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A few more fixes

This commit is contained in:
James Agnew 2019-10-28 17:00:23 -04:00
parent 2b8426114f
commit 493ec707ca
2 changed files with 226 additions and 176 deletions
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207
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamExtractorDstu3Test.java
View File

@ -1,21 +1,21 @@
package ca.uhn.fhir.jpa.searchparam.extractor;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeResourceDefinition;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.*;
import ca.uhn.fhir.jpa.model.util.StringNormalizer;
import ca.uhn.fhir.jpa.searchparam.JpaRuntimeSearchParam;
import ca.uhn.fhir.jpa.searchparam.SearchParamConstants;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Sets;
import org.hl7.fhir.dstu3.hapi.ctx.DefaultProfileValidationSupport;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Questionnaire;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
@ -37,63 +37,7 @@ public class SearchParamExtractorDstu3Test {
Observation obs = new Observation();
obs.addCategory().addCoding().setSystem("SYSTEM").setCode("CODE");
ISearchParamRegistry searchParamRegistry = new ISearchParamRegistry() {
@Override
public void forceRefresh() {
// nothing
}
@Override
public RuntimeSearchParam getActiveSearchParam(String theResourceName, String theParamName) {
throw new UnsupportedOperationException();
}
@Override
public boolean refreshCacheIfNecessary() {
// nothing
return false;
}
@Override
public Map<String, Map<String, RuntimeSearchParam>> getActiveSearchParams() {
throw new UnsupportedOperationException();
}
@Override
public Map<String, RuntimeSearchParam> getActiveSearchParams(String theResourceName) {
RuntimeResourceDefinition nextResDef = ourCtx.getResourceDefinition(theResourceName);
Map<String, RuntimeSearchParam> sps = new HashMap<>();
for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
sps.put(nextSp.getName(), nextSp);
}
return sps;
}
@Override
public List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName, Set<String> theParamNames) {
throw new UnsupportedOperationException();
}
@Override
public List<JpaRuntimeSearchParam> getActiveUniqueSearchParams(String theResourceName) {
throw new UnsupportedOperationException();
}
@Override
public void requestRefresh() {
// nothing
}
@Override
public RuntimeSearchParam getSearchParamByName(RuntimeResourceDefinition theResourceDef, String theParamName) {
return null;
}
@Override
public Collection<RuntimeSearchParam> getSearchParamsByResourceType(RuntimeResourceDefinition theResourceDef) {
return null;
}
};
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
@ -116,7 +60,131 @@ public class SearchParamExtractorDstu3Test {
Questionnaire questionnaire = new Questionnaire();
questionnaire.setDescription(value);
ISearchParamRegistry searchParamRegistry = new ISearchParamRegistry() {
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
Set<ResourceIndexedSearchParamString> params = extractor.extractSearchParamStrings(questionnaire);
assertEquals(1, params.size());
}
@Test
public void testEncounterDuration_Normalized() {
Encounter enc = new Encounter();
Duration value = new Duration();
value.setSystem(SearchParamConstants.UCUM_NS);
value.setCode("min");
value.setValue(2 * 24 * 60);
enc.setLength(value);
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
Set<ResourceIndexedSearchParamNumber> params = extractor.extractSearchParamNumber(enc);
assertEquals(1, params.size());
// Normalized to days
assertEquals("2", params.iterator().next().getValue().toPlainString());
}
@Test
public void testEncounterDuration_NotNormalized() {
Encounter enc = new Encounter();
Duration value = new Duration();
value.setValue(15);
enc.setLength(value);
ISearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
Set<ResourceIndexedSearchParamNumber> params = extractor.extractSearchParamNumber(enc);
