package org.hl7.fhir.convertors;
/*
* #%L
* HAPI FHIR - Converter
* %%
* Copyright (C) 2014 - 2017 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%
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.InputStream;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.hl7.fhir.dstu3.context.IWorkerContext;
import org.hl7.fhir.dstu3.model.AllergyIntolerance;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCriticality;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceReactionComponent;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceSeverity;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceType;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceVerificationStatus;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Comparison;
import org.hl7.fhir.dstu3.model.Composition;
import org.hl7.fhir.dstu3.model.Composition.CompositionAttestationMode;
import org.hl7.fhir.dstu3.model.Composition.CompositionAttesterComponent;
import org.hl7.fhir.dstu3.model.Composition.DocumentConfidentiality;
import org.hl7.fhir.dstu3.model.Composition.SectionComponent;
import org.hl7.fhir.dstu3.model.ContactPoint;
import org.hl7.fhir.dstu3.model.Device;
import org.hl7.fhir.dstu3.model.DomainResource;
import org.hl7.fhir.dstu3.model.Encounter;
import org.hl7.fhir.dstu3.model.Extension;
import org.hl7.fhir.dstu3.model.Factory;
import org.hl7.fhir.dstu3.model.Identifier;
import org.hl7.fhir.dstu3.model.InstantType;
import org.hl7.fhir.dstu3.model.ListResource;
import org.hl7.fhir.dstu3.model.ListResource.ListEntryComponent;
import org.hl7.fhir.dstu3.model.Location;
import org.hl7.fhir.dstu3.model.Meta;
import org.hl7.fhir.dstu3.model.Narrative;
import org.hl7.fhir.dstu3.model.Narrative.NarrativeStatus;
import org.hl7.fhir.dstu3.model.Observation;
import org.hl7.fhir.dstu3.model.Observation.ObservationRelatedComponent;
import org.hl7.fhir.dstu3.model.Observation.ObservationRelationshipType;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.dstu3.model.Organization;
import org.hl7.fhir.dstu3.model.Patient;
import org.hl7.fhir.dstu3.model.Period;
import org.hl7.fhir.dstu3.model.Practitioner;
import org.hl7.fhir.dstu3.model.Procedure;
import org.hl7.fhir.dstu3.model.Procedure.ProcedurePerformerComponent;
import org.hl7.fhir.dstu3.model.Reference;
import org.hl7.fhir.dstu3.model.ResourceFactory;
import org.hl7.fhir.dstu3.utils.NarrativeGenerator;
import org.hl7.fhir.dstu3.utils.ToolingExtensions;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.ucum.UcumService;
import org.w3c.dom.Element;
/**
Advance Directives Section 42348-3 :
Allergies, Adverse Reactions, Alerts Section 48765-2 : List(AlleryIntolerance) processAdverseReactionsSection
Anesthesia Section 59774-0 :
Assessment Section 51848-0 :
Assessment and Plan Section 51487-2 :
Chief Complaint Section 10154-3 :
Chief Complaint and Reason for Visit Section 46239-0 :
Complications 55109-3:
DICOM Object Catalog Section - DCM 121181 :
Discharge Diet Section 42344-2 :
Encounters Section 46240-8:
Family History Section 10157-6 :
Findings Section 18782-3 :
Functional Status Section 47420-5 :
General Status Section 10210-3 :
History of Past Illness Section 11348-0 :
History of Present Illness Section 10164-2 :
Hospital Admission Diagnosis Section 46241-6 :
Hospital Consultations Section 18841-7 :
Hospital Course Section 8648-8 :
Hospital Discharge Diagnosis Section 11535-2 :
Hospital Discharge Instructions Section :
Hospital Discharge Medications Section (entries optional) 10183-2 :
Hospital Discharge Physical Section 10184-0 :
Hospital Discharge Studies Summary Section 11493-4 :
Immunizations Section 11369-6 :
Interventions Section 62387-6 :
Medical Equipment Section 46264-8 :
Medical (General) History Section 11329-0 :
Medications Section 10160-0 :
Medications Administered Section 29549-3 :
Objective Section 61149-1 :
Operative Note Fluid Section 10216-0 :
Operative Note Surgical Procedure Section 10223-6 :
Payers Section 48768-6 :
Physical Exam Section 29545-1 :
Plan of Care Section 18776-5 :
Planned Procedure Section 59772-:
Postoperative Diagnosis Section 10218-6 :
Postprocedure Diagnosis Section 59769-0 :
Preoperative Diagnosis Section 10219-4 :
Problem Section 11450-4 :
Procedure Description Section 29554-3:
Procedure Disposition Section 59775-7 :
Procedure Estimated Blood Loss Section 59770-8 :
Procedure Findings Section 59776-5 :
Procedure Implants Section 59771-6 :
Procedure Indications Section 59768-2 :
Procedure Specimens Taken Section 59773-2 :
Procedures Section 47519-4 : List (Procedure) processProceduresSection
Reason for Referral Section 42349-1 :
Reason for Visit Section 29299-5 :
Results Section 30954-2 :
Review of Systems Section 10187-3 :
Social History Section 29762-2 : List (Observation) processSocialHistorySection
Subjective Section 61150-9:
Surgical Drains Section 11537-8 :
Vital Signs Section 8716-3 : List(Observation) processVitalSignsSection
MU Sections:
Allergies/Adverse Reactions
Problems
Encounters
Medications
Results
Vital Signs
Procedures
Immunizations
Reason for Referral
Hospital Discharge Instructions
Functional Status
Plan of Care
Hospital Discharge Medication
All of General Header
* @author Grahame
*
*/
public class CCDAConverter {
public enum SocialHistoryType {
SocialHistory, Pregnancy, SmokingStatus, TobaccoUse
}
public enum ProcedureType {
Observation, Procedure, Act
}
protected CDAUtilities cda;
protected Element doc;
protected Convert convert;
protected Bundle feed;
protected Composition composition;
protected Map<String, Practitioner> practitionerCache = new HashMap<String, Practitioner>();
protected Integer refCounter = 0;
protected UcumService ucumSvc;
protected IWorkerContext context;
public CCDAConverter(UcumService ucumSvc, IWorkerContext context) {
super();
this.ucumSvc = ucumSvc;
this.context = context;
}
public Bundle convert(InputStream stream) throws Exception {
cda = new CDAUtilities(stream);
doc = cda.getElement();
cda.checkTemplateId(doc, "2.16.840.1.113883.10.20.22.1.1");
convert = new Convert(cda, ucumSvc, "Z");
// check it's a CDA/CCD
feed = new Bundle();
feed.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
feed.setId(makeUUIDReference());
