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org.hl7.fhir.core
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Merge branch 'master' of https://github.com/hapifhir/org.hl7.fhir.core

This commit is contained in:
Grahame Grieve 2019-07-10 22:40:52 +00:00
parent da4fc1f860 881fdc9284
commit 17b6b26ef2
27 changed files with 912 additions and 126 deletions
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57
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_40.java
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@ -8258,6 +8258,9 @@ public class VersionConvertor_30_40 {
tgt.addNote(convertAnnotation(t));
return tgt;
}
private static final String CODE_SYSTEM_CONDITION_CLINICAL_URL = "http://terminology.hl7.org/CodeSystem/condition-clinical";
private static final String CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL = "http://hl7.org/fhir/condition-clinical";
private static org.hl7.fhir.r4.model.CodeableConcept convertConditionClinicalStatus(org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus src) throws FHIRException {
if (src == null)
@ -8265,19 +8268,19 @@ public class VersionConvertor_30_40 {
org.hl7.fhir.r4.model.CodeableConcept cc = new org.hl7.fhir.r4.model.CodeableConcept();
switch (src) {
case ACTIVE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("active");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("active");
return cc;
case RECURRENCE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("recurrence");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("recurrence");
return cc;
case INACTIVE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("inactive");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("inactive");
return cc;
case REMISSION:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("remission");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("remission");
return cc;
case RESOLVED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("resolved");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("resolved");
return cc;
default: return null;
}
@ -8286,33 +8289,41 @@ public class VersionConvertor_30_40 {
private static org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus convertConditionClinicalStatus(org.hl7.fhir.r4.model.CodeableConcept src) throws FHIRException {
if (src == null)
return null;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "active")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.ACTIVE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "recurrence")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RECURRENCE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "inactive")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.INACTIVE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "remission")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.REMISSION;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "resolved")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RESOLVED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "active")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "active")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.ACTIVE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "recurrence")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "recurrence")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RECURRENCE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "inactive")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "inactive")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.INACTIVE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "remission")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "remission")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.REMISSION;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "resolved")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "resolved")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RESOLVED;
return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.NULL;
}
private static final String CODE_SYSTEM_CONDITION_VER_CLINICAL_URL = "http://terminology.hl7.org/CodeSystem/condition-ver-status";
private static final String CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL = "http://hl7.org/fhir/condition-ver-status";
private static org.hl7.fhir.r4.model.CodeableConcept convertConditionVerificationStatus(org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus src) throws FHIRException {
if (src == null)
return null;
org.hl7.fhir.r4.model.CodeableConcept cc = new org.hl7.fhir.r4.model.CodeableConcept();
switch (src) {
case PROVISIONAL:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("provisional");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("provisional");
return cc;
case DIFFERENTIAL:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("differential");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("differential");
return cc;
case CONFIRMED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("confirmed");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("confirmed");
return cc;
case REFUTED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("refuted");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("refuted");
return cc;
case ENTEREDINERROR:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("entered-in-error");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("entered-in-error");
return cc;
default: return null;
}
@ -8321,15 +8332,19 @@ public class VersionConvertor_30_40 {
private static org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus convertConditionVerificationStatus(org.hl7.fhir.r4.model.CodeableConcept src) throws FHIRException {
if (src == null)
return null;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "provisional")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.PROVISIONAL;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "differential")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.DIFFERENTIAL;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "confirmed")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.CONFIRMED;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "refuted")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.REFUTED;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "entered-in-error")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.ENTEREDINERROR;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "provisional")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "provisional")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.PROVISIONAL;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "differential")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "differential")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.DIFFERENTIAL;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "confirmed")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "confirmed")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.CONFIRMED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "refuted")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "refuted")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.REFUTED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "entered-in-error")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "entered-in-error")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.ENTEREDINERROR;
return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.NULL;
}
public static org.hl7.fhir.r4.model.Condition.ConditionStageComponent convertConditionStageComponent(org.hl7.fhir.dstu3.model.Condition.ConditionStageComponent src) throws FHIRException {
if (src == null)
return null;

57
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/VersionConvertor_30_50.java
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@ -8249,25 +8249,28 @@ public class VersionConvertor_30_50 {
return tgt;
}
private static final String CODE_SYSTEM_CONDITION_CLINICAL_URL = "http://terminology.hl7.org/CodeSystem/condition-clinical";
private static final String CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL = "http://hl7.org/fhir/condition-clinical";
private static org.hl7.fhir.r5.model.CodeableConcept convertConditionClinicalStatus(org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus src) throws FHIRException {
if (src == null)
return null;
org.hl7.fhir.r5.model.CodeableConcept cc = new org.hl7.fhir.r5.model.CodeableConcept();
switch (src) {
case ACTIVE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("active");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("active");
return cc;
case RECURRENCE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("recurrence");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("recurrence");
return cc;
case INACTIVE:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("inactive");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("inactive");
return cc;
case REMISSION:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("remission");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("remission");
return cc;
case RESOLVED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-clinical").setCode("resolved");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_CLINICAL_URL).setCode("resolved");
return cc;
default: return null;
}
@ -8276,33 +8279,41 @@ public class VersionConvertor_30_50 {
private static org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus convertConditionClinicalStatus(org.hl7.fhir.r5.model.CodeableConcept src) throws FHIRException {
if (src == null)
return null;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "active")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.ACTIVE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "recurrence")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RECURRENCE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "inactive")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.INACTIVE;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "remission")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.REMISSION;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "resolved")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RESOLVED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "active")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "active")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.ACTIVE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "recurrence")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "recurrence")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RECURRENCE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "inactive")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "inactive")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.INACTIVE;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "remission")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "remission")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.REMISSION;
if (src.hasCoding(CODE_SYSTEM_CONDITION_CLINICAL_URL, "resolved")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_CLINICAL_URL, "resolved")) return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.RESOLVED;
return org.hl7.fhir.dstu3.model.Condition.ConditionClinicalStatus.NULL;
}
private static final String CODE_SYSTEM_CONDITION_VER_CLINICAL_URL = "http://terminology.hl7.org/CodeSystem/condition-ver-status";
private static final String CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL = "http://hl7.org/fhir/condition-ver-status";
private static org.hl7.fhir.r5.model.CodeableConcept convertConditionVerificationStatus(org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus src) throws FHIRException {
if (src == null)
return null;
org.hl7.fhir.r5.model.CodeableConcept cc = new org.hl7.fhir.r5.model.CodeableConcept();
switch (src) {
case PROVISIONAL:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("provisional");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("provisional");
return cc;
case DIFFERENTIAL:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("differential");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("differential");
return cc;
case CONFIRMED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("confirmed");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("confirmed");
return cc;
case REFUTED:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("refuted");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("refuted");
return cc;
case ENTEREDINERROR:
cc.addCoding().setSystem("http://hl7.org/fhir/condition-ver-status").setCode("entered-in-error");
cc.addCoding().setSystem(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL).setCode("entered-in-error");
return cc;
default: return null;
}
@ -8311,15 +8322,19 @@ public class VersionConvertor_30_50 {
private static org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus convertConditionVerificationStatus(org.hl7.fhir.r5.model.CodeableConcept src) throws FHIRException {
if (src == null)
return null;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "provisional")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.PROVISIONAL;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "differential")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.DIFFERENTIAL;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "confirmed")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.CONFIRMED;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "refuted")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.REFUTED;
if (src.hasCoding("http://hl7.org/fhir/condition-clinical", "entered-in-error")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.ENTEREDINERROR;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "provisional")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "provisional")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.PROVISIONAL;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "differential")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "differential")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.DIFFERENTIAL;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "confirmed")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "confirmed")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.CONFIRMED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "refuted")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "refuted")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.REFUTED;
if (src.hasCoding(CODE_SYSTEM_CONDITION_VER_CLINICAL_URL, "entered-in-error")
||src.hasCoding(CODE_SYSTEM_LEGACY_CONDITION_VER_CLINICAL_URL, "entered-in-error")) return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.ENTEREDINERROR;
return org.hl7.fhir.dstu3.model.Condition.ConditionVerificationStatus.NULL;
}
public static org.hl7.fhir.r5.model.Condition.ConditionStageComponent convertConditionStageComponent(org.hl7.fhir.dstu3.model.Condition.ConditionStageComponent src) throws FHIRException {
if (src == null)
return null;

