Java tutorial
package ca.uhn.fhir.jpa.dao; /* * #%L * HAPI FHIR JPA Server * %% * Copyright (C) 2014 - 2016 University Health Network * %% * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. * #L% */ import static org.apache.commons.lang3.StringUtils.isBlank; import static org.apache.commons.lang3.StringUtils.isNotBlank; import java.math.BigDecimal; import java.util.ArrayList; import java.util.Collections; import java.util.HashSet; import java.util.List; import java.util.Set; import javax.measure.quantity.Quantity; import javax.measure.unit.NonSI; import javax.measure.unit.Unit; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Pair; import org.hl7.fhir.instance.model.api.IBaseResource; 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.entity.BaseResourceIndexedSearchParam; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamCoords; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamDate; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamNumber; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamQuantity; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamToken; import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamUri; import ca.uhn.fhir.jpa.entity.ResourceTable; import ca.uhn.fhir.model.api.IDatatype; import ca.uhn.fhir.model.api.IPrimitiveDatatype; import ca.uhn.fhir.model.api.IValueSetEnumBinder; import ca.uhn.fhir.model.base.composite.BaseHumanNameDt; import ca.uhn.fhir.model.dstu2.composite.AddressDt; import ca.uhn.fhir.model.dstu2.composite.BoundCodeableConceptDt; import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt; import ca.uhn.fhir.model.dstu2.composite.CodingDt; import ca.uhn.fhir.model.dstu2.composite.ContactPointDt; import ca.uhn.fhir.model.dstu2.composite.DurationDt; import ca.uhn.fhir.model.dstu2.composite.HumanNameDt; import ca.uhn.fhir.model.dstu2.composite.IdentifierDt; import ca.uhn.fhir.model.dstu2.composite.PeriodDt; import ca.uhn.fhir.model.dstu2.composite.QuantityDt; import ca.uhn.fhir.model.dstu2.resource.Conformance.RestSecurity; import ca.uhn.fhir.model.dstu2.resource.Location; import ca.uhn.fhir.model.dstu2.resource.Patient; import ca.uhn.fhir.model.dstu2.resource.Patient.Communication; import ca.uhn.fhir.model.dstu2.resource.Questionnaire; import ca.uhn.fhir.model.dstu2.resource.ValueSet; import ca.uhn.fhir.model.dstu2.valueset.RestfulSecurityServiceEnum; import ca.uhn.fhir.model.primitive.BaseDateTimeDt; import ca.uhn.fhir.model.primitive.BoundCodeDt; import ca.uhn.fhir.model.primitive.IntegerDt; import ca.uhn.fhir.model.primitive.StringDt; import ca.uhn.fhir.model.primitive.UriDt; import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum; public class SearchParamExtractorDstu2 extends BaseSearchParamExtractor implements ISearchParamExtractor { private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory .getLogger(SearchParamExtractorDstu2.class); private void addSearchTerm(ResourceTable theEntity, Set<ResourceIndexedSearchParamString> retVal, String resourceName, String searchTerm) { if (isBlank(searchTerm)) { return; } if (searchTerm.length() > ResourceIndexedSearchParamString.MAX_LENGTH) { searchTerm = searchTerm.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH); } ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(resourceName, BaseHapiFhirDao.normalizeString(searchTerm), searchTerm); nextEntity.setResource(theEntity); retVal.add(nextEntity); } private void addStringParam(ResourceTable theEntity, Set<BaseResourceIndexedSearchParam> retVal, RuntimeSearchParam nextSpDef, String value) { if (value.length() > ResourceIndexedSearchParamString.MAX_LENGTH) { value = value.substring(0, ResourceIndexedSearchParamString.MAX_LENGTH); } ResourceIndexedSearchParamString nextEntity = new ResourceIndexedSearchParamString(nextSpDef.getName(), BaseHapiFhirDao.normalizeString(value), value); nextEntity.setResource(theEntity); retVal.add(nextEntity); } @Override public Set<ResourceIndexedSearchParamCoords> extractSearchParamCoords(ResourceTable theEntity, IBaseResource theResource) { // TODO: implement return