feed.getMeta().getTag().add(new Coding()); // todo-bundle ("http://hl7.org/fhir/tag", "http://hl7.org/fhir/tag/document", "Document"));
// process the header
makeDocument();
composition.setSubject(Factory.makeReference(makeSubject()));
for (Element e : cda.getChildren(doc, "author"))
composition.getAuthor().add(Factory.makeReference(makeAuthor(e)));
// todo: data enterer & informant goes in provenance
composition.setCustodian(Factory.makeReference(makeOrganization(
cda.getDescendent(doc, "custodian/assignedCustodian/representedCustodianOrganization"), "Custodian")));
// todo: informationRecipient
for (Element e : cda.getChildren(doc, "legalAuthenticator"))
composition.getAttester().add(makeAttester(e, CompositionAttestationMode.LEGAL, "Legal Authenticator"));
for (Element e : cda.getChildren(doc, "authenticator"))
composition.getAttester().add(makeAttester(e, CompositionAttestationMode.PROFESSIONAL, "Authenticator"));
// process the contents
// we do this by section - keep the original section order
Element body = cda.getDescendent(doc, "component/structuredBody");
processComponentSections(composition.getSection(), body);
return feed;
}
protected String addReference(DomainResource r, String title, String id) throws Exception {
if (r.getText() == null)
r.setText(new Narrative());
if (r.getText().getDiv() == null) {
r.getText().setStatus(NarrativeStatus.GENERATED);
// new NarrativeGenerator("", "", context).generate(r);
}
r.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));
r.setId(id);
feed.getEntry().add(new BundleEntryComponent().setResource(r));
return id;
}
protected void makeDocument() throws Exception {
composition = (Composition) ResourceFactory.createResource("Composition");
addReference(composition, "Composition", makeUUIDReference());
Element title = cda.getChild(doc, "title");
composition.setTitle(title.getTextContent());
if (cda.getChild(doc, "setId") != null) {
feed.setId(convert.makeURIfromII(cda.getChild(doc, "id")));
composition.setIdentifier(convert.makeIdentifierFromII(cda.getChild(doc, "setId")));
} else
composition.setIdentifier(convert.makeIdentifierFromII(cda.getChild(doc, "id"))); // well, we fall back to id
composition.setDateElement(convert.makeDateTimeFromTS(cda.getChild(doc, "effectiveTime")));
composition.setType(convert.makeCodeableConceptFromCD(cda.getChild(doc, "code")));
composition.setConfidentiality(convertConfidentiality(cda.getChild(doc, "confidentialityCode")));
if (cda.getChild(doc, "confidentialityCode") != null)
composition.setLanguage(cda.getChild(doc, "confidentialityCode").getAttribute("value")); // todo - fix streaming for this
Element ee = cda.getChild(doc, "componentOf");
if (ee != null)
ee = cda.getChild(ee, "encompassingEncounter");
if (ee != null) {
Encounter visit = new Encounter();
for (Element e : cda.getChildren(ee, "id"))
visit.getIdentifier().add(convert.makeIdentifierFromII(e));
visit.setPeriod(convert.makePeriodFromIVL(cda.getChild(ee, "effectiveTime")));
composition.getEvent().add(new Composition.CompositionEventComponent());
composition.getEvent().get(0).getCode().add(convert.makeCodeableConceptFromCD(cda.getChild(ee, "code")));
composition.getEvent().get(0).setPeriod(visit.getPeriod());
composition.getEvent().get(0).getDetail().add(Factory.makeReference(addReference(visit, "Encounter", makeUUIDReference())));
}
// main todo: fill out the narrative, but before we can do that, we have to convert everything else
}
protected DocumentConfidentiality convertConfidentiality(Element child) throws FHIRException, org.hl7.fhir.exceptions.FHIRException {
// TODO Auto-generated method stub
return DocumentConfidentiality.fromCode(child.getAttribute("code"));
}
protected String makeSubject() throws Exception {
Element rt = cda.getChild(doc, "recordTarget");
Element pr = cda.getChild(rt, "patientRole");
Element p = cda.getChild(pr, "patient");
Patient pat = (Patient) ResourceFactory.createResource("Patient");
for (Element e : cda.getChildren(pr, "id"))
pat.getIdentifier().add(convert.makeIdentifierFromII(e));
for (Element e : cda.getChildren(pr, "addr"))
pat.getAddress().add(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(pr, "telecom"))
pat.getTelecom().add(convert.makeContactFromTEL(e));
for (Element e : cda.getChildren(p, "name"))
pat.getName().add(convert.makeNameFromEN(e));
pat.setGender(convert.makeGenderFromCD(cda.getChild(p, "administrativeGenderCode")));
pat.setBirthDateElement(convert.makeDateFromTS(cda.getChild(p, "birthTime")));
pat.setMaritalStatus(convert.makeCodeableConceptFromCD(cda.getChild(p, "maritalStatusCode")));
pat.getExtension().add(Factory.newExtension(CcdaExtensions.NAME_RELIGION, convert.makeCodeableConceptFromCD(cda.getChild(p, "religiousAffiliationCode")), false));
pat.getExtension().add(Factory.newExtension(CcdaExtensions.DAF_NAME_RACE, convert.makeCodeableConceptFromCD(cda.getChild(p, "raceCode")), false));
pat.getExtension().add(Factory.newExtension(CcdaExtensions.DAF_NAME_ETHNICITY, convert.makeCodeableConceptFromCD(cda.getChild(p, "ethnicGroupCode")), false));
pat.getExtension().add(Factory.newExtension(CcdaExtensions.NAME_BIRTHPLACE, convert.makeAddressFromAD(cda.getChild(p, new String[] {"birthplace", "place", "addr"})), false));
Patient.ContactComponent guardian = new Patient.ContactComponent();
pat.getContact().add(guardian);
guardian.getRelationship().add(Factory.newCodeableConcept("GUARD", "urn:oid:2.16.840.1.113883.5.110", "guardian"));
Element g = cda.getChild(p, "guardian");
for (Element e : cda.getChildren(g, "addr"))
if (guardian.getAddress() == null)
guardian.setAddress(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(g, "telecom"))
guardian.getTelecom().add(convert.makeContactFromTEL(e));
g = cda.getChild(g, "guardianPerson");
for (Element e : cda.getChildren(g, "name"))
if (guardian.getName() == null)
guardian.setName(convert.makeNameFromEN(e));
Element l = cda.getChild(p, "languageCommunication");
CodeableConcept cc = new CodeableConcept();
Coding c = new Coding();
c.setCode(cda.getChild(l, "languageCode").getAttribute("code"));
cc.getCoding().add(c);
pat.addCommunication().setLanguage(cc);
// todo: this got broken.... lang.setMode(convert.makeCodeableConceptFromCD(cda.getChild(l, "modeCode")));