297
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/SearchParameterProcessor.java Normal file
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@ -0,0 +1,297 @@
package org.hl7.fhir.convertors.misc;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import org.hl7.fhir.convertors.misc.SearchParameterProcessor.SPRelationship;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.exceptions.FHIRFormatError;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.JsonParser;
import org.hl7.fhir.r5.model.ConceptMap;
import org.hl7.fhir.r5.model.ConceptMap.ConceptMapGroupComponent;
import org.hl7.fhir.r5.model.ConceptMap.SourceElementComponent;
import org.hl7.fhir.r5.model.Enumerations.ConceptMapEquivalence;
import org.hl7.fhir.r5.model.Enumerations.PublicationStatus;
import org.hl7.fhir.utilities.CSVReader;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
public class SearchParameterProcessor {
public class SPRelationship {
private String r4;
private String r3;
private String r2b;
private String r2;
public SPRelationship(String r4, String r3, String r2b, String r2) {
super();
this.r4 = r4;
this.r3 = r3;
this.r2b = r2b;
this.r2 = r2;
}
public String getR4() {
return r4;
}
public String getR3() {
return r3;
}
public String getR2b() {
return r2b;
}
public String getR2() {
return r2;
}
public String getByCode(String code) {
if ("R4".equals(code))
return r4;
if ("R3".equals(code))
return r3;
if ("R2b".equals(code))
return r2b;
if ("R2".equals(code))
return r2;
return null;
}
}
private static final String ROOT = "C:\\work\\org.hl7.fhir\\org.fhir.interversion\\package";
private List<SPRelationship> list = new ArrayList<>();
private List<String> list4 = new ArrayList<>();
private List<String> list3 = new ArrayList<>();
private List<String> list2 = new ArrayList<>();
private List<String> list2b = new ArrayList<>();
private void load() throws FileNotFoundException, IOException, FHIRException {
load4();
load3();
load2b();
load2();
loadCsv();
check4();
check3();
check2b();
check2();
generate("R3", "R4", "STU3", "R4");
generate("R4", "R3", "R4", "STU3");
generate("R2", "R4", "DSTU2", "R4");
generate("R4", "R2", "R4", "DSTU2");
generate("R2", "R3", "DSTU2", "STU3");
generate("R3", "R2", "STU3", "DSTU2");
}
private void generate(String src, String dst, String srcURL, String tgtURL) throws FileNotFoundException, IOException {
ConceptMap map = new ConceptMap();
map.setId("search-parameters-"+src+"-to-"+dst);
map.setUrl("http://hl7.org/fhir/interversion/ConceptMap/"+map.getId());
map.setName("SearchParameterMap"+src+dst);
map.setTitle("Search Parameter Map - "+src+" to "+dst);
map.setStatus(PublicationStatus.DRAFT);
map.setDate(new Date());
map.setExperimental(false);
map.setPublisher("HL7");
ConceptMapGroupComponent group = map.addGroup();
group.setSource("http://hl7.org/fhir/"+srcURL);
group.setTarget("http://hl7.org/fhir/"+tgtURL);
for (SPRelationship sp : list) {
String s = sp.getByCode(src);
String d = sp.getByCode(dst);
if (!Utilities.noString(s) && !Utilities.noString(d)) {
SourceElementComponent e = makeElement(s, group);
e.addTarget().setCode(d).setEquivalence(ConceptMapEquivalence.RELATEDTO);
}
}
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(ROOT, "ConceptMap-"+map.getId()+".json")), map);
}
private SourceElementComponent makeElement(String code, ConceptMapGroupComponent group) {
for (SourceElementComponent e : group.getElement()) {
if (e.getCode().equals(code))
return e;
}
return group.addElement().setCode(code);
}
private void check4() {
for (String s : list4) {
boolean ok = false;
for (SPRelationship t : list) {
if (s.equals(t.r4))
ok = true;
}
if (!ok)
System.out.println("R4 missing : "+s);
}
for (SPRelationship sp : list) {
if (!Utilities.noString(sp.r4)) {
boolean ok = list4.contains(sp.r4);
if (!ok)
System.out.println("R4 extra : "+sp.r4);
}
}
}
private void check3() {
for (String s : list3) {
boolean ok = false;
for (SPRelationship t : list) {
if (s.equals(t.r3))
ok = true;
}
if (!ok)
System.out.println("R3 : "+s);
}
for (SPRelationship sp : list) {
if (!Utilities.noString(sp.r3)) {
boolean ok = list3.contains(sp.r3);
if (!ok)
System.out.println("R3 extra : "+sp.r3);
}
}
}
private void check2b() {
for (String s : list2b) {
boolean ok = false;
for (SPRelationship t : list) {
if (s.equals(t.r2b))
ok = true;
}
if (!ok)
System.out.println("R2b : "+s);
}
for (SPRelationship sp : list) {
if (!Utilities.noString(sp.r2b)) {
boolean ok = list2b.contains(sp.r2b);
if (!ok)
System.out.println("R2b extra : "+sp.r2b);
}
}
}
private void check2() {
for (String s : list2) {
boolean ok = false;
for (SPRelationship t : list) {
if (s.equals(t.r2))
ok = true;
}
if (!ok)
System.out.println("R2 : "+s);
}
for (SPRelationship sp : list) {
if (!Utilities.noString(sp.r2)) {
boolean ok = list2.contains(sp.r2);
if (!ok)
System.out.println("R2 extra : "+sp.r2);
}
}
}
private void load4() throws FHIRFormatError, FileNotFoundException, IOException {
org.hl7.fhir.r4.model.Bundle bundle = (org.hl7.fhir.r4.model.Bundle) new org.hl7.fhir.r4.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp4.json"));
for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.r4.model.SearchParameter sp = (org.hl7.fhir.r4.model.SearchParameter) be.getResource();
for (org.hl7.fhir.r4.model.CodeType br : sp.getBase()) {
if (!Utilities.existsInList(br.asStringValue(), "DomainResource", "Resource"))
list4.add(br.asStringValue()+"."+sp.getCode());//+", "+sp.getType().toCode());
}
}
Collections.sort(list4);
System.out.println("R4 loaded - "+list4.size()+" parameters");
}
private void load3() throws FHIRFormatError, FileNotFoundException, IOException {
org.hl7.fhir.dstu3.model.Bundle bundle = (org.hl7.fhir.dstu3.model.Bundle) new org.hl7.fhir.dstu3.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp3.json"));
for (org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu3.model.SearchParameter sp = (org.hl7.fhir.dstu3.model.SearchParameter) be.getResource();
for (org.hl7.fhir.dstu3.model.CodeType br : sp.getBase()) {
if (!Utilities.existsInList(br.asStringValue(), "DomainResource", "Resource"))
list3.add(br.asStringValue()+"."+sp.getCode());//+", "+sp.getType().toCode());
}
}
Collections.sort(list3);
System.out.println("R3 loaded - "+list3.size()+" parameters");
}
private void load2() throws FHIRFormatError, FileNotFoundException, IOException {
org.hl7.fhir.dstu2.model.Bundle bundle = (org.hl7.fhir.dstu2.model.Bundle) new org.hl7.fhir.dstu2.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp2.json"));
for (org.hl7.fhir.dstu2.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu2.model.SearchParameter sp = (org.hl7.fhir.dstu2.model.SearchParameter) be.getResource();
String br = sp.getBase();
if (!Utilities.existsInList(br, "DomainResource", "Resource"))
list2.add(br+"."+sp.getCode());//+", "+sp.getType().toCode());
}
Collections.sort(list2);
System.out.println("R2 loaded - "+list2.size()+" parameters");
}
private void load2b() throws FHIRFormatError, FileNotFoundException, IOException {
org.hl7.fhir.dstu2016may.model.Bundle bundle = (org.hl7.fhir.dstu2016may.model.Bundle) new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(new FileInputStream("c:\\temp\\sp2b.json"));
for (org.hl7.fhir.dstu2016may.model.Bundle.BundleEntryComponent be : bundle.getEntry()) {
org.hl7.fhir.dstu2016may.model.SearchParameter sp = (org.hl7.fhir.dstu2016may.model.SearchParameter) be.getResource();
String br = sp.getBase();
if (!Utilities.existsInList(br, "DomainResource", "Resource"))
list2b.add(br+"."+sp.getCode());//+", "+sp.getType().toCode());
}
Collections.sort(list2b);
System.out.println("R2b loaded - "+list2b.size()+" parameters");
}
private void loadCsv() throws IOException, FHIRException {
CSVReader csv = new CSVReader(new FileInputStream("C:\\work\\org.hl7.fhir\\org.fhir.interversion\\work\\search-params.csv"));
csv.readHeaders();
while (csv.line()) {
String r4 = csv.cell("R4");
String r3 = csv.cell("R3");
String r2b = csv.cell("R2b");
String r2 = csv.cell("R2");
if (!Utilities.noString(r4) || !Utilities.noString(r3) || !Utilities.noString(r2b) || !Utilities.noString(r2)) {
boolean ok = (!Utilities.noString(r4) && r4.contains(".")) ||
(!Utilities.noString(r3) && r3.contains(".")) ||
(!Utilities.noString(r2b) && r2b.contains(".")) ||
(!Utilities.noString(r2) && r2.contains("."));
if (ok) {
list.add(new SPRelationship(r4, r3, r2b, r2));
}
}
}
System.out.println("Map loaded - "+list.size()+" entries");
}
// private void generate(String name) throws IOException {
// StringBuilder b = new StringBuilder();
//
// String rn = "";
// Collections.sort(list);
// for (String s : list) {
// String rnn = s.substring(0, s.indexOf("."));
// if (!rnn.equals(rn)) {
// rn = rnn;
// b.append(rn+"\r\n");
// }
// b.append(s+"\r\n");
// }
// TextFile.stringToFile(b.toString(), name);
// }
//
public static void main(String[] args) throws FileNotFoundException, IOException, FHIRException {
new SearchParameterProcessor().load();
}
}

