use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.
the class BaseWorkerContext method supportsSystem.
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
synchronized (lock) {
if (codeSystems.has(system) && codeSystems.get(system).getContent() != CodeSystemContentMode.NOTPRESENT) {
return true;
} else if (supportedCodeSystems.contains(system)) {
return true;
} else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com") || system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:")) {
return false;
} else {
if (noTerminologyServer) {
return false;
}
if (txcaps == null) {
try {
log("Terminology server: Check for supported code systems for " + system);
setTxCaps(txClient.getTerminologyCapabilities());
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
log("==============!! Running without terminology server !! ==============");
if (txClient != null) {
log("txServer = " + txClient.getAddress());
log("Error = " + e.getMessage() + "");
}
log("=====================================================================");
return false;
} else {
e.printStackTrace();
throw new TerminologyServiceException(e);
}
}
if (supportedCodeSystems.contains(system)) {
return true;
}
}
}
return false;
}
}
use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.
the class BaseWorkerContext method supportsSystem.
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
synchronized (lock) {
if (codeSystems.has(system) && codeSystems.get(system).getContent() != CodeSystemContentMode.NOTPRESENT) {
return true;
} else if (supportedCodeSystems.contains(system)) {
return true;
} else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com") || system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:")) {
return false;
} else {
if (noTerminologyServer) {
return false;
}
if (txcaps == null) {
try {
logger.logMessage("Terminology server: Check for supported code systems for " + system);
final TerminologyCapabilities capabilityStatement = txCache.hasTerminologyCapabilities() ? txCache.getTerminologyCapabilities() : txClient.getTerminologyCapabilities();
txCache.cacheTerminologyCapabilities(capabilityStatement);
setTxCaps(capabilityStatement);
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
logger.logMessage("==============!! Running without terminology server !! ==============");
if (txClient != null) {
logger.logMessage("txServer = " + txClient.getAddress());
logger.logMessage("Error = " + e.getMessage() + "");
}
logger.logMessage("=====================================================================");
return false;
} else {
e.printStackTrace();
throw new TerminologyServiceException(e);
}
}
if (supportedCodeSystems.contains(system)) {
return true;
}
}
}
return false;
}
}
use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.
the class ValueSetExpanderSimple method doInternalIncludeCodes.
public void doInternalIncludeCodes(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive) throws NoTerminologyServiceException, TerminologyServiceException, FHIRException {
if (cs == null) {
if (context.isNoTerminologyServer())
throw failTSE("Unable to find code system " + inc.getSystem().toString());
else
throw failTSE("Unable to find code system " + inc.getSystem().toString());
}
cs.checkNoModifiers("Code System", "expanding");
if (cs.getContent() != CodeSystemContentMode.COMPLETE && cs.getContent() != CodeSystemContentMode.FRAGMENT)
throw failTSE("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion())
if (!existsInParams(exp.getParameter(), "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
exp.getParameter().add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
}
}
if (!inc.getConcept().isEmpty()) {
canBeHeirarchy = false;
for (ConceptReferenceComponent c : inc.getConcept()) {
c.checkNoModifiers("Code in Code System", "expanding");
ConceptDefinitionComponent def = CodeSystemUtilities.findCode(cs.getConcept(), c.getCode());
// default is true if we're a fragment and
Boolean inactive = false;
if (def == null) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
} else if (cs.getContent() == CodeSystemContentMode.EXAMPLE) {
addExampleWarning(exp, cs);
} else {
if (checkCodesWhenExpanding) {
throw failTSE("Unable to find code '" + c.getCode() + "' in code system " + cs.getUrl());
}
}
} else {
inactive = CodeSystemUtilities.isInactive(cs, def);
}
addCode(inc.getSystem(), c.getCode(), !Utilities.noString(c.getDisplay()) ? c.getDisplay() : def == null ? null : def.getDisplay(), null, convertDesignations(c.getDesignation()), expParams, false, inactive, imports, noInactive);
}
}
if (inc.getFilter().size() > 1) {
// which will bt the case if we get around to supporting this
canBeHeirarchy = false;
// need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
throw failTSE("Multiple filters not handled yet");
}
if (inc.getFilter().size() == 1) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
ConceptSetFilterComponent fc = inc.getFilter().get(0);
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISNOTA) {
// special: all codes in the target code system that are not under the value
ConceptDefinitionComponent defEx = getConceptForCode(cs.getConcept(), fc.getValue());
if (defEx == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(), noInactive);
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children) addCodeAndDescendents(cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(), noInactive);
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
// gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
canBeHeirarchy = false;
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports, noInactive);
}
}
}
} else if (isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(fc, getPropertyDefinition(cs, fc.getProperty())), noInactive);
}
} else {
throw fail("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
}
use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.