Collections.emptySet(); } /* * (non-Javadoc) * * @see ca.uhn.fhir.jpa.dao.ISearchParamExtractor#extractSearchParamDates(ca.uhn.fhir.jpa.entity.ResourceTable, * ca.uhn.fhir.model.api.IResource) */ @Override public Set<ResourceIndexedSearchParamDate> extractSearchParamDates(ResourceTable theEntity, IBaseResource theResource) { HashSet<ResourceIndexedSearchParamDate> retVal = new HashSet<ResourceIndexedSearchParamDate>(); RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.DATE) { continue; } String nextPath = nextSpDef.getPath(); if (isBlank(nextPath)) { continue; } boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } for (Object nextObject : extractValues(nextPath, theResource)) { if (nextObject == null) { continue; } ResourceIndexedSearchParamDate nextEntity; if (nextObject instanceof BaseDateTimeDt) { BaseDateTimeDt nextValue = (BaseDateTimeDt) nextObject; if (nextValue.isEmpty()) { continue; } nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getValue(), nextValue.getValue()); } else if (nextObject instanceof PeriodDt) { PeriodDt nextValue = (PeriodDt) nextObject; if (nextValue.isEmpty()) { continue; } nextEntity = new ResourceIndexedSearchParamDate(nextSpDef.getName(), nextValue.getStart(), nextValue.getEnd()); } else { if (!multiType) { throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass()); } else { continue; } } if (nextEntity != null) { nextEntity.setResource(theEntity); retVal.add(nextEntity); } } } return retVal; } /* * (non-Javadoc) * * @see ca.uhn.fhir.jpa.dao.ISearchParamExtractor#extractSearchParamNumber(ca.uhn.fhir.jpa.entity.ResourceTable, * ca.uhn.fhir.model.api.IResource) */ @Override public HashSet<ResourceIndexedSearchParamNumber> extractSearchParamNumber(ResourceTable theEntity, IBaseResource theResource) { HashSet<ResourceIndexedSearchParamNumber> retVal = new HashSet<ResourceIndexedSearchParamNumber>(); RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.NUMBER) { continue; } String nextPath = nextSpDef.getPath(); if (isBlank(nextPath)) { continue; } for (Object nextObject : extractValues(nextPath, theResource)) { if (nextObject == null || ((IDatatype) nextObject).isEmpty()) { continue; } String resourceName = nextSpDef.getName(); boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } if (nextObject instanceof DurationDt) { DurationDt nextValue = (DurationDt) nextObject; if (nextValue.getValueElement().isEmpty()) { continue; } if (new UriDt(BaseHapiFhirDao.UCUM_NS).equals(nextValue.getSystemElement())) { if (isNotBlank(nextValue.getCode())) { Unit<? extends Quantity> unit = Unit.valueOf(nextValue.getCode()); javax.measure.converter.UnitConverter dayConverter = unit.getConverterTo(NonSI.DAY); double dayValue = dayConverter.convert(nextValue.getValue().doubleValue()); DurationDt newValue = new DurationDt(); newValue.setSystem(BaseHapiFhirDao.UCUM_NS); newValue.setCode(NonSI.DAY.toString()); newValue.setValue(dayValue); nextValue = newValue; /* * @SuppressWarnings("unchecked") PhysicsUnit<? extends * org.unitsofmeasurement.quantity.Quantity<?>> unit = (PhysicsUnit<? extends * org.unitsofmeasurement.quantity.Quantity<?>>) * UCUMFormat.getCaseInsensitiveInstance().parse(nextValue.getCode().getValue(), null); if * (unit.isCompatible(UCUM.DAY)) { * * @SuppressWarnings("unchecked") PhysicsUnit<org.unitsofmeasurement.quantity.Time> timeUnit = * (PhysicsUnit<Time>) unit; UnitConverter conv = timeUnit.getConverterTo(UCUM.DAY); double * dayValue = conv.convert(nextValue.getValue().getValue().doubleValue()); DurationDt newValue = * new DurationDt(); newValue.setSystem(UCUM_NS); newValue.setCode(UCUM.DAY.getSymbol()); * newValue.setValue(dayValue); nextValue=newValue; } */ } } ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue()); nextEntity.setResource(theEntity); retVal.add(nextEntity); } else if (nextObject instanceof QuantityDt) { QuantityDt nextValue = (QuantityDt) nextObject; if (nextValue.getValueElement().isEmpty()) { continue; } ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, nextValue.getValue()); nextEntity.setResource(theEntity); retVal.add(nextEntity); } else