3
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/OperationOutcomeUtilities.java
View File

@ -27,6 +27,7 @@ import org.hl7.fhir.dstu2.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu2.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu2.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.dstu2.model.StringType;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class OperationOutcomeUtilities {
@ -37,7 +38,7 @@ public class OperationOutcomeUtilities {
issue.setCode(convert(message.getType()));
if (message.getLocation() != null) {
StringType s = new StringType();
s.setValue(message.getLocation()+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
s.setValue(Utilities.fhirPathToXPath(message.getLocation())+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
issue.getLocation().add(s);
}
issue.setSeverity(convert(message.getLevel()));

6
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/utils/OperationOutcomeUtilities.java
View File

@ -27,6 +27,7 @@ import org.hl7.fhir.dstu3.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.dstu3.model.OperationOutcome.IssueType;
import org.hl7.fhir.dstu3.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class OperationOutcomeUtilities {
@ -36,8 +37,11 @@ public class OperationOutcomeUtilities {
OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
issue.setCode(convert(message.getType()));
if (message.getLocation() != null) {
// message location has a fhirPath in it. We need to populate the expression
issue.addExpression(message.getLocation());
// also, populate the XPath variant
StringType s = new StringType();
s.setValue(message.getLocation()+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
s.setValue(Utilities.fhirPathToXPath(message.getLocation())+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
issue.getLocation().add(s);
}
issue.setSeverity(convert(message.getLevel()));

1
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/context/SimpleWorkerContext.java
View File

@ -289,6 +289,7 @@ public class SimpleWorkerContext extends BaseWorkerContext implements IWorkerCon
}
}
}
this.version = pi.version();
}
public void loadFromFile(String file, IContextResourceLoader loader) throws IOException, FHIRException {

9
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/model/XhtmlType.java
View File

@ -73,8 +73,13 @@ public class XhtmlType extends Element {
@Override
public Base setProperty(int hash, String name, Base value) throws FHIRException {
if ("value".equals(name)) {
place.setDiv(castToXhtml(value));
return value;
if (value instanceof StringType) {
// div is already generated with getValue, we cannot just overwrite it
place.getDiv().setValueAsString(((StringType) value).asStringValue());
} else {
place.setDiv(castToXhtml(value));
}
return value;
} else
return super.setProperty(hash, name, value);
}

2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/FHIRPathEngine.java
View File

@ -2889,7 +2889,7 @@ public class FHIRPathEngine {
if (!Utilities.noString(f)) {
if (exp.getParameters().size() != 2) {
if (exp.getParameters().size() == 2) {
String t = convertToString(execute(context, focus, exp.getParameters().get(0), true));
String r = convertToString(execute(context, focus, exp.getParameters().get(1), true));

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/OperationOutcomeUtilities.java
View File

@ -27,6 +27,7 @@ import org.hl7.fhir.r4.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.r4.model.OperationOutcome.IssueType;
import org.hl7.fhir.r4.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class OperationOutcomeUtilities {
@ -36,8 +37,11 @@ public class OperationOutcomeUtilities {
OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
issue.setCode(convert(message.getType()));
if (message.getLocation() != null) {
// message location has a fhirPath in it. We need to populate the expression
issue.addExpression(message.getLocation());
// also, populate the XPath variant
StringType s = new StringType();
s.setValue(message.getLocation()+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
s.setValue(Utilities.fhirPathToXPath(message.getLocation())+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
issue.getLocation().add(s);
}
issue.setSeverity(convert(message.getLevel()));

6
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/utils/StructureMapUtilities.java
View File

@ -1402,7 +1402,7 @@ public class StructureMapUtilities {
}
} else if (rule.getSource().size() == 1 && rule.getSourceFirstRep().hasVariable() && rule.getTarget().size() == 1 && rule.getTargetFirstRep().hasVariable() && rule.getTargetFirstRep().getTransform() == StructureMapTransform.CREATE && !rule.getTargetFirstRep().hasParameter()) {
// simple inferred, map by type
System.out.println(v.summary());
log(v.summary());
Base src = v.get(VariableMode.INPUT, rule.getSourceFirstRep().getVariable());
Base tgt = v.get(VariableMode.OUTPUT, rule.getTargetFirstRep().getVariable());
String srcType = src.fhirType();
@ -1493,7 +1493,9 @@ public class StructureMapUtilities {
if (value.contains("*")) {
for (StructureMap sm : worker.listTransforms()) {
if (urlMatches(value, sm.getUrl())) {
res.add(sm);
if (!res.contains(sm)) {
res.add(sm);
}
}
}
} else {

1
org.hl7.fhir.r4/src/test/java/org/hl7/fhir/r4/test/SnapShotGenerationTests.java
View File