assertEquals(1, params.size());
// Normalized to days
assertEquals("15", params.iterator().next().getValue().toPlainString());
}
@Test
public void testInvalidType() {
MySearchParamRegistry searchParamRegistry = new MySearchParamRegistry();
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.STRING, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamStrings(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.TOKEN, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamTokens(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.QUANTITY, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamQuantity(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.DATE, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamDates(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.NUMBER, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamNumber(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
searchParamRegistry.addSearchParam(new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.URI, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE));
Patient resource = new Patient();
extractor.extractSearchParamUri(resource);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
try {
RuntimeSearchParam sp = new RuntimeSearchParam("foo", "foo", "Patient", RestSearchParameterTypeEnum.REFERENCE, Sets.newHashSet(), Sets.newHashSet(), RuntimeSearchParam.RuntimeSearchParamStatusEnum.ACTIVE);
searchParamRegistry.addSearchParam(sp);
Patient resource = new Patient();
extractor.extractResourceLinks(resource, sp);
} catch (ConfigurationException e) {
assertEquals("Search param foo is of unexpected datatype: class org.hl7.fhir.dstu3.model.Patient", e.getMessage());
}
}
private static class MySearchParamRegistry implements ISearchParamRegistry {
private List<RuntimeSearchParam> myAddedSearchParams = new ArrayList<>();
public void addSearchParam(RuntimeSearchParam... theSearchParam) {
myAddedSearchParams.clear();
for (RuntimeSearchParam next : theSearchParam) {
myAddedSearchParams.add(next);
}
}
@Override
public void forceRefresh() {
// nothing
@ -145,6 +213,9 @@ public class SearchParamExtractorDstu3Test {
for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
sps.put(nextSp.getName(), nextSp);
}
for (RuntimeSearchParam next : myAddedSearchParams) {
sps.put(next.getName(), next);
}
return sps;
}
@ -172,12 +243,6 @@ public class SearchParamExtractorDstu3Test {
public Collection<RuntimeSearchParam> getSearchParamsByResourceType(RuntimeResourceDefinition theResourceDef) {
return null;
}
};
SearchParamExtractorDstu3 extractor = new SearchParamExtractorDstu3(new ModelConfig(), ourCtx, ourValidationSupport, searchParamRegistry);
extractor.start();
Set<ResourceIndexedSearchParamString> params = extractor.extractSearchParamStrings(questionnaire);
assertEquals(1, params.size());
}
@AfterClass

79
hapi-fhir-jpaserver-searchparam/src/test/java/ca/uhn/fhir/jpa/searchparam/extractor/SearchParamFinder.java
View File

@ -14,80 +14,65 @@ public class SearchParamFinder {
public static void main(String[] args) {
FhirContext ctx = FhirContext.forR5();
RestSearchParameterTypeEnum wantType = RestSearchParameterTypeEnum.NUMBER;
RestSearchParameterTypeEnum type = RestSearchParameterTypeEnum.TOKEN;
process(FhirContext.forDstu2(), type);
process(FhirContext.forDstu3(), type);
process(FhirContext.forR4(), type);
process(FhirContext.forR5(), type);
for (String nextResourceName : ctx.getResourceNames()) {
RuntimeResourceDefinition nextResDef = ctx.getResourceDefinition(nextResourceName);
}
public static void process(FhirContext theCtx, RestSearchParameterTypeEnum theWantType) {
for (String nextResourceName : theCtx.getResourceNames()) {
RuntimeResourceDefinition nextResDef = theCtx.getResourceDefinition(nextResourceName);
for (RuntimeSearchParam nextSp : nextResDef.getSearchParams()) {
if (nextSp.getParamType() == wantType) {