if (nextObject instanceof IntegerDt) { IntegerDt nextValue = (IntegerDt) nextObject; if (nextValue.getValue() == null) { continue; } ResourceIndexedSearchParamNumber nextEntity = new ResourceIndexedSearchParamNumber(resourceName, new BigDecimal(nextValue.getValue())); nextEntity.setResource(theEntity); retVal.add(nextEntity); } else { if (!multiType) { throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass()); } else { continue; } } } } return retVal; } /* * (non-Javadoc) * * @see ca.uhn.fhir.jpa.dao.ISearchParamExtractor#extractSearchParamQuantity(ca.uhn.fhir.jpa.entity.ResourceTable, * ca.uhn.fhir.model.api.IResource) */ @Override public Set<ResourceIndexedSearchParamQuantity> extractSearchParamQuantity(ResourceTable theEntity, IBaseResource theResource) { HashSet<ResourceIndexedSearchParamQuantity> retVal = new HashSet<ResourceIndexedSearchParamQuantity>(); RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.QUANTITY) { continue; } String nextPath = nextSpDef.getPath(); if (isBlank(nextPath)) { continue; } for (Object nextObject : extractValues(nextPath, theResource)) { if (nextObject == null || ((IDatatype) nextObject).isEmpty()) { continue; } String resourceName = nextSpDef.getName(); boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } if (nextObject instanceof QuantityDt) { QuantityDt nextValue = (QuantityDt) nextObject; if (nextValue.getValueElement().isEmpty()) { continue; } ResourceIndexedSearchParamQuantity nextEntity = new ResourceIndexedSearchParamQuantity( resourceName, nextValue.getValueElement().getValue(), nextValue.getSystemElement().getValueAsString(), nextValue.getCode()); nextEntity.setResource(theEntity); retVal.add(nextEntity); } else { if (!multiType) { throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass()); } else { continue; } } } } return retVal; } /* * (non-Javadoc) * * @see ca.uhn.fhir.jpa.dao.ISearchParamExtractor#extractSearchParamStrings(ca.uhn.fhir.jpa.entity.ResourceTable, * ca.uhn.fhir.model.api.IResource) */ @Override public Set<ResourceIndexedSearchParamString> extractSearchParamStrings(ResourceTable theEntity, IBaseResource theResource) { HashSet<ResourceIndexedSearchParamString> retVal = new HashSet<ResourceIndexedSearchParamString>(); RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.STRING) { continue; } String nextPath = nextSpDef.getPath(); String resourceName = nextSpDef.getName(); if (isBlank(nextPath)) { // TODO: implement phonetic, and any others that have no path if ("Questionnaire".equals(def.getName()) && nextSpDef.getName().equals("title")) { Questionnaire q = (Questionnaire) theResource; String title = q.getGroup().getTitle(); addSearchTerm(theEntity, retVal, resourceName, title); } continue; } for (Object nextObject : extractValues(nextPath, theResource)) { if (nextObject == null || ((IDatatype) nextObject).isEmpty()) { continue; } boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } if (nextObject instanceof IPrimitiveDatatype<?>) { IPrimitiveDatatype<?> nextValue = (IPrimitiveDatatype<?>) nextObject; String searchTerm = nextValue.getValueAsString(); addSearchTerm(theEntity, retVal, resourceName, searchTerm); } else { if (nextObject instanceof BaseHumanNameDt) { ArrayList<StringDt> allNames = new ArrayList<StringDt>(); HumanNameDt nextHumanName = (HumanNameDt) nextObject; allNames.addAll(nextHumanName.getFamily()); allNames.addAll(nextHumanName.getGiven()); for (StringDt nextName : allNames) { addSearchTerm(theEntity, retVal, resourceName, nextName.getValue()); } } else if (nextObject instanceof AddressDt) { ArrayList<StringDt> allNames = new ArrayList<StringDt>(); AddressDt nextAddress = (AddressDt) nextObject; allNames.addAll(nextAddress.getLine()); allNames.add(nextAddress.getCityElement()); allNames.add(nextAddress.getStateElement()); allNames.add(nextAddress.getCountryElement()); allNames.add(nextAddress.getPostalCodeElement()); for (StringDt nextName : allNames) { addSearchTerm(theEntity, retVal, resourceName, nextName.getValue()); } } else if (nextObject instanceof