@ -277,6 +277,7 @@ public class SnapShotGenerationTests {
@Parameters(name = "{index}: file {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, IOException, FHIRFormatError {
SnapShotGenerationTestsContext context = new SnapShotGenerationTestsContext();
System.out.println("Snapshot tests using "+TestingUtilities.resourceNameToFile("snapshot-generation-tests.xml"));
context.tests = (TestScript) new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("snapshot-generation-tests.xml")));
context.checkTestsDetails();

4
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ExpressionNode.java
View File

@ -61,7 +61,7 @@ public class ExpressionNode {
Empty, Not, Exists, SubsetOf, SupersetOf, IsDistinct, Distinct, Count, Where, Select, All, Repeat, Aggregate, Item /*implicit from name[]*/, As, Is, Single,
First, Last, Tail, Skip, Take, Union, Combine, Intersect, Exclude, Iif, Upper, Lower, ToChars, Substring, StartsWith, EndsWith, Matches, ReplaceMatches, Contains, Replace, Length,
Children, Descendants, MemberOf, Trace, Today, Now, Resolve, Extension, AllFalse, AnyFalse, AllTrue, AnyTrue,
Children, Descendants, MemberOf, Trace, Check, Today, Now, Resolve, Extension, AllFalse, AnyFalse, AllTrue, AnyTrue,
HasValue, AliasAs, Alias, HtmlChecks, OfType, Type,
ConvertsToBoolean, ConvertsToInteger, ConvertsToString, ConvertsToDecimal, ConvertsToQuantity, ConvertsToDateTime, ConvertsToTime, ToBoolean, ToInteger, ToString, ToDecimal, ToQuantity, ToDateTime, ToTime, ConformsTo;
@ -108,6 +108,7 @@ public class ExpressionNode {
if (name.equals("descendants")) return Function.Descendants;
if (name.equals("memberOf")) return Function.MemberOf;
if (name.equals("trace")) return Function.Trace;
if (name.equals("check")) return Function.Check;
if (name.equals("today")) return Function.Today;
if (name.equals("now")) return Function.Now;
if (name.equals("resolve")) return Function.Resolve;
@ -183,6 +184,7 @@ public class ExpressionNode {
case Descendants : return "descendants";
case MemberOf : return "memberOf";
case Trace : return "trace";
case Check : return "check";
case Today : return "today";
case Now : return "now";
case Resolve : return "resolve";

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/XhtmlType.java
View File

@ -25,6 +25,7 @@ import java.io.IOException;
import java.util.List;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.utilities.xhtml.NodeType;
import org.hl7.fhir.utilities.xhtml.XhtmlComposer;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
@ -72,7 +73,12 @@ public class XhtmlType extends Element {
@Override
public Base setProperty(int hash, String name, Base value) throws FHIRException {
if ("value".equals(name)) {
place.setDiv(castToXhtml(value));
if (value instanceof StringType) {
// div is already generated with getValue, we cannot just overwrite it
place.getDiv().setValueAsString(((StringType) value).asStringValue());
} else {
place.setDiv(castToXhtml(value));
}
return value;
} else
return super.setProperty(hash, name, value);

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/FHIRPathEngine.java
View File

@ -1110,6 +1110,7 @@ public class FHIRPathEngine {
case Descendants: return checkParamCount(lexer, location, exp, 0);
case MemberOf: return checkParamCount(lexer, location, exp, 1);
case Trace: return checkParamCount(lexer, location, exp, 1, 2);
case Check: return checkParamCount(lexer, location, exp, 2);
case Today: return checkParamCount(lexer, location, exp, 0);
case Now: return checkParamCount(lexer, location, exp, 0);
case Resolve: return checkParamCount(lexer, location, exp, 0);
@ -2549,6 +2550,10 @@ public class FHIRPathEngine {
checkParamTypes(exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return focus;
}
case Check : {
checkParamTypes(exp.getFunction().toCode(), paramTypes, new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_String));
return focus;
}
case Today :
return new TypeDetails(CollectionStatus.SINGLETON, TypeDetails.FP_DateTime);
case Now :
@ -2741,6 +2746,7 @@ public class FHIRPathEngine {
case Descendants : return funcDescendants(context, focus, exp);
case MemberOf : return funcMemberOf(context, focus, exp);
case Trace : return funcTrace(context, focus, exp);
case Check : return funcCheck(context, focus, exp);
case Today : return funcToday(context, focus, exp);
case Now : return funcNow(context, focus, exp);
case Resolve : return funcResolve(context, focus, exp);
@ -2896,7 +2902,7 @@ public class FHIRPathEngine {
if (!Utilities.noString(f)) {
if (exp.getParameters().size() != 2) {
if (exp.getParameters().size() == 2) {
String t = convertToString(execute(context, focus, exp.getParameters().get(0), true));
String r = convertToString(execute(context, focus, exp.getParameters().get(1), true));
@ -3484,6 +3490,16 @@ public class FHIRPathEngine {
return focus;
}
private List<Base> funcCheck(ExecutionContext context, List<Base> focus, ExpressionNode exp) throws FHIRException {
List<Base> n1 = execute(context, focus, exp.getParameters().get(0), true);
if (!convertToBoolean(n1)) {
List<Base> n2 = execute(context, focus, exp.getParameters().get(1), true);
String name = n2.get(0).primitiveValue();
throw new FHIRException("check failed: "+name);
}
return focus;
}
private List<Base> funcDistinct(ExecutionContext context, List<Base> focus, ExpressionNode exp) {
if (focus.size() <= 1)
return focus;

8
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/utils/OperationOutcomeUtilities.java
View File

@ -28,6 +28,7 @@ import org.hl7.fhir.r5.model.OperationOutcome.IssueSeverity;
import org.hl7.fhir.r5.model.OperationOutcome.IssueType;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.StringType;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
public class OperationOutcomeUtilities {
@ -36,11 +37,16 @@ public class OperationOutcomeUtilities {
public static OperationOutcomeIssueComponent convertToIssue(ValidationMessage message, OperationOutcome op) {
OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
issue.setCode(convert(message.getType()));
if (message.getLocation() != null) {
// message location has a fhirPath in it. We need to populate the expression
issue.addExpression(message.getLocation());
// also, populate the XPath variant
StringType s = new StringType();
s.setValue(message.getLocation()+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
s.setValue(Utilities.fhirPathToXPath(message.getLocation())+(message.getLine()>= 0 && message.getCol() >= 0 ? " (line "+Integer.toString(message.getLine())+", col"+Integer.toString(message.getCol())+")" : "") );
issue.getLocation().add(s);
}
// pass through line/col if they're present
if (message.getLine() != 0)
issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
if (message.getCol() != 0)

2
org.hl7.fhir.r5/src/main/resources/gen/gen.xml
View File

@ -111,7 +111,7 @@
<a href="Patient/f201">Roel</a>
</p>
<p>
<b>authored</b>: Jun 17, 2013 11:00:00 PM
<b>authored</b>: 18/06/2013 9:00:00 AM
</p>
<p>
<b>author</b>:

