honeymoose
/
org.hl7.fhir.core
mirror of https://github.com/hapifhir/org.hl7.fhir.core.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

handle value set with exclusion filters when expanding

This commit is contained in:
Grahame Grieve 2024-01-15 15:05:01 +11:00
parent 449821a4b4
commit e6df130e3a
1 changed files with 81 additions and 14 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

95
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/terminologies/expansion/ValueSetExpander.java
View File

@ -522,6 +522,32 @@ public class ValueSetExpander extends ValueSetProcessBase {
}
private void excludeCodeAndDescendents(WorkingContext wc, CodeSystem cs, String system, ConceptDefinitionComponent def, Parameters expParams, List<ValueSet> filters,
ConceptDefinitionComponent exclusion, ConceptFilter filterFunc, List<WorkingContext> otherFilters, ValueSetExpansionComponent exp) throws FHIRException, ETooCostly {
opContext.deadCheck();
def.checkNoModifiers("Code in Code System", "expanding");
if (exclusion != null) {
if (exclusion.getCode().equals(def.getCode()))
return; // excluded.
}
boolean abs = CodeSystemUtilities.isNotSelectable(cs, def);
if ((includeAbstract || !abs) && filterFunc.includeConcept(cs, def) && passesOtherFilters(otherFilters, cs, def.getCode())) {
for (String code : getCodesForConcept(def, expParams)) {
if (!(filters != null && !filters.isEmpty() && !filterContainsCode(filters, system, code, exp)))
excludeCode(wc, system, code);
}
}
for (ConceptDefinitionComponent c : def.getConcept()) {
excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp);
}
if (def.hasUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK)) {
List<ConceptDefinitionComponent> children = (List<ConceptDefinitionComponent>) def.getUserData(CodeSystemUtilities.USER_DATA_CROSS_LINK);
for (ConceptDefinitionComponent c : children)
excludeCodeAndDescendents(wc, cs, system, c, expParams, filters, exclusion, filterFunc, otherFilters, exp);
}
}
private List<String> getCodesForConcept(ConceptDefinitionComponent focus, Parameters expParams) {
List<String> codes = new ArrayList<>();
codes.add(focus.getCode());
@ -590,8 +616,20 @@ public class ValueSetExpander extends ValueSetProcessBase {
excludeCode(wc, exc.getSystem(), c.getCode());
}
if (exc.getFilter().size() > 0)
throw fail("not done yet - multiple filters");
if (exc.getFilter().size() > 0) {
if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
addFragmentWarning(exp, cs);
}
List<WorkingContext> filters = new ArrayList<>();
for (int i = 1; i < exc.getFilter().size(); i++) {
WorkingContext wc1 = new WorkingContext();
filters.add(wc1);
processFilter(exc, exp, expParams, null, cs, false, exc.getFilter().get(i), wc1, null, true);
}
ConceptSetFilterComponent fc = exc.getFilter().get(0);
WorkingContext wc1 = dwc;
processFilter(exc, exp, expParams, null, cs, false, fc, wc1, filters, false);
}
}
private void excludeCodes(WorkingContext wc, ValueSetExpansionComponent expand) {
@ -1083,16 +1121,16 @@ public class ValueSetExpander extends ValueSetProcessBase {
for (int i = 1; i < inc.getFilter().size(); i++) {
WorkingContext wc = new WorkingContext();
filters.add(wc);
processFilter(inc, exp, expParams, imports, cs, noInactive, inc.getFilter().get(i), wc, null);
processFilter(inc, exp, expParams, imports, cs, noInactive, inc.getFilter().get(i), wc, null, false);
}
ConceptSetFilterComponent fc = inc.getFilter().get(0);
WorkingContext wc = dwc;
processFilter(inc, exp, expParams, imports, cs, noInactive, fc, wc, filters);
processFilter(inc, exp, expParams, imports, cs, noInactive, fc, wc, filters, false);
}
}
private void processFilter(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams,
List<ValueSet> imports, CodeSystem cs, boolean noInactive, ConceptSetFilterComponent fc, WorkingContext wc, List<WorkingContext> filters)
private void processFilter(ConceptSetComponent inc, ValueSetExpansionComponent exp, Parameters expParams, List<ValueSet> imports, CodeSystem cs, boolean noInactive,
ConceptSetFilterComponent fc, WorkingContext wc, List<WorkingContext> filters, boolean exclude)
throws ETooCostly {
opContext.deadCheck();
if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.ISA) {
@ -1100,14 +1138,22 @@ public class ValueSetExpander extends ValueSetProcessBase {
ConceptDefinitionComponent def = getConceptForCode(cs.getConcept(), fc.getValue());
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
} 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(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, defEx, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, defEx, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
}
} else if ("concept".equals(fc.getProperty()) && fc.getOp() == FilterOperator.DESCENDENTOF) {
// special: all codes in the target code system under the value
@ -1115,11 +1161,20 @@ public class ValueSetExpander extends ValueSetProcessBase {
if (def == null)
throw failTSE("Code '" + fc.getValue() + "' not found in system '" + inc.getSystem() + "'");
for (ConceptDefinitionComponent c : def.getConcept())
addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
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(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
for (ConceptDefinitionComponent c : children) {
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), c, null, imports, null, new AllConceptsFilter(allErrors), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), c, null, expParams, imports, null, new AllConceptsFilter(allErrors), noInactive, exp.getProperty(), filters, exp);
}
}
}
} else if ("display".equals(fc.getProperty()) && fc.getOp() == FilterOperator.EQUAL) {
@ -1131,19 +1186,31 @@ public class ValueSetExpander extends ValueSetProcessBase {
if (def.getDisplay().contains(fc.getValue()) && passesOtherFilters(filters, cs, def.getCode())) {
for (String code : getCodesForConcept(def, expParams)) {
opContext.deadCheck();
ValueSetExpansionContainsComponent t = addCode(wc, inc.getSystem(), code, def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
if (exclude) {
excludeCode(wc, inc.getSystem(), code);
} else {
addCode(wc, inc.getSystem(), code, def.getDisplay(), cs.getLanguage(), null, def.getDesignation(), expParams, CodeSystemUtilities.isNotSelectable(cs, def), CodeSystemUtilities.isInactive(cs, def),
imports, noInactive, false, exp.getProperty(), makeCSProps(def.getDefinition(), def.getProperty()), cs, null, def.getExtension(), null, exp);
}
}
}
}
}
} else if (isDefinedProperty(cs, fc.getProperty())) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(allErrors, fc, getPropertyDefinition(cs, fc.getProperty())), noInactive, exp.getProperty(), filters, exp);
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new PropertyFilter(allErrors, fc, getPropertyDefinition(cs, fc.getProperty())), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new PropertyFilter(allErrors, fc, getPropertyDefinition(cs, fc.getProperty())), noInactive, exp.getProperty(), filters, exp);
}
}
} else if ("code".equals(fc.getProperty()) && fc.getOp() == FilterOperator.REGEX) {
for (ConceptDefinitionComponent def : cs.getConcept()) {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters, exp);
if (exclude) {
excludeCodeAndDescendents(wc, cs, inc.getSystem(), def, null, imports, null, new RegexFilter(allErrors, fc.getValue()), filters, exp);
} else {
addCodeAndDescendents(wc, cs, inc.getSystem(), def, null, expParams, imports, null, new RegexFilter(allErrors, fc.getValue()), noInactive, exp.getProperty(), filters, exp);
}
}
} else {
throw fail("Filter by property[" + fc.getProperty() + "] and op[" + fc.getOp() + "] is not supported yet");