ContactPointDt) { ContactPointDt nextContact = (ContactPointDt) nextObject; if (nextContact.getValueElement().isEmpty() == false) { addSearchTerm(theEntity, retVal, resourceName, nextContact.getValue()); } } else { if (!multiType) { throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass()); } } } } } return retVal; } /* * (non-Javadoc) * * @see ca.uhn.fhir.jpa.dao.ISearchParamExtractor#extractSearchParamTokens(ca.uhn.fhir.jpa.entity.ResourceTable, * ca.uhn.fhir.model.api.IResource) */ @Override public Set<BaseResourceIndexedSearchParam> extractSearchParamTokens(ResourceTable theEntity, IBaseResource theResource) { HashSet<BaseResourceIndexedSearchParam> retVal = new HashSet<BaseResourceIndexedSearchParam>(); String useSystem = null; if (theResource instanceof ValueSet) { ValueSet vs = (ValueSet) theResource; useSystem = vs.getCodeSystem().getSystem(); } RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.TOKEN) { continue; } String nextPath = nextSpDef.getPath(); if (isBlank(nextPath)) { continue; } boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } List<String> systems = new ArrayList<String>(); List<String> codes = new ArrayList<String>(); String needContactPointSystem = null; if (nextPath.endsWith("(system=phone)")) { nextPath = nextPath.substring(0, nextPath.length() - "(system=phone)".length()); needContactPointSystem = "phone"; } if (nextPath.endsWith("(system=email)")) { nextPath = nextPath.substring(0, nextPath.length() - "(system=email)".length()); needContactPointSystem = "email"; } for (Object nextObject : extractValues(nextPath, theResource)) { // Patient:language if (nextObject instanceof Patient.Communication) { Communication nextValue = (Patient.Communication) nextObject; nextObject = nextValue.getLanguage(); } if (nextObject instanceof IdentifierDt) { IdentifierDt nextValue = (IdentifierDt) nextObject; if (nextValue.isEmpty()) { continue; } String system = StringUtils.defaultIfBlank(nextValue.getSystemElement().getValueAsString(), null); String value = nextValue.getValueElement().getValue(); if (isNotBlank(value)) { systems.add(system); codes.add(value); } if (isNotBlank(nextValue.getType().getText())) { addStringParam(theEntity, retVal, nextSpDef, nextValue.getType().getText()); } } else if (nextObject instanceof ContactPointDt) { ContactPointDt nextValue = (ContactPointDt) nextObject; if (nextValue.isEmpty()) { continue; } if (isNotBlank(needContactPointSystem)) { if (!needContactPointSystem.equals(nextValue.getSystemElement().getValueAsString())) { continue; } } systems.add(nextValue.getSystemElement().getValueAsString()); codes.add(nextValue.getValueElement().getValue()); } else if (nextObject instanceof BoundCodeDt) { BoundCodeDt<?> obj = (BoundCodeDt<?>) nextObject; String system = extractSystem(obj); String code = obj.getValue(); if (isNotBlank(code)) { systems.add(system); codes.add(code); } } else if (nextObject instanceof IPrimitiveDatatype<?>) { IPrimitiveDatatype<?> nextValue = (IPrimitiveDatatype<?>) nextObject; if (nextValue.isEmpty()) { continue; } if ("ValueSet.codeSystem.concept.code".equals(nextPath)) { systems.add(useSystem); } else { systems.add(null); } codes.add(nextValue.getValueAsString()); } else if (nextObject instanceof CodingDt) { CodingDt nextValue = (CodingDt) nextObject; extractTokensFromCoding(systems, codes, theEntity, retVal, nextSpDef, nextValue); } else if (nextObject instanceof CodeableConceptDt) { CodeableConceptDt nextCC = (CodeableConceptDt) nextObject; if (!nextCC.getTextElement().isEmpty()) { addStringParam(theEntity, retVal, nextSpDef, nextCC.getTextElement().getValue()); } extractTokensFromCodeableConcept(systems, codes, nextCC, theEntity, retVal, nextSpDef); } else if (nextObject instanceof RestSecurity) { // Conformance.security search param points to something kind of useless right now - This should probably // be fixed. RestSecurity sec = (RestSecurity) nextObject; for (BoundCodeableConceptDt<RestfulSecurityServiceEnum> nextCC : sec.getService()) { extractTokensFromCodeableConcept(systems, codes, nextCC, theEntity, retVal, nextSpDef); } } else