290
org.hl7.fhir.r5/src/main/resources/snapshot-generation-tests.xml
View File

@ -2086,7 +2086,7 @@
</element>
<element>
<path value="Observation.value[x]"/>
<sliceName value="quantity"/>
<sliceName value="Quantity"/>
<short value="some text for quantity"/>
<type>
<code value="Quantity"/>
@ -2168,7 +2168,7 @@
</element>
<element>
<path value="Observation.value[x]"/>
<sliceName value="quantity"/>
<sliceName value="Quantity"/>
<short value="some text for quantity"/>
<type>
<code value="Quantity"/>
@ -2180,7 +2180,7 @@
</element>
<element>
<path value="Observation.value[x]"/>
<sliceName value="codeable"/>
<sliceName value="CodeableConcept"/>
<short value="some text for CodeableConcept"/>
<type>
<code value="CodeableConcept"/>
@ -4310,4 +4310,288 @@
</assert>
</action>
</test>
<test>
<name value="Test40"/>
<description value="40. Choice Types: constrain minimum cardinality"/>
<action>
<operation>
<type>
<system value="http://hl7.org/fhir/testscript-operation-codes"/>
<code value="snapshot"/>
</type>
<resource value="StructureDefinition"/>
<encodeRequestUrl value="false"/>
<params value="sort=true"/>
<responseId value="t40o"/>
<sourceId value="t40"/>
</operation>
</action>
<action>
<assert>
<label value="test40-1"/>
<description value="Snapshot must generate ok"/>
<response value="okay"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test40-2"/>
<description value="There should only be one element definition for value[x]"/>
<direction value="response"/>
<expression value="fixture('t40o').snapshot.element.where(path.startsWith('Observation.value')).count() = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test40-3"/>
<description value="The element definition for value[x] should have min = 1"/>
<direction value="response"/>
<expression value="fixture('t40o').snapshot.element.where(path.startsWith('Observation.value')).min = 1"/>
<warningOnly value="false"/>
</assert>
</action>
</test>
<test>
<name value="Test41"/>
<description value="41. Choice Types: constrain list of choices to 2"/>
<action>
<operation>
<type>
<system value="http://hl7.org/fhir/testscript-operation-codes"/>
<code value="snapshot"/>
</type>
<resource value="StructureDefinition"/>
<encodeRequestUrl value="false"/>
<params value="sort=true"/>
<responseId value="t41o"/>
<sourceId value="t41"/>
</operation>
</action>
<action>
<assert>
<label value="test41-1"/>
<description value="Snapshot must generate ok"/>
<response value="okay"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test41-2"/>
<description value="There should only be one element definition for value[x]"/>
<direction value="response"/>
<expression value="fixture('t41o').snapshot.element.where(path.startsWith('Observation.value')).count() = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test41-3"/>
<description value="The element definition for value[x] should have 2 types"/>
<direction value="response"/>
<expression value="fixture('t41o').snapshot.element.where(path.startsWith('Observation.value')).type.count() = 2"/>
<warningOnly value="false"/>
</assert>
</action>
</test>
<test>
<name value="Test42"/>
<description value="Choice Types: constrain list of choices to 1"/>
<action>
<operation>
<type>
<system value="http://hl7.org/fhir/testscript-operation-codes"/>
<code value="snapshot"/>
</type>
<resource value="StructureDefinition"/>
<encodeRequestUrl value="false"/>
<params value="sort=true"/>
<responseId value="t42o"/>
<sourceId value="t42"/>
</operation>
</action>
<action>
<assert>
<label value="test42-1"/>
<description value="Snapshot must generate ok"/>
<response value="okay"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test42-2"/>
<description value="There should only be one element definition for value[x]"/>
<direction value="response"/>
<expression value="fixture('t42o').snapshot.element.where(path.startsWith('Observation.value')).count() = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test42-3"/>
<description value="The element definition for value[x] should have 1 type"/>
<direction value="response"/>
<expression value="fixture('t42o').snapshot.element.where(path.startsWith('Observation.value')).type.count() = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test42-4"/>
<description value="The element definition for value[x] should have short = 'some text'"/>
<direction value="response"/>
<expression value="fixture('t42o').snapshot.element.where(path.startsWith('Observation.value')).short = 'some text'"/>
<warningOnly value="false"/>
</assert>
</action>
</test>
<test>
<name value="Test43"/>
<description value="Choice Types: constrain list of choices to 1 and constrain the type (slicing)"/>
<action>
<operation>
<type>
<system value="http://hl7.org/fhir/testscript-operation-codes"/>
<code value="snapshot"/>
</type>
<resource value="StructureDefinition"/>
<encodeRequestUrl value="false"/>
<params value="sort=true"/>
<responseId value="t43o"/>
<sourceId value="t43"/>
</operation>
</action>
<action>
<assert>
<label value="test43-1"/>
<description value="Snapshot must generate ok"/>
<response value="okay"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test43-2"/>
<description value="There should be 9 element definitions for value[x] (base + quantity + walking into quantity"/>
<direction value="response"/>
<expression value="fixture('t43o').snapshot.element.where(path.startsWith('Observation.value')).count() = 9"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test43-3"/>
<description value="The element definition for value[x] should have 1 type"/>
<direction value="response"/>
<expression value="fixture('t43o').snapshot.element.where(id = 'Observation.value[x]').type.count().trace('count') = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test43-4"/>
<description value="The element definition for value[x] should have short = 'some text'"/>
<direction value="response"/>
<expression value="fixture('t43o').snapshot.element.where(id = 'Observation.value[x]').short = 'some text'"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test43-5"/>
<description value="The element definition for value[x] quantity slice should have sliceName = 'Quantity'"/>
<direction value="response"/>
<expression value="fixture('t43o').snapshot.element.where(id = 'Observation.value[x]:Quantity').check(exists(), 'no slice').sliceName = 'Quantity'"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test43-6"/>
<description value="The element definition for value[x].value quantity slice should have sliceName = 'Quantity'"/>
<direction value="response"/>
<expression value="fixture('t43o').snapshot.element.where(id = 'Observation.value[x]:Quantity.value').check(exists(), 'no slice').min = 1"/>
<warningOnly value="false"/>
</assert>
</action>
</test>
<test>
<name value="Test44"/>
<description value="Choice Types: constrain list of choices to 1 and constrain the type (shortcut)"/>
<action>
<operation>
<type>
<system value="http://hl7.org/fhir/testscript-operation-codes"/>
<code value="snapshot"/>
</type>
<resource value="StructureDefinition"/>
<encodeRequestUrl value="false"/>
<params value="sort=true"/>
<responseId value="t44o"/>
<sourceId value="t44"/>
</operation>
</action>
<action>
<assert>
<label value="test44-1"/>
<description value="Snapshot must generate ok"/>
<response value="okay"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test44-2"/>
<description value="There should be 9 element definitions for value[x] (base + quantity + walking into quantity"/>
<direction value="response"/>
<expression value="fixture('t44o').snapshot.element.where(path.startsWith('Observation.value')).count() = 9"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test44-3"/>
<description value="The element definition for value[x] should have 1 type"/>
<direction value="response"/>
<expression value="fixture('t44o').snapshot.element.where(id = 'Observation.value[x]').type.count().trace('count') = 1"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test44-4"/>
<description value="The element definition for value[x] should have short = 'some text'"/>
<direction value="response"/>
<expression value="fixture('t44o').snapshot.element.where(id = 'Observation.value[x]').short = 'some text'"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test44-5"/>
<description value="The element definition for value[x] quantity slice should have sliceName = 'Quantity'"/>
<direction value="response"/>
<expression value="fixture('t44o').snapshot.element.where(id = 'Observation.value[x]:Quantity').check(exists(), 'no slice').sliceName = 'Quantity'"/>
<warningOnly value="false"/>
</assert>
</action>
<action>
<assert>
<label value="test44-6"/>
<description value="The element definition for value[x].value quantity slice should have sliceName = 'Quantity'"/>
<direction value="response"/>
<expression value="fixture('t44o').snapshot.element.where(id = 'Observation.value[x]:Quantity.value').check(exists(), 'no slice').min = 1"/>
<warningOnly value="false"/>
</assert>
</action>
</test>
</TestScript>