the class ValueSetExpanderSimple method includeCodes.
private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, ExpansionProfile profile) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
List<ValueSet> imports = new ArrayList<ValueSet>();
for (UriType imp : inc.getValueSet()) imports.add(importValueSet(imp.getValue(), params, profile));
if (!inc.hasSystem()) {
if (// though this is not supposed to be the case
imports.isEmpty())
return;
ValueSet base = imports.get(0);
imports.remove(0);
copyImportContains(base.getExpansion().getContains(), null, profile, imports);
} else {
CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE) && context.supportsSystem(inc.getSystem())) {
addCodes(context.expandVS(inc, canBeHeirarchy), params, profile, imports);
return;
}
if (cs == null) {
if (context.isNoTerminologyServer())
throw new NoTerminologyServiceException("unable to find code system " + inc.getSystem().toString());
else
throw new TerminologyServiceException("unable to find code system " + inc.getSystem().toString());
}
if (cs.getContent() != CodeSystemContentMode.COMPLETE)
throw new TerminologyServiceException("Code system " + inc.getSystem().toString() + " is incomplete");
if (cs.hasVersion())
if (!existsInParams(params, "version", new UriType(cs.getUrl() + "|" + cs.getVersion())))
params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(cs.getUrl() + "|" + cs.getVersion())));
if (inc.getConcept().size() == 0 && inc.getFilter().size() == 0) {
// special case - add all the code system
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
}
}
if (!inc.getConcept().isEmpty()) {
canBeHeirarchy = false;
for (ConceptReferenceComponent c : inc.getConcept()) {
addCode(inc.getSystem(), c.getCode(), Utilities.noString(c.getDisplay()) ? getCodeDisplay(cs, c.getCode()) : c.getDisplay(), null, convertDesignations(c.getDesignation()), profile, false, CodeSystemUtilities.isInactive(cs, c.getCode()), imports);
}
}
if (inc.getFilter().size() > 1) {
// which will bt the case if we get around to supporting this
canBeHeirarchy = false;
// need to and them, and this isn't done yet. But this shouldn't arise in non loinc and snomed value sets
throw new TerminologyServiceException("Multiple filters not handled yet");
}
if (inc.getFilter().size() == 1) {
ConceptSetFilterComponent fc = inc.getFilter().get(0);
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(cs, inc.getSystem(), def, null, profile, imports);
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw new TerminologyServiceException("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept()) addCodeAndDescendents(cs, inc.getSystem(), c, null, profile, imports);
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
// gg; note: wtf is this: if the filter is display=v, look up the code 'v', and see if it's diplsay is 'v'?
canBeHeirarchy = false;
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def != null) {
if (isNotBlank(def.getDisplay()) && isNotBlank(fc.getValue())) {
if (def.getDisplay().contains(fc.getValue())) {
addCode(inc.getSystem(), def.getCode(), def.getDisplay(), null, def.getDesignation(), profile, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def), imports);
}
}
}
} else
throw new NotImplementedException("Search by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");
}
}
}
use of org.hl7.fhir.exceptions.TerminologyServiceException in project org.hl7.fhir.core by hapifhir.
the class BaseWorkerContext method supportsSystem.
@Override
public boolean supportsSystem(String system) throws TerminologyServiceException {
synchronized (lock) {
if (codeSystems.containsKey(system) && codeSystems.get(system).getContent() != CodeSystemContentMode.NOTPRESENT)
return true;
else if (supportedCodeSystems.contains(system))
return true;
else if (system.startsWith("http://example.org") || system.startsWith("http://acme.com") || system.startsWith("http://hl7.org/fhir/valueset-") || system.startsWith("urn:oid:"))
return false;
else {
if (noTerminologyServer)
return false;
if (txcaps == null) {
try {
log("Terminology server: Check for supported code systems for " + system);
txcaps = txClient.getTerminologyCapabilities();
} catch (Exception e) {
if (canRunWithoutTerminology) {
noTerminologyServer = true;
log("==============!! Running without terminology server !! ==============");
if (txClient != null) {
log("txServer = " + txClient.getAddress());
log("Error = " + e.getMessage() + "");
}
log("=====================================================================");
return false;
} else
throw new TerminologyServiceException(e);
}
if (txcaps != null) {
for (TerminologyCapabilitiesCodeSystemComponent tccs : txcaps.getCodeSystem()) {
supportedCodeSystems.add(tccs.getUri());
}
}
if (supportedCodeSystems.contains(system))
return true;
}
}
return false;
}
}
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