boolean logged = false;
if (nextSp.getParamType() == theWantType) {
for (String nextPath : nextSp.getPathsSplit()) {
List<String> pathsPart = new ArrayList<>(Arrays.asList(nextPath.split("\\.")));
BaseRuntimeElementCompositeDefinition def = null;
traverse(ctx, pathsPart, def);
// for (int i = 0; i < pathsPart.length; i++) {
// String nextPart = pathsPart[i];
//
// if (i == 0) {
// def = ctx.getResourceDefinition(nextPart);
// } else {
// BaseRuntimeChildDefinition child = def.getChildByName(nextPart);
// if (child == null) {
// child = def.getChildByName(nextPart + "[x]");
// }
// BaseRuntimeElementDefinition<?> childDef = child.getChildByName(nextPart);
// if (childDef instanceof RuntimePrimitiveDatatypeDefinition) {
// ourLog.info("SearchParam {} : {} : {} has {}", nextResourceName, nextSp.getName(), nextSp.getPath(), childDef.getName());
// logged = true;
// break;
// }
// def = (BaseRuntimeElementCompositeDefinition) childDef;
// }
//
// }
traverse(theCtx, nextSp, pathsPart, theCtx, pathsPart, def);
}
if (!logged) {
ourLog.info("SearchParam {} : {} : {}", nextResourceName, nextSp.getName(), nextSp.getPath());
}
}
}
}
}
private static void traverse(FhirContext theContext, List<String> thePathsPart, BaseRuntimeElementCompositeDefinition theDef) {
private static void traverse(FhirContext theCtx, RuntimeSearchParam theSearchParam, List<String> theFullPath, FhirContext theContext, List<String> thePathsPart, BaseRuntimeElementCompositeDefinition theDef) {
if (thePathsPart.size() == 0) {
ourLog.info("{} - {}", thePathsPart, theDef.getName());
ourLog.info("Found {} - {} - {} - {}", theCtx.getVersion().getVersion(), theSearchParam.getName(), String.join(".", theFullPath), theDef.getName());
return;
}
String nextName = thePathsPart.get(0);
if (theDef == null) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(nextName);
traverse(theContext, thePathsPart.subList(1, thePathsPart.size()), def);
traverse(theCtx, theSearchParam, theFullPath, theContext, thePathsPart.subList(1, thePathsPart.size()), def);
} else {
BaseRuntimeChildDefinition child = theDef.getChildByName(nextName);
if (child != null) {
BaseRuntimeElementCompositeDefinition def = (BaseRuntimeElementCompositeDefinition) child.getChildByName(nextName);
traverse(theContext, thePathsPart.subList(1, thePathsPart.size()), def);
BaseRuntimeElementDefinition<?> subChild = child.getChildByName(nextName);
if (subChild instanceof RuntimePrimitiveDatatypeDefinition) {
assert thePathsPart.size() == 1;
ourLog.info("Found {} - {} - {} - {}", theCtx.getVersion().getVersion(), theSearchParam.getName(), String.join(".", theFullPath), subChild.getName());
return;
}
BaseRuntimeElementCompositeDefinition def = (BaseRuntimeElementCompositeDefinition) subChild;
traverse(theCtx, theSearchParam, theFullPath, theContext, thePathsPart.subList(1, thePathsPart.size()), def);
}
RuntimeChildChoiceDefinition choiceChild = (RuntimeChildChoiceDefinition) theDef.getChildByName(nextName + "[x]");
if (choiceChild != null){
for (String nextChildName : choiceChild.getValidChildNames()) {
if (nextChildName.startsWith(nextName)) {
BaseRuntimeElementCompositeDefinition def = (BaseRuntimeElementCompositeDefinition) choiceChild.getChildByName(nextChildName);
traverse(theContext, thePathsPart.subList(1, thePathsPart.size()), def);
BaseRuntimeElementDefinition<?> subChild = choiceChild.getChildByName(nextChildName);
if (subChild instanceof RuntimePrimitiveDatatypeDefinition) {
assert thePathsPart.size() == 1;
ourLog.info("Found {} - {} - {} - {}", theCtx.getVersion().getVersion(), theSearchParam.getName(), String.join(".", theFullPath), subChild.getName());
return;
}
BaseRuntimeElementCompositeDefinition def = (BaseRuntimeElementCompositeDefinition) subChild;
traverse(theCtx, theSearchParam, theFullPath, theContext, thePathsPart.subList(1, thePathsPart.size()), def);
}
}
}