4
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/CSVProcessor.java
View File

@ -70,7 +70,7 @@ public class CSVProcessor {
public class DataReader extends CSVReader {
public DataReader(InputStream data) throws UnsupportedEncodingException {
public DataReader(InputStream data) throws FHIRException, IOException {
super(data);
}
@ -125,7 +125,7 @@ public class CSVProcessor {
this.source = source;
}
public void setData(InputStream data) {
public void setData(InputStream data) throws FHIRException, IOException {
try {
this.data = new DataReader(data);
} catch (UnsupportedEncodingException e) {

13
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/CSVReader.java
View File

@ -65,11 +65,18 @@ import org.hl7.fhir.exceptions.FHIRException;
*/
public class CSVReader extends InputStreamReader {
public CSVReader(InputStream in) throws UnsupportedEncodingException {
public CSVReader(InputStream in) throws FHIRException, IOException {
super(in, "UTF-8");
checkBOM();
}
private String[] cols;
private void checkBOM() throws FHIRException, IOException {
if (peek() == '\uFEFF')
next();
}
private String[] cols;
private String[] cells;
public void readHeaders() throws IOException, FHIRException {
@ -92,7 +99,7 @@ public class CSVReader extends InputStreamReader {
public String cell(String name) {
int index = -1;
for (int i = 0; i < cols.length; i++) {
if (name.equals(cols[i]))
if (name.equals(cols[i].trim()))
index = i;
}
if (index == -1)

26
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
View File

@ -1195,6 +1195,32 @@ public class Utilities {
}
/**
* Only handles simple FHIRPath expressions of the type produced by the validator
*
* @param path
* @return
*/
public static String fhirPathToXPath(String path) {
String[] p = path.split("\\.");
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder(".");
int i = 0;
while (i < p.length) {
String s = p[i];
if (s.contains("[")) {
String si = s.substring(s.indexOf("[")+1, s.length()-1);
s = s.substring(0, s.indexOf("["))+"["+Integer.toString(Integer.parseInt(si)+1)+"]";
}
if (i < p.length - 1 && p[i+1].startsWith(".ofType(")) {
i++;
s = s + capitalize(p[i].substring(8, p.length-1));
}
b.append(s);
i++;
}
return b.toString();
}
}

2
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/validation/ValidationMessage.java
View File

@ -479,7 +479,7 @@ public class ValidationMessage implements Comparator<ValidationMessage>, Compara
private Source source;
private int line;
private int col;
private String location;
private String location; // fhirPath
private String message;
private IssueType type;
private IssueSeverity level;

4
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/BaseValidator.java
View File

@ -331,8 +331,8 @@ public class BaseValidator {
protected boolean warning(List<ValidationMessage> errors, IssueType type, int line, int col, String path, boolean thePass, String msg, Object... theMessageArguments) {
if (!thePass) {
msg = formatMessage(msg, theMessageArguments);
IssueSeverity severity = IssueSeverity.WARNING;
addValidationMessage(errors, type, line, col, path, msg, severity);
IssueSeverity severity = IssueSeverity.WARNING;
addValidationMessage(errors, type, line, col, path, msg, severity);
}
return thePass;

45
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/InstanceValidator.java
View File

@ -22,6 +22,7 @@ package org.hl7.fhir.r5.validation;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.junit.Assert.assertNotNull;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
@ -2922,6 +2923,20 @@ public class InstanceValidator extends BaseValidator implements IResourceValidat
}
}
}
// security tags are a set (system|code)
Element meta = element.getNamedChild("meta");
if (meta != null) {
Set<String> tags = new HashSet<>();
List<Element> list = new ArrayList<>();
meta.getNamedChildren("security", list);
int i = 0;
for (Element e : list) {
String s = e.getNamedChildValue("system") + "#" + e.getNamedChildValue("code");
rule(errors, IssueType.BUSINESSRULE, e.line(), e.col(), stack.getLiteralPath()+".meta.profile["+Integer.toString(i)+"]", !tags.contains(s), "Duplicate Security Label "+s);
tags.add(s);
i++;
}
}
}
private void validateCodeSystem(List<ValidationMessage> errors, Element cs, NodeStack stack) {
@ -4416,7 +4431,7 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
String nb = cursor == 0 ? "--" : parent.getChildren().get(cursor-1).getName();
String na = cursor >= parent.getChildren().size() - 1 ? "--" : parent.getChildren().get(cursor+1).getName();
if (name().equals(nb) || name().equals(na) ) {
return lastCount + 1;
return lastCount;
} else
return -1;
}
@ -4447,10 +4462,21 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
public String path() {
int i = count();
String sfx = "";
if (i > -1) {
sfx = "[" + Integer.toString(lastCount + 1) + "]";
String n = name();
String fn = "";
if (element().getProperty().isChoice()) {
String en = element().getProperty().getName();
en = en.substring(0, en.length()-3);
String t = n.substring(en.length());
if (isPrimitiveType(Utilities.uncapitalize(t)))
t = Utilities.uncapitalize(t);
n = en;
fn = ".ofType("+t+")";
}
return basePath + "." + name() + sfx;
if (i > -1 || (element().getSpecial() == null && element().isList())) {
sfx = "[" + Integer.toString(lastCount) + "]";
}
return basePath + "." + n + sfx+fn;
}
}
@ -4519,6 +4545,17 @@ private boolean isAnswerRequirementFulfilled(QuestionnaireItemComponent qItem, L
res.literalPath = getLiteralPath() + "." + element.getName();
if (count > -1)
res.literalPath = res.literalPath + "[" + Integer.toString(count) + "]";
else if (element.getSpecial() == null && element.getProperty().isList())
res.literalPath = res.literalPath + "[0]";
else if (element.getProperty().isChoice()) {
String n = res.literalPath.substring(res.literalPath.lastIndexOf(".")+1);
String en = element.getProperty().getName();
en = en.substring(0, en.length()-3);
String t = n.substring(en.length());
if (isPrimitiveType(Utilities.uncapitalize(t)))
t = Utilities.uncapitalize(t);
res.literalPath = res.literalPath.substring(0, res.literalPath.lastIndexOf("."))+"."+en+".ofType("+t+")";
}
res.logicalPaths = new ArrayList<String>();
if (type != null) {
// type will be bull if we on a stitching point of a contained resource, or if....

16
org.hl7.fhir.validation/src/main/java/org/hl7/fhir/r5/validation/Validator.java
View File

@ -72,6 +72,7 @@ import org.hl7.fhir.r5.model.Constants;
import org.hl7.fhir.r5.model.DomainResource;
import org.hl7.fhir.r5.model.FhirPublication;
import org.hl7.fhir.r5.model.ImplementationGuide;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.OperationOutcome;
import org.hl7.fhir.r5.model.OperationOutcome.OperationOutcomeIssueComponent;
import org.hl7.fhir.r5.model.Resource;
@ -287,6 +288,7 @@ public class Validator {
if ("1.0".equals(sv)) sv = "1.0.2";
if ("1.4".equals(sv)) sv = "1.4.0";
if ("3.0".equals(sv)) sv = "3.0.1";
if ("4.0".equals(sv)) sv = "4.0.0";
if (sv.startsWith(Constants.VERSION)) sv = Constants.VERSION;
definitions = "hl7.fhir.core#"+sv;
} else if (args[i].equals("-output"))
@ -527,7 +529,19 @@ public class Validator {
}
private static String getIssueSummary(OperationOutcomeIssueComponent issue) {
return " " + issue.getSeverity().getDisplay() + " @ " + issue.getLocation().get(0).asStringValue() + " : " + issue.getDetails().getText();
String loc = null;
if (issue.hasExpression()) {
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
loc = issue.getExpression().get(0).asStringValue() + (line >= 0 && col >= 0 ? " (line "+Integer.toString(line)+", col"+Integer.toString(col)+")" : "");
} else if (issue.hasLocation()) {
loc = issue.getLocation().get(0).asStringValue();
} else {
int line = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_LINE, -1);
int col = ToolingExtensions.readIntegerExtension(issue, ToolingExtensions.EXT_ISSUE_COL, -1);
loc = (line >= 0 && col >= 0 ? "line "+Integer.toString(line)+", col"+Integer.toString(col) : "??");
}
return " " + issue.getSeverity().getDisplay() + " @ " + loc + " : " + issue.getDetails().getText();
}