cc.getExtension().add(Factory.newExtension(CcdaExtensions.NAME_LANG_PROF, convert.makeCodeableConceptFromCD(cda.getChild(l, "modeCode")), false));
pat.getExtension().add(Factory.newExtension(CcdaExtensions.NAME_RELIGION, convert.makeCodeableConceptFromCD(cda.getChild(p, "religiousAffiliationCode")), false));
pat.setManagingOrganization(Factory.makeReference(makeOrganization(cda.getChild(pr, "providerOrganization"), "Provider")));
return addReference(pat, "Subject", makeUUIDReference());
}
protected String makeOrganization(Element org, String name) throws Exception {
Organization o = new Organization();
for (Element e : cda.getChildren(org, "id"))
o.getIdentifier().add(convert.makeIdentifierFromII(e));
for (Element e : cda.getChildren(org, "name"))
o.setName(e.getTextContent());
for (Element e : cda.getChildren(org, "addr"))
o.getAddress().add(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(org, "telecom"))
o.getTelecom().add(convert.makeContactFromTEL(e));
return addReference(o, name, makeUUIDReference());
}
protected String makeAuthor(Element auth) throws Exception {
Element aa = cda.getChild(auth, "assignedAuthor");
Element ap = cda.getChild(aa, "assignedPerson");
Practitioner pr = (Practitioner) ResourceFactory.createResource("Practitioner");
for (Element e : cda.getChildren(aa, "id"))
pr.getIdentifier().add(convert.makeIdentifierFromII(e));
for (Element e : cda.getChildren(aa, "addr"))
if (pr.getAddress() == null)
pr.getAddress().add(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(aa, "telecom"))
pr.getTelecom().add(convert.makeContactFromTEL(e));
for (Element e : cda.getChildren(ap, "name"))
if (pr.getName() != null)
pr.addName(convert.makeNameFromEN(e));
return addReference(pr, "Author", makeUUIDReference());
}
protected String makeUUIDReference() {
return "urn:uuid:"+UUID.randomUUID().toString().toLowerCase();
}
protected CompositionAttesterComponent makeAttester(Element a1, CompositionAttestationMode mode, String title) throws Exception {
Practitioner pr = (Practitioner) ResourceFactory.createResource("Practitioner");
Element ass = cda.getChild(a1, "assignedEntity");
for (Element e : cda.getChildren(ass, "id"))
pr.getIdentifier().add(convert.makeIdentifierFromII(e));
for (Element e : cda.getChildren(ass, "addr"))
if (pr.getAddress() == null) // just take the first
pr.getAddress().add(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(ass, "telecom"))
pr.getTelecom().add(convert.makeContactFromTEL(e));
Element ap = cda.getChild(ass, "assignedPerson");
for (Element e : cda.getChildren(ap, "name"))
if (pr.getName() == null) // just take the first
pr.addName(convert.makeNameFromEN(e));
CompositionAttesterComponent att = new CompositionAttesterComponent();
att.addMode(mode);
att.setTimeElement(convert.makeDateTimeFromTS(cda.getChild(a1,"time")));
att.setParty(Factory.makeReference(addReference(pr, title, makeUUIDReference())));
return att;
}
protected void processComponentSections(List<SectionComponent> sections, Element container) throws Exception {
for (Element c : cda.getChildren(container, "component")) {
SectionComponent s = processSection(cda.getChild(c, "section"));
if (s != null)
sections.add(s);
}
}
protected SectionComponent processSection(Element section) throws Exception {
checkNoSubject(section, "Section");
// this we do by templateId
if (cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.6") || cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.6.1"))
return processAdverseReactionsSection(section);
else if (cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.7") || cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.7.1"))
return processProceduresSection(section);
else if (cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.17"))
return processSocialHistorySection(section);
else if (cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.4") || cda.hasTemplateId(section, "2.16.840.1.113883.10.20.22.2.4.1"))
return processVitalSignsSection(section);
else
// todo: error?
return null;
}
protected void checkNoSubject(Element act, String path) throws Exception {
if (cda.getChild(act, "subject") != null)
throw new Exception("The conversion program cannot accept a nullFlavor at the location "+path);
}
protected SectionComponent processProceduresSection(Element section) throws Exception {
ListResource list = new ListResource();
for (Element entry : cda.getChildren(section, "entry")) {
Element procedure = cda.getlastChild(entry);
if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.14")) {
processProcedure(list, procedure, ProcedureType.Procedure);
} else if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.13")) {
processProcedure(list, procedure, ProcedureType.Observation);
} else if (cda.hasTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.12")) {
processProcedure(list, procedure, ProcedureType.Act);
} else
throw new Exception("Unhandled Section template ids: "+cda.showTemplateIds(procedure));
}
// todo: text
SectionComponent s = new Composition.SectionComponent();
s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
// todo: check subject
s.addEntry(Factory.makeReference(addReference(list, "Procedures", makeUUIDReference())));
return s;
}
protected void processProcedure(ListResource list, Element procedure, ProcedureType type) throws Exception {
switch (type) {
case Procedure :
cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.14");
break;
case Observation:
cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.13");
break;
case Act:
cda.checkTemplateId(procedure, "2.16.840.1.113883.10.20.22.4.12");
}
checkNoNegationOrNullFlavor(procedure, "Procedure ("+type.toString()+")");
checkNoSubject(procedure, "Procedure ("+type.toString()+")");
Procedure p = new Procedure();
addItemToList(list, p);
// moodCode is either INT or EVN. INT is not handled yet. INT is deprecated anyway
if (procedure.getAttribute("moodCode").equals("INT"))
p.getModifierExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-planned", Factory.newBoolean(true), false));
// SHALL contain at least one [1..*] id (CONF:7655).
for (Element e : cda.getChildren(procedure, "id"))
p.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] code (CONF:7656).
