct");
break;
default:
}
return urls;
return new OIDSummary(urls);
}
private Connection connectToOidSource(String folder) {
try {
File ff = ManagedFileAccess.file(folder);
File of = ManagedFileAccess.file(Utilities.path(ff.getAbsolutePath(), ".oid-map.db"));
File of = ManagedFileAccess.file(Utilities.path(ff.getAbsolutePath(), ".oid-map-2.db"));
if (!of.exists()) {
OidIndexBuilder oidBuilder = new OidIndexBuilder(ff, of);
oidBuilder.build();