126
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/conversion/tests/R3R4ConversionTests.java
View File

@ -33,18 +33,20 @@ import org.hl7.fhir.r4.model.Resource;
import org.hl7.fhir.r4.model.ResourceFactory;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.StructureDefinition.StructureDefinitionKind;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.model.StructureMap;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.test.utils.TestingUtilities;
import org.hl7.fhir.r4.utils.IResourceValidator;
import org.hl7.fhir.r4.utils.IResourceValidator.IValidatorResourceFetcher;
import org.hl7.fhir.r4.utils.IResourceValidator.ReferenceValidationPolicy;
import org.hl7.fhir.r4.utils.StructureMapUtilities;
import org.hl7.fhir.r4.utils.StructureMapUtilities.ITransformerServices;
import org.hl7.fhir.r5.validation.InstanceValidatorFactory;
import org.hl7.fhir.r4.validation.InstanceValidatorFactory;
import org.hl7.fhir.utilities.IniFile;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.cache.PackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.junit.Test;
@ -63,12 +65,14 @@ import com.google.gson.JsonPrimitive;
public class R3R4ConversionTests implements ITransformerServices, IValidatorResourceFetcher {
private static final boolean SAVING = true;
private PackageCacheManager pcm = null;
@Parameters(name = "{index}: id {0}")
public static Iterable<Object[]> data() throws ParserConfigurationException, SAXException, IOException {
if (!(new File(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")).exists()))
throw new Error("You must set the default directory to the build directory when you execute these tests");
r3r4Outcomes = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
r3r4Outcomes = (JsonObject) new com.google.gson.JsonParser().parse(
TextFile.fileToString(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
rules = new IniFile(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-rules.ini"));
String srcFile = Utilities.path(TestingUtilities.home(), "source", "release3", "examples.zip");
@ -79,7 +83,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
filter = filter.toLowerCase();
Map<String, byte[]> examples = new HashMap<String, byte[]>();
ZipEntry entry;
while((entry = stream.getNextEntry())!=null) {
while ((entry = stream.getNextEntry()) != null) {
String n = entry.getName();
byte[] buffer = new byte[2048];
ByteArrayOutputStream output = null;
@ -97,7 +101,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
List<Object[]> objects = new ArrayList<Object[]>(examples.size());
for (String id : names) {
objects.add(new Object[] { id, examples.get(id)});
objects.add(new Object[] { id, examples.get(id) });
}
return objects;
@ -137,7 +141,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
extras = new ArrayList<Resource>();
// load the example (r3)
org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3).parse(new ByteArrayInputStream(content));
org.hl7.fhir.r4.elementmodel.Element r3 = new org.hl7.fhir.r4.elementmodel.XmlParser(contextR3)
.parse(new ByteArrayInputStream(content));
tn = r3.fhirType();
workingid = r3.getChildValue("id");
if (SAVING) {
@ -145,13 +150,14 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(r3, bso, OutputStyle.PRETTY, null);
cnt = bso.toByteArray();
Utilities.createDirectory(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output"));
TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".input.json"));
TextFile.bytesToFile(cnt, Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output",
tn + "-" + workingid + ".input.json"));
}
// load the r3 to R4 map
String mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4", r3.fhirType()+".map");
if (new File(mapFile).exists()) {
StructureMap sm = smu4.parse(TextFile.fileToString(mapFile), mapFile);
tn = smu4.getTargetType(sm).getType();
// convert from r3 to r4
@ -161,11 +167,13 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
ByteArrayOutputStream bs = new ByteArrayOutputStream();
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r4);
if (SAVING) {
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".r4.json"));
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", tn + "-" + workingid + ".r4.json"));
for (Resource r : extras) {
bs = new ByteArrayOutputStream();
new org.hl7.fhir.r4.formats.JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(bs, r);
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", r.fhirType()+"-"+r.getId()+".r4.json"));
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", r.fhirType() + "-" + r.getId() + ".r4.json"));
}
}
@ -176,8 +184,6 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
validator.validate(null, r4validationErrors, r4);
// load the R4 to R3 map
// mapFile = Utilities.path(root, "implementations", "r3maps", "R4toR3", r3.fhirType()+".map");
// s = sm.parse(TextFile.fileToString(mapFile));
mapFile = Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3", getMapFor(r4.fhirType(), r3.fhirType())+".map");
sm = smu3.parse(TextFile.fileToString(mapFile), mapFile);
@ -190,15 +196,17 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
bs = new ByteArrayOutputStream();
new org.hl7.fhir.r4.elementmodel.JsonParser(contextR3).compose(ro3, bs, OutputStyle.PRETTY, null);
if (SAVING)
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "test-output", tn+"-"+workingid+".output.json"));
TextFile.bytesToFile(bs.toByteArray(), Utilities.path(TestingUtilities.home(), "implementations", "r3maps",
"test-output", tn + "-" + workingid + ".output.json"));
// check(errors, tn, workingid);
roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()), filter != null);
if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn+"/"+workingid, "roundtrip")))
// check(errors, tn, workingid);
roundTripError = TestingUtilities.checkJsonSrcIsSame(new String(cnt), new String(bs.toByteArray()),
filter != null);
if (roundTripError != null && roundTripError.equals(rules.getStringProperty(tn + "/" + workingid, "roundtrip")))
roundTripError = null;
} else {
if (loadErrors.containsKey(r3.fhirType()+".map")) {
executionError = loadErrors.get(r3.fhirType()+".map");
if (loadErrors.containsKey(r3.fhirType() + ".map")) {
executionError = loadErrors.get(r3.fhirType() + ".map");
}
}
} catch (Exception e) {
@ -216,10 +224,11 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (r3.equals("ReferralRequest"))
return "ServiceRequestRR";
// if (r3.equals("ProcedureRequest"))
return "ServiceRequestPR";
return "ServiceRequestPR";
}
private void updateOutcomes(String tn, String id, Exception executionError, List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
private void updateOutcomes(String tn, String id, Exception executionError,
List<ValidationMessage> r4validationErrors, String roundTripError) throws IOException {
JsonObject r = r3r4Outcomes.getAsJsonObject(tn);
if (r == null) {
r = new JsonObject();
@ -238,7 +247,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
i.addProperty("execution", true);
else
i.addProperty("execution", executionError.getMessage());
// round-trip check
// round-trip check
if (i.has("round-trip"))
i.remove("round-trip");
if (roundTripError != null)
@ -251,11 +260,12 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
JsonArray arr = new JsonArray();
i.add("r4.errors", arr);
for (ValidationMessage e : r4validationErrors)
arr.add(new JsonPrimitive(e.summary()));
arr.add(new JsonPrimitive(e.summary()));
}
Gson gson = new GsonBuilder().setPrettyPrinting().create();
String json = gson.toJson(r3r4Outcomes);
TextFile.stringToFile(json, (Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
TextFile.stringToFile(json,
(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "outcomes.json")));
}
@ -266,7 +276,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
break;
if (vm.getMessage().contains("Error null validating Coding"))
break;
String s = rules.getStringProperty(tn+"/"+id, "validation");