// This code @code in a procedure activity SHOULD be selected from LOINC or SNOMED CT and MAY be selected from CPT-4, ICD9 Procedures, ICD10 Procedures
p.setCode(convert.makeCodeableConceptFromCD(cda.getChild(procedure, "code")));
// SHALL contain exactly one [1..1] statusCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.11.20.9.22 ProcedureAct
// completed | active | aborted | cancelled - not in FHIR
p.getModifierExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-status", Factory.newCode(cda.getStatus(procedure)), false));
// SHOULD contain zero or one [0..1] effectiveTime (CONF:7662).
p.setPerformed(convert.makePeriodFromIVL(cda.getChild(procedure, "effectiveTime")));
// MAY contain zero or one [0..1] priorityCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.1.11.16866 ActPriority DYNAMIC (CONF:7668)
p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-priority", convert.makeCodeableConceptFromCD(cda.getChild(procedure, "priorityCode")), false));
// MAY contain zero or one [0..1] methodCode (CONF:7670).
p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-method", convert.makeCodeableConceptFromCD(cda.getChild(procedure, "methodCode")), false));
if (type == ProcedureType.Observation) {
// for Procedure-Observation:
// 9. SHALL contain exactly one [1..1] value (CONF:16846).
// don't know what this is. It's not the actual result of the procedure (that goes in results "This section records ... procedure observations"), and there seems to be no value. The example as <value xsi:type="CD"/> which is not valid
// so we ignore this for now
}
// SHOULD contain zero or more [0..*] targetSiteCode/@code, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.8.9 Body site DYNAMIC (CONF:7683).
for (Element e : cda.getChildren(procedure, "targetSiteCode"))
p.addBodySite(convert.makeCodeableConceptFromCD(e));
// MAY contain zero or more [0..*] specimen (CONF:7697).
// todo: add these as extensions when specimens are done.
// SHOULD contain zero or more [0..*] performer (CONF:7718) such that it
for (Element e : cda.getChildren(procedure, "performer")) {
ProcedurePerformerComponent pp = new ProcedurePerformerComponent();
p.getPerformer().add(pp);
pp.setActor(makeReferenceToPractitionerForAssignedEntity(e, p));
}
for (Element participant : cda.getChildren(procedure, "participant")) {
Element participantRole = cda.getlastChild(participant);
if (type == ProcedureType.Procedure && cda.hasTemplateId(participantRole, "2.16.840.1.113883.10.20.22.4.37")) {
// MAY contain zero or more [0..*] participant (CONF:7751) such that it SHALL contain exactly one [1..1] @typeCode="DEV" Device
// implanted devices
p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/implanted-devices", Factory.makeReference(processDevice(participantRole, p)), false));
} else if (cda.hasTemplateId(participantRole, "2.16.840.1.113883.10.20.22.4.32")) {
// MAY contain zero or more [0..*] participant (CONF:7765) such that it SHALL contain exactly one [1..1] Service Delivery Location (templateId:2.16.840.1.113883.10.20.22.4.32) (CONF:7767)
p.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/location", Factory.makeReference(processSDLocation(participantRole, p)), false));
}
}
for (Element e : cda.getChildren(procedure, "entryRelationship")) {
Element a /* act*/ = cda.getlastChild(e);
if (a.getLocalName().equals("encounter")) {
// MAY contain zero or more [0..*] entryRelationship (CONF:7768) such that it SHALL contain exactly one encounter which SHALL contain exactly one [1..1] id (CONF:7773).
// todo - and process as a full encounter while we're at it
} else if (cda.hasTemplateId(a, "2.16.840.1.113883.10.20.22.4.20")) {
// MAY contain zero or one [0..1] entryRelationship (CONF:7775) such that it SHALL contain exactly one [1..1] Instructions (templateId:2.16.840.1.113883.10.20.22.4.20) (CONF:7778).
// had code for type, plus text for instructions
Extension n = Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions", null, true);
n.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions-type", convert.makeCodeableConceptFromCD(cda.getChild(a, "code")), false));
n.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/procedure-instructions-text", convert.makeStringFromED(cda.getChild(a, "text")), false));
p.getExtension().add(n);
} else if (cda.hasTemplateId(a, "2.16.840.1.113883.10.20.22.4.19")) {
// MAY contain zero or more [0..*] entryRelationship (CONF:7779) such that it SHALL contain exactly one [1..1] Indication (templateId:2.16.840.1.113883.10.20.22.4.19) (CONF:7781).
p.addReasonCode(processIndication(a));
} else if (cda.hasTemplateId(cda.getlastChild(e), "2.16.840.1.113883.10.20.22.4.16")) {
// MAY contain zero or one [0..1] entryRelationship (CONF:7886) such that it SHALL contain exactly one [1..1] Medication Activity (templateId:2.16.840.1.113883.10.20.22.4.16) (CONF:7888).
// todo
}
}
}
protected String processSDLocation(Element participantRole, DomainResource r) throws Exception {
Location l = new Location();
l.setType(convert.makeCodeableConceptFromCD(cda.getChild(participantRole, "code")));
for (Element id : cda.getChildren(participantRole, "id")) {
if (l.getIdentifier() == null)
l.getIdentifier().add(convert.makeIdentifierFromII(id));
}
for (Element addr : cda.getChildren(participantRole, "addr")) {
if (l.getAddress() == null)
l.setAddress(convert.makeAddressFromAD(addr));
}
for (Element telecom : cda.getChildren(participantRole, "telecom")) {
l.getTelecom().add(convert.makeContactFromTEL(telecom));
}
Element place = cda.getChild(participantRole, "playingDevice");
if (cda.getChild(place, "name") != null)
l.setName(cda.getChild(place, "name").getTextContent());
String id = nextRef();
l.setId(id);
r.getContained().add(l);
return "#"+id;
}
protected String processDevice(Element participantRole, DomainResource r) throws Exception {
Device d = new Device();
for (Element id : cda.getChildren(participantRole, "id")) {
// todo: check for UDIs, how?
d.getIdentifier().add(convert.makeIdentifierFromII(id));
}
Element device = cda.getChild(participantRole, "playingDevice");
// todo: if (cda.getChild(device, "code") != null)
d.setType(convert.makeCodeableConceptFromCD(cda.getChild(device, "code")));
// CCDA has an id - this is manufacturer? We just call it the name, but what to do about this?
