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Merge pull request #574 from LouisRolland78/issue-555 

fix: #555 Handling minValue/maxValue in generate snapshot process
This commit is contained in:
Grahame Grieve 2021-08-25 06:10:27 +10:00 committed by GitHub
parent aa5ab74003 b5723bab50
commit 104fe321f5
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7 changed files with 393 additions and 237 deletions
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9
RELEASE_NOTES.md
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@ -1 +1,8 @@
Exposed showMessagesFromReferences on the command line interface to support reporting validation errors on referenced types (particularly useful when validating messages & documents)
* Differential element fields minValue/maxValue are now correctly treated in the snapshot generation process
* Conversion context added to conversions process
* Users can now define custom behavior for CodeSystems, Extensions, BundleEntries, and Types by extending BaseAdvisor.
* Resource Conversions are now thread-safe, each using their own instance of the conversion context that is unique
* ConversionFactory classes are statically accessed, to minimize changes downstream
* I need to add more tests, there were very few to begin with, and it's my next task
* All conversion libraries and no play makes Mark a dull boy
* Exposed showMessagesFromReferences on the command line interface to support reporting validation errors on referenced types (particularly useful when validating messages & documents)