if (nextObject instanceof Location.Position) { ourLog.warn("Position search not currently supported, not indexing location"); continue; } else { if (!multiType) { throw new ConfigurationException("Search param " + nextSpDef.getName() + " is of unexpected datatype: " + nextObject.getClass()); } else { continue; } } } assert systems.size() == codes.size() : "Systems contains " + systems + ", codes contains: " + codes; Set<Pair<String, String>> haveValues = new HashSet<Pair<String, String>>(); for (int i = 0; i < systems.size(); i++) { String system = systems.get(i); String code = codes.get(i); if (isBlank(system) && isBlank(code)) { continue; } if (system != null && system.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) { system = system.substring(0, ResourceIndexedSearchParamToken.MAX_LENGTH); } if (code != null && code.length() > ResourceIndexedSearchParamToken.MAX_LENGTH) { code = code.substring(0, ResourceIndexedSearchParamToken.MAX_LENGTH); } Pair<String, String> nextPair = Pair.of(system, code); if (haveValues.contains(nextPair)) { continue; } haveValues.add(nextPair); ResourceIndexedSearchParamToken nextEntity; nextEntity = new ResourceIndexedSearchParamToken(nextSpDef.getName(), system, code); nextEntity.setResource(theEntity); retVal.add(nextEntity); } } return retVal; } @Override public Set<ResourceIndexedSearchParamUri> extractSearchParamUri(ResourceTable theEntity, IBaseResource theResource) { HashSet<ResourceIndexedSearchParamUri> retVal = new HashSet<ResourceIndexedSearchParamUri>(); RuntimeResourceDefinition def = getContext().getResourceDefinition(theResource); for (RuntimeSearchParam nextSpDef : def.getSearchParams()) { if (nextSpDef.getParamType() != RestSearchParameterTypeEnum.URI) { continue; } String nextPath = nextSpDef.getPath(); if (isBlank(nextPath)) { continue; } for (Object nextObject : extractValues(nextPath, theResource)) { if (nextObject == null || ((IDatatype) nextObject).isEmpty()) { continue; } String resourceName = nextSpDef.getName(); boolean multiType = false; if (nextPath.endsWith("[x]")) { multiType = true; } if (nextObject instanceof UriDt) { UriDt nextValue = (UriDt) nextObject; if (isBlank(nextValue.getValue())) { continue; } ourLog.trace("Adding param: {}, {}", resourceName, nextValue.getValue()); ResourceIndexedSearchParamUri nextEntity = new ResourceIndexedSearchParamUri(resourceName, nextValue.getValue()); nextEntity.setResource(theEntity); retVal.add(nextEntity); } else { if (!multiType) { throw new ConfigurationException("Search param " + resourceName + " is of unexpected datatype: " + nextObject.getClass()); } else { continue; } } } } return retVal; } private void extractTokensFromCodeableConcept(List<String> theSystems, List<String> theCodes, CodeableConceptDt theCodeableConcept, ResourceTable theEntity, Set<BaseResourceIndexedSearchParam> theListToPopulate, RuntimeSearchParam theParameterDef) { for (CodingDt nextCoding : theCodeableConcept.getCoding()) { extractTokensFromCoding(theSystems, theCodes, theEntity, theListToPopulate, theParameterDef, nextCoding); } } private void extractTokensFromCoding(List<String> theSystems, List<String> theCodes, ResourceTable theEntity, Set<BaseResourceIndexedSearchParam> theListToPopulate, RuntimeSearchParam theParameterDef, CodingDt nextCoding) { if (nextCoding != null && !nextCoding.isEmpty()) { String nextSystem = nextCoding.getSystemElement().getValueAsString(); String nextCode = nextCoding.getCodeElement().getValue(); if (isNotBlank(nextSystem) || isNotBlank(nextCode)) { theSystems.add(nextSystem); theCodes.add(nextCode); } if (!nextCoding.getDisplayElement().isEmpty()) { addStringParam(theEntity, theListToPopulate, theParameterDef, nextCoding.getDisplayElement().getValue()); } } } private static <T extends Enum<?>> String extractSystem(BoundCodeDt<T> theBoundCode) { if (theBoundCode.getValueAsEnum() != null) { IValueSetEnumBinder<T> binder = theBoundCode.getBinder(); return binder.toSystemString(theBoundCode.getValueAsEnum()); } return null; } }