Element org = cda.getChild(participantRole, "scopingEntity");
d.setManufacturer(convert.makeURIfromII(cda.getChild(org, "id")));
String id = nextRef();
d.setId(id);
r.getContained().add(d);
return "#"+id;
}
protected CodeableConcept processIndication(Element obs) throws Exception {
Element v = cda.getChild(obs, "value");
if (v == null) {
// have to find it by ID
Element o = cda.getById(cda.getChild(obs, "id"), "value");
if (o != null)
v = cda.getChild(obs, "value");
}
if (v != null)
return convert.makeCodeableConceptFromCD(v);
else
return null;
}
protected Reference makeReferenceToPractitionerForAssignedEntity(Element assignedEntity, DomainResource r) throws Exception {
Reference ref = null;
// do we have this by id?
String uri = getIdForEntity(assignedEntity);
Practitioner p = null;
if (uri != null) {
ref = Factory.makeReference(uri);
p = practitionerCache.get(uri);
}
if (p == null) {
p = new Practitioner();
if (uri == null) {
// make a contained practitioner
String n = nextRef();
p.setId(n);
r.getContained().add(p);
ref = Factory.makeReference("#"+n);
} else {
// add this to feed
ref = Factory.makeReference(addReference(p, "Practitioner", uri));
}
}
// ref and p are both sorted. now we fill out p as much as we can (remembering it might already be populated)
// p.addRole().setCode(convert.makeCodeableConceptFromCD(cda.getChild(assignedEntity, "code")));
for (Element e : cda.getChildren(assignedEntity, "id"))
addToIdList(p.getIdentifier(), convert.makeIdentifierFromII(e));
for (Element e : cda.getChildren(assignedEntity, "addr"))
if (p.getAddress() == null)
p.getAddress().add(convert.makeAddressFromAD(e));
for (Element e : cda.getChildren(assignedEntity, "telecom"))
addToContactList(p.getTelecom(), convert.makeContactFromTEL(e));
for (Element e : cda.getChildren(cda.getChild(assignedEntity, "assignedPerson"), "name"))
if (p.getName() == null)
p.addName(convert.makeNameFromEN(e));
// todo:
// representedOrganization
return ref;
}
protected void addToContactList(List<ContactPoint> list, ContactPoint c) throws Exception {
for (ContactPoint item : list) {
if (Comparison.matches(item, c, null))
Comparison.merge(item, c);
}
list.add(c);
}
protected void addToIdList(List<Identifier> list, Identifier id) throws Exception {
for (Identifier item : list) {
if (Comparison.matches(item, id, null))
Comparison.merge(item, id);
}
list.add(id);
}
protected void addToCodeableList(List<CodeableConcept> list, CodeableConcept code) throws Exception {
for (CodeableConcept item : list) {
if (Comparison.matches(item, code, null))
Comparison.merge(item, code);
}
list.add(code);
}
protected String getIdForEntity(Element assignedEntity) throws Exception {
Element id = cda.getChild(assignedEntity, "id"); // for now, just grab the first
if (id == null)
return null;
if (id.getAttribute("extension") == null) {
if (convert.isGuid(id.getAttribute("root")))
return "urn:uuid:"+id.getAttribute("root");
else
return "urn:oid:"+id.getAttribute("root");
} else
return "ii:"+id.getAttribute("root")+"::"+id.getAttribute("extension");
}
protected SectionComponent processAdverseReactionsSection(Element section) throws Exception {
ListResource list = new ListResource();
for (Element entry : cda.getChildren(section, "entry")) {
Element concern = cda.getChild(entry, "act");
if (cda.hasTemplateId(concern, "2.16.840.1.113883.10.20.22.4.30")) {
processAllergyProblemAct(list, concern);
} else
throw new Exception("Unhandled Section template ids: "+cda.showTemplateIds(concern));
}
// todo: text
SectionComponent s = new Composition.SectionComponent();
s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
// todo: check subject
s.addEntry(Factory.makeReference(addReference(list, "Allergies, Adverse Reactions, Alerts", makeUUIDReference())));
return s;
}
protected void processAllergyProblemAct(ListResource list, Element concern) throws Exception {
cda.checkTemplateId(concern, "2.16.840.1.113883.10.20.22.4.30");
// Allergy Problem Act - this is a concern - we treat the concern as information about it's place in the list
checkNoNegationOrNullFlavor(concern, "Allergy Problem Act");
checkNoSubject(concern, "Allergy Problem Act");
// SHALL contain at least one [1..*] entryRelationship (CONF:7509) such that it
// SHALL contain exactly one [1..1] Allergy - intolerance Observation
for (Element entry : cda.getChildren(concern, "entryRelationship")) {
Element obs = cda.getChild(entry, "observation");
cda.checkTemplateId(obs, "2.16.840.1.113883.10.20.22.4.7");
checkNoNegationOrNullFlavor(obs, "Allergy - intolerance Observation");
checkNoSubject(obs, "Allergy Problem Act");
AllergyIntolerance ai = new AllergyIntolerance();
ListEntryComponent item = addItemToList(list, ai);
// this first section comes from the concern, and is processed once for each observation in the concern group
// SHALL contain at least one [1..*] id (CONF:7472).
for (Element e : cda.getChildren(concern, "id"))
ai.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] statusCode, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.80.68 HITSPProblemStatus DYNAMIC (CONF:7485)
// the status code is about the concern (e.g. the entry in the list)
// possible values: active, suspended, aborted, completed, with an effective time
String s = cda.getStatus(concern);
item.setFlag(Factory.newCodeableConcept(s, "http://hl7.org/fhir/v3/ActStatus", s));
if (s.equals("aborted")) // only on this condition?