String s = rules.getStringProperty(tn + "/" + id, "validation");
if (!Utilities.noString(s)) {
boolean ok = false;
for (String m : s.split("\\;"))
@ -285,7 +295,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
break;
}
if (vm.getLevel() == IssueSeverity.ERROR || vm.getLevel() == IssueSeverity.FATAL) {
b.append("[R4 validation error] "+vm.getLocation()+": "+vm.getMessage()+"\r\n");
b.append("[R4 validation error] " + vm.getLocation() + ": " + vm.getMessage() + "\r\n");
}
}
if (b.length() > 0)
@ -293,32 +303,31 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
}
/*
* Supporting multiple versions at once is a little tricky. We're going to have 2 contexts:
* - an R3 context which is used to read/write R3 instances
* - an R4 context which is used to perform the transforms
* Supporting multiple versions at once is a little tricky. We're going to have
* 2 contexts: - an R3 context which is used to read/write R3 instances - an R4
* context which is used to perform the transforms
*
* R3 structure definitions are cloned into R3 context with a modified URL (as
* 3.0/)
*
* R3 structure definitions are cloned into R3 context with a modified URL (as 3.0/)
*
*/
private void checkLoad() throws IOException, FHIRException {
private void checkLoad() throws IOException, FHIRException, Exception {
if (contextR3 != null)
return;
pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
R3ToR4Loader ldr = new R3ToR4Loader().setPatchUrls(true).setKillPrimitives(true);
System.out.println("loading R3");
contextR3 = new SimpleWorkerContext();
contextR3.setAllowLoadingDuplicates(true);
contextR3.setOverrideVersionNs("http://hl7.org/fhir/3.0/StructureDefinition");
contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","profiles-types.xml"), ldr);
contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","profiles-resources.xml"), ldr);
contextR3.loadFromFile(Utilities.path(TestingUtilities.home(),"source","release3","expansions.xml"), ldr);
contextR3.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "3.0.1"), ldr, new String[] {});
System.out.println("loading R4");
contextR4 = new SimpleWorkerContext();
contextR4.setAllowLoadingDuplicates(true);
contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"profiles-types.xml"), null);
contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"profiles-resources.xml"), null);
contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"extension-definitions.xml"), null);
contextR4.loadFromFile(Utilities.path(TestingUtilities.content(),"valuesets.xml"), null);
contextR4 = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
contextR4.setCanRunWithoutTerminology(true);
for (StructureDefinition sd : contextR3.allStructures()) {
@ -332,7 +341,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR3.cacheResource(sd);
StructureDefinition sdn = sd.copy();
sdn.setUrl(sdn.getUrl().replace("http://hl7.org/fhir/", "http://hl7.org/fhir/3.0/"));
sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace").setValue(new UriType("http://hl7.org/fhir"));
sdn.addExtension().setUrl("http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace")
.setValue(new UriType("http://hl7.org/fhir"));
contextR3.cacheResource(sdn);
contextR4.cacheResource(sdn);
}
@ -342,11 +352,15 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
contextR4.setExpansionProfile(new org.hl7.fhir.r4.model.Parameters());
contextR3.setName("R3");
contextR4.setName("R4");
contextR4.setValidatorFactory(new InstanceValidatorFactory());
// TODO: this has to be R% now... contextR4.setValidatorFactory(new InstanceValidatorFactory());
System.out.println("loading Maps");
loadLib(Utilities.path(TestingUtilities.home(),"implementations","r3maps", "R3toR4"));
loadLib(Utilities.path(TestingUtilities.home(),"implementations","r3maps", "R4toR3"));
loadLib(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R4toR3"));
loadLib(Utilities.path(TestingUtilities.home(), "implementations", "r3maps", "R3toR4"));
System.out.println("loaded");
}
@ -361,30 +375,31 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
for (Resource r : sm.getContained()) {
if (r instanceof MetadataResource) {
MetadataResource mr = (MetadataResource) r.copy();
mr.setUrl(sm.getUrl()+"#"+r.getId());
mr.setUrl(sm.getUrl() + "#" + r.getId());
contextR3.cacheResource(mr);
contextR4.cacheResource(mr);
}
}
} catch (FHIRException e) {
System.out.println("Unable to load "+Utilities.path(dir, s)+": "+e.getMessage());
System.out.println("Unable to load " + Utilities.path(dir, s) + ": " + e.getMessage());
loadErrors.put(s, e);
// e.printStackTrace();
// e.printStackTrace();
}
}
}
@Override
public void log(String message) {
System.out.println(message);
System.out.println(message);
}
@Override
public Base createResource(Object appInfo, Base res, boolean atRootofTransform) {
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")) || res.fhirType().equals("PractitionerRole")) {
if (res instanceof Resource && (res.fhirType().equals("CodeSystem") || res.fhirType().equals("CareTeam")
|| res.fhirType().equals("PractitionerRole"))) {
Resource r = (Resource) res;
extras.add(r);
r.setId(workingid+"-"+extras.size());
r.setId(workingid + "-" + extras.size());
}
return res;
}
@ -398,9 +413,10 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
public Base createType(Object appInfo, String name) throws FHIRException {
BaseWorkerContext context = (BaseWorkerContext) appInfo;
if (context == contextR3) {
StructureDefinition sd = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/3.0/StructureDefinition/"+name);
StructureDefinition sd = context.fetchResource(StructureDefinition.class,
"http://hl7.org/fhir/3.0/StructureDefinition/" + name);
if (sd == null)
throw new FHIRException("Type not found: '"+name+"'");
throw new FHIRException("Type not found: '" + name + "'");
return Manager.build(context, sd);
} else
return ResourceFactory.createResourceOrType(name);
@ -414,7 +430,7 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
if (url.equals(mr.getUrl()))
return mr;
}
if (url.equals(r.fhirType()+"/"+r.getId()))
if (url.equals(r.fhirType() + "/" + r.getId()))
return r;
}
@ -429,7 +445,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
String[] vals = parts[1].split("\\=");
if (vals.length == 2 && vals[0].equals("practitioner"))
for (Resource r : extras) {
if (r instanceof PractitionerRole && ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/"+vals[1])) {
if (r instanceof PractitionerRole
&& ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/" + vals[1])) {
results.add(r);
}
}
@ -438,7 +455,8 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
}
@Override
public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException {
public Element fetch(Object appContext, String url)
throws FHIRFormatError, DefinitionException, IOException, FHIRException {
return null;
}
@ -451,6 +469,4 @@ public class R3R4ConversionTests implements ITransformerServices, IValidatorReso
public boolean resolveURL(Object appContext, String path, String url) throws IOException, FHIRException {
return true;
}
}

23
org.hl7.fhir.validation/src/test/resources/validation-examples/duplicate-security-tags.xml Normal file
View File

@ -0,0 +1,23 @@
<Patient xmlns="http://hl7.org/fhir">
<id value="pat-good"/>
<meta>
<security>
<system value="http://test.org"/>
<code value="x"/>
</security>
<security>
<system value="http://test.org"/>
<code value="y"/>
</security>
<security>
<system value="http://test.org"/>
<code value="x"/>
</security>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">
some text in no particular language
</div>
</text>
</Patient>

4
org.hl7.fhir.validation/src/test/resources/validation-examples/manifest.json
View File

@ -783,6 +783,10 @@
"errorCount": 0,
"warningCount": 0
},
"duplicate-security-tags.xml" : {
"errorCount": 1,
"warningCount": 3
},
"azatadha/example-params-1.xml" : {
"errorCount": 0,
"warningCount": 1,