item.setDeleted(true);
// SHALL contain exactly one [1..1] effectiveTime (CONF:7498)
Period p = convert.makePeriodFromIVL(cda.getChild(concern, "effectiveTime"));
item.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/list-period", p, false));
if (p.getEnd() != null)
item.setDate(p.getEnd());
else
item.setDate(p.getStart());
//ok, now process the actual observation
// SHALL contain at least one [1..*] id (CONF:7382)
for (Element e : cda.getChildren(obs, "id"))
ai.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] effectiveTime (CONF:7387)
ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergyintolerance-period", convert.makePeriodFromIVL(cda.getChild(obs, "effectiveTime")), false));
// SHALL contain exactly one [1..1] value with @xsi:type="CD" (CONF:7390)
CodeableConcept type = convert.makeCodeableConceptFromCD(cda.getChild(obs, "value"));
// This value SHALL contain @code, which SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.6.2 Allergy/Adverse Event Type
String ss = type.getCoding().get(0).getCode();
if (ss.equals("416098002") || ss.equals("414285001"))
ai.setType(AllergyIntoleranceType.ALLERGY);
else if (ss.equals("59037007") || ss.equals("235719002"))
ai.setType(AllergyIntoleranceType.INTOLERANCE);
ai.getExtension().add(Factory.newExtension("http://www.healthintersections.com.au/fhir/extensions/allergy-category", type, false));
// SHOULD contain zero or one [0..1] participant (CONF:7402) such that it
// ......This playingEntity SHALL contain exactly one [1..1] code
ai.setCode(convert.makeCodeableConceptFromCD(cda.getDescendent(obs, "participant/participantRole/playingEntity/code")));
// MAY contain zero or one [0..1] entryRelationship (CONF:7440) such that it SHALL contain exactly one [1..1] Alert Status Observation
// SHOULD contain zero or more [0..*] entryRelationship (CONF:7447) such that it SHALL contain exactly one [1..1] Reaction Observation (templateId:2.16.840.1.113883.10.20.22.4.9) (CONF:7450).
for (Element e : cda.getChildren(obs, "entryRelationship")) {
Element child = cda.getChild(e, "observation");
if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.28") && ai.getClinicalStatus() == null) {
// SHALL contain exactly one [1..1] value with @xsi:type="CE", where the @code SHALL be selected from ValueSet Problem Status Value Set 2.16.840.1.113883.3.88.12.80.68 DYNAMIC (CONF:7322).
// 55561003 SNOMED CT Active
// 73425007 SNOMED CT Inactive
// 413322009 SNOMED CT Resolved
String sc = cda.getChild(child, "value").getAttribute("code");
if (sc.equals("55561003")) {
ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.ACTIVE);
ai.setVerificationStatus(AllergyIntoleranceVerificationStatus.CONFIRMED);
} else
ai.setClinicalStatus(AllergyIntoleranceClinicalStatus.RESOLVED);
} else if (cda.hasTemplateId(child, "2.16.840.1.113883.10.20.22.4.9")) {
ai.getReaction().add(processAdverseReactionObservation(child));
}
}
// SHOULD contain zero or one [0..1] entryRelationship (CONF:9961) such that it SHALL contain exactly one [1..1] Severity Observation (templateId:2.16.840.1.113883.10.20.22.4.8) (CONF:9963).
ai.setCriticality(readCriticality(cda.getSeverity(obs)));
}
}
// this is going to be a contained resource, so we aren't going to generate any narrative
protected AllergyIntoleranceReactionComponent processAdverseReactionObservation(Element reaction) throws Exception {
checkNoNegationOrNullFlavor(reaction, "Adverse Reaction Observation");
checkNoSubject(reaction, "Adverse Reaction Observation");
// This clinical statement represents an undesired symptom, finding, etc., due to an administered or exposed substance. A reaction can be defined with respect to its severity, and can have been treated by one or more interventions.
AllergyIntoleranceReactionComponent ar = new AllergyIntoleranceReactionComponent();
// SHALL contain exactly one [1..1] id (CONF:7329).
for (Element e : cda.getChildren(reaction, "id"))
ToolingExtensions.addIdentifier(ar, convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] code (CONF:7327). The value set for this code element has not been specified.
// todo: what the heck is this?
// SHOULD contain zero or one [0..1] text (CONF:7330).
// todo: so what is this? how can we know whether to ignore it?
// 8. SHOULD contain zero or one [0..1] effectiveTime (CONF:7332).
// a. This effectiveTime SHOULD contain zero or one [0..1] low (CONF:7333).
// b. This effectiveTime SHOULD contain zero or one [0..1] high (CONF:7334).
// !this is a problem because FHIR just has a date, not a period.
ar.setOnsetElement(convert.makeDateTimeFromIVL(cda.getChild(reaction, "effectiveTime")));
// SHALL contain exactly one [1..1] value with @xsi:type="CD", where the @code SHALL be selected from ValueSet 2.16.840.1.113883.3.88.12.3221.7.4 Problem DYNAMIC (CONF:7335).
ar.getManifestation().add(convert.makeCodeableConceptFromCD(cda.getChild(reaction, "value")));
// SHOULD contain zero or one [0..1] entryRelationship (CONF:7580) such that it SHALL contain exactly one [1..1] Severity Observation (templateId:2.16.840.1.113883.10.20.22.4.8) (CONF:7582).
ar.setSeverity(readSeverity(cda.getSeverity(reaction)));
// MAY contain zero or more [0..*] entryRelationship (CONF:7337) such that it SHALL contain exactly one [1..1] Procedure Activity Procedure (templateId:2.16.840.1.113883.10.20.22.4.14) (CONF:7339).
// i. This procedure activity is intended to contain information about procedures that were performed in response to an allergy reaction
// todo: process these into an procedure and add as an extension
// MAY contain zero or more [0..*] entryRelationship (CONF:7340) such that it SHALL contain exactly one [1..1] Medication Activity (templateId:2.16.840.1.113883.10.20.22.4.16) (CONF:7342).
// i. This medication activity is intended to contain information about medications that were administered in response to an allergy reaction. (CONF:7584).
// todo: process these into an medication statement and add as an extension
return ar;
}
protected SectionComponent processSocialHistorySection(Element section) throws Exception {
ListResource list = new ListResource();
for (Element entry : cda.getChildren(section, "entry")) {
Element observation = cda.getlastChild(entry);
if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.38")) {
processSocialObservation(list, observation, SocialHistoryType.SocialHistory);
} else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.15.3.8")) {
processSocialObservation(list, observation, SocialHistoryType.Pregnancy);
} else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.78")) {
processSocialObservation(list, observation, SocialHistoryType.SmokingStatus);
} else if (cda.hasTemplateId(observation, "2.16.840.1.113883.10.20.22.4.85")) {
processSocialObservation(list, observation, SocialHistoryType.TobaccoUse);
} else
throw new Exception("Unhandled Section template ids: "+cda.showTemplateIds(observation));
}
// todo: text
SectionComponent s = new Composition.SectionComponent();
s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
// todo: check subject
s.addEntry(Factory.makeReference(addReference(list, "Procedures", makeUUIDReference())));
return s;
}
protected void processSocialObservation(ListResource list, Element so, SocialHistoryType type) throws Exception {
Observation obs = new Observation();
addItemToList(list, obs);
switch (type) {
case SocialHistory :
cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.38");
// SHALL contain exactly one [1..1] code (CONF:8558/).
obs.setCode(convert.makeCodeableConceptFromCD(cda.getChild(so, "code")));
break;
case Pregnancy:
cda.checkTemplateId(so, "2.16.840.1.113883.10.20.15.3.8");
// SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
obs.setCode(Factory.newCodeableConcept("11449-6", "http://loinc.org", "Pregnancy Status"));
break;
case SmokingStatus:
cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.78");
// SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
obs.setCode(Factory.newCodeableConcept("72166-2", "http://loinc.org", "Tobacco Smoking Status"));
break;
case TobaccoUse:
cda.checkTemplateId(so, "2.16.840.1.113883.10.20.22.4.12");
// SHALL contain exactly one [1..1] code (CONF:8558/), which SHALL be an assertion
obs.setCode(Factory.newCodeableConcept("11367-0", "http://loinc.org", "History of Tobacco Use"));
}
// SHALL contain at least one [1..*] id (8551).
for (Element e : cda.getChildren(so, "id"))
obs.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] statusCode (CONF:8553/455/14809).
// a. This statusCode SHALL contain exactly one [1..1] @code="completed" Completed (CodeSystem: ActStatus 2.16.840.1.113883.5.14 STATIC) (CONF:19117).
obs.setStatus(ObservationStatus.FINAL);
// SHOULD contain zero or one [0..1] effectiveTime (CONF:2018/14814).
// for smoking status/tobacco: low only. in R2, this is just value. So we treat low only as just a value
Element et = cda.getChild(so, "effectiveTime");
if (et != null) {
if (cda.getChild(et, "low") != null)
obs.setEffective(convert.makeDateTimeFromTS(cda.getChild(et, "low")));
else
obs.setEffective(convert.makeDateTimeFromIVL(et));
}
// SHOULD contain zero or one [0..1] value (CONF:8559).
// a. Observation/value can be any data type.
for (Element e : cda.getChildren(so, "value"))
if (obs.getValue() == null) { // only one in FHIR
// special case for pregnancy:
if (type == SocialHistoryType.Pregnancy && "true".equals(e.getAttribute("negationInd"))) {
obs.setValue(Factory.newCodeableConcept("60001007", "http://snomed.info/sct", "Not pregnant"));
} else {
// negationInd is not described. but it might well be used. For now, we blow up
checkNoNegation(so, "Social Observation ("+type.toString()+")");
if (so.hasAttribute("nullFlavor"))
obs.setValue(convert.makeCodeableConceptFromNullFlavor(so.getAttribute("nullFlavor")));
else if (e.hasAttribute("nullFlavor") && !"OTH".equals(e.getAttribute("nullFlavor")))
obs.setValue(convert.makeCodeableConceptFromNullFlavor(e.getAttribute("nullFlavor")));
else
obs.setValue(convert.makeTypeFromANY(e));
}
} else
throw new Exception("too many values on Social Observation");
if (type == SocialHistoryType.Pregnancy) {
for (Element e : cda.getChildren(so, "entyRelationship")) {
Element dd = cda.getChild(e, "observation");
checkNoNegationOrNullFlavor(dd, "Estimated Date of Delivery");
// MAY contain zero or one [0..1] entryRelationship (CONF:458) such that it
// SHALL contain exactly one [1..1] @typeCode="REFR" Refers to (CodeSystem: HL7ActRelationshipType 2.16.840.1.113883.5.1002 STATIC) (CONF:459).
// SHALL contain exactly one [1..1] Estimated Date of Delivery (templateId:2.16.840.1.113883.10.20.15.3.1) (CONF:15584).
Observation co = new Observation();
String id = nextRef();
co.setId(id);
obs.getContained().add(co);
ObservationRelatedComponent or = new ObservationRelatedComponent();
obs.getRelated().add(or);
or.setType(ObservationRelationshipType.HASMEMBER);
or.setTarget(Factory.makeReference("#"+id));
co.setCode(Factory.newCodeableConcept("11778-8", "http://loinc.org", "Delivery date Estimated"));
co.setValue(convert.makeDateTimeFromTS(cda.getChild(dd, "value"))); // not legal, see gForge http://gforge.hl7.org/gf/project/fhir/tracker/?action=TrackerItemEdit&tracker_item_id=3125&start=0
}
}
}
protected void checkNoNegation(Element act, String path) throws Exception {
if ("true".equals(act.getAttribute("negationInd")))
throw new Exception("The conversion program cannot accept a negationInd at the location "+path);
}
protected void checkNoNegationOrNullFlavor(Element act, String path) throws Exception {
if (act.hasAttribute("nullFlavor"))
throw new Exception("The conversion program cannot accept a nullFlavor at the location "+path);
if ("true".equals(act.getAttribute("negationInd")))
throw new Exception("The conversion program cannot accept a negationInd at the location "+path);
}
protected ListEntryComponent addItemToList(ListResource list, DomainResource ai)
throws Exception {
list.getContained().add(ai);
String n = nextRef();
ai.setId(n);
ListEntryComponent item = new ListResource.ListEntryComponent();
list.getEntry().add(item);
item.setItem(Factory.makeReference("#"+n));
return item;
}
protected String nextRef() {
refCounter++;
String n = refCounter.toString();
return n;
}
protected AllergyIntoleranceCriticality readCriticality(String severity) {
if ("255604002".equals(severity)) // Mild
return AllergyIntoleranceCriticality.LOW;
if ("371923003".equals(severity)) // Mild to moderate
return AllergyIntoleranceCriticality.LOW;
if ("6736007".equals(severity)) // Moderate
return AllergyIntoleranceCriticality.LOW;
if ("371924009".equals(severity)) // Moderate to severe
return AllergyIntoleranceCriticality.HIGH;
if ("24484000".equals(severity)) // Severe
return AllergyIntoleranceCriticality.HIGH;
if ("399166001".equals(severity)) // Fatal
return AllergyIntoleranceCriticality.HIGH;
return null;
}
protected AllergyIntoleranceSeverity readSeverity(String severity) {
if ("255604002".equals(severity)) // Mild
return AllergyIntoleranceSeverity.MILD;
if ("371923003".equals(severity)) // Mild to moderate
return AllergyIntoleranceSeverity.MODERATE;
if ("6736007".equals(severity)) // Moderate
return AllergyIntoleranceSeverity.MODERATE;
if ("371924009".equals(severity)) // Moderate to severe
return AllergyIntoleranceSeverity.SEVERE;
if ("24484000".equals(severity)) // Severe
return AllergyIntoleranceSeverity.SEVERE;
if ("399166001".equals(severity)) // Fatal
return AllergyIntoleranceSeverity.SEVERE;
return null;
}
protected SectionComponent processVitalSignsSection(Element section) throws Exception {
ListResource list = new ListResource();
for (Element entry : cda.getChildren(section, "entry")) {
Element organizer = cda.getlastChild(entry);
if (cda.hasTemplateId(organizer, "2.16.840.1.113883.10.20.22.4.26")) {
processVitalSignsOrganizer(list, organizer);
} else
throw new Exception("Unhandled Section template ids: "+cda.showTemplateIds(organizer));
}
// todo: text
SectionComponent s = new Composition.SectionComponent();
s.setCode(convert.makeCodeableConceptFromCD(cda.getChild(section, "code")));
// todo: check subject
s.addEntry(Factory.makeReference(addReference(list, "Vital Signs", makeUUIDReference())));
return s;
}
protected void processVitalSignsOrganizer(ListResource list, Element organizer) throws Exception {
cda.checkTemplateId(organizer, "2.16.840.1.113883.10.20.22.4.26");
checkNoNegationOrNullFlavor(organizer, "Vital Signs Organizer");
checkNoSubject(organizer, "Vital Signs Organizer");
// moodCode is EVN.
Observation obs = new Observation();
addItemToList(list, obs);
// SHALL contain at least one [1..*] id (CONF:7282).
for (Element e : cda.getChildren(organizer, "id"))
obs.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] code (CONF:19176).
// This code SHALL contain exactly one [1..1] @code="46680005" Vital signs (CodeSystem: SNOMED-CT 2.16.840.1.113883.6.96 STATIC) (CONF:19177).
obs.setCode(convert.makeCodeableConceptFromCD(cda.getChild(organizer, "code")));
// SHALL contain exactly one [1..1] effectiveTime (CONF:7288).
obs.setEffective(convert.makeMatchingTypeFromIVL(cda.getChild(organizer, "effectiveTime")));
// SHALL contain at least one [1..*] component (CONF:7285) such that it
// SHALL contain exactly one [1..1] Vital Sign Observation (templateId:2.16.840.1.113883.10.20.22.4.27) (CONF:15946).
for (Element e : cda.getChildren(organizer, "component")){
ObservationRelatedComponent ro = new ObservationRelatedComponent();
ro.setType(ObservationRelationshipType.HASMEMBER);
ro.setTarget(Factory.makeReference("#"+processVitalSignsObservation(e, list)));
}
}
protected String processVitalSignsObservation(Element comp, ListResource list) throws Exception {
Element observation = cda.getChild(comp, "observation");
cda.checkTemplateId(observation, "2.16.840.1.113883.10.20.22.4.27");
checkNoNegationOrNullFlavor(observation, "Vital Signs Observation");
checkNoSubject(observation, "Vital Signs Observation");
Observation obs = new Observation();
// SHALL contain at least one [1..*] id (CONF:7300).
for (Element e : cda.getChildren(observation, "id"))
obs.getIdentifier().add(convert.makeIdentifierFromII(e));
// SHALL contain exactly one [1..1] code, which SHOULD be selected from ValueSet Vital Sign Result Value Set 2.16.840.1.113883.3.88.12.80.62 DYNAMIC (CONF:7301).
obs.setCode(convert.makeCodeableConceptFromCD(cda.getChild(observation, "code"))); // all loinc codes
// SHOULD contain zero or one [0..1] text (CONF:7302).
// The text, if present, SHOULD contain zero or one [0..1] reference (CONF:15943).
// The reference, if present, SHOULD contain zero or one [0..1] @value (CONF:15944).
// This reference/@value SHALL begin with a '#' and SHALL point to its corresponding narrative (using the approach defined in CDA Release 2, section 4.3.5.1) (CONF:15945).
// todo: put this in narrative if it exists?
// SHALL contain exactly one [1..1] statusCode (CONF:7303). This statusCode SHALL contain exactly one [1..1] @code="completed" Completed (CodeSystem: ActStatus 2.16.840.1.113883.5.14 STATIC) (CONF:19119).
// ignore
// SHALL contain exactly one [1..1] effectiveTime (CONF:7304).
obs.setEffective(convert.makeMatchingTypeFromIVL(cda.getChild(observation, "effectiveTime")));
// SHALL contain exactly one [1..1] value with @xsi:type="PQ" (CONF:7305).
obs.setValue(convert.makeQuantityFromPQ(cda.getChild(observation, "value")));
// MAY contain zero or one [0..1] interpretationCode (CONF:7307).
obs.setInterpretation(convert.makeCodeableConceptFromCD(cda.getChild(observation, "interpretationCode")));
// MAY contain zero or one [0..1] methodCode (CONF:7308).
obs.setMethod(convert.makeCodeableConceptFromCD(cda.getChild(observation, "methodCode")));
// MAY contain zero or one [0..1] targetSiteCode (CONF:7309).
obs.setBodySite(convert.makeCodeableConceptFromCD(cda.getChild(observation, "targetSiteCode")));
// MAY contain zero or one [0..1] author (CONF:7310).
if (cda.getChild(observation, "author") != null)
obs.getPerformer().add(makeReferenceToPractitionerForAssignedEntity(cda.getChild(observation, "author"), composition));
// make a contained practitioner
String n = nextRef();
obs.setId(n);
list.getContained().add(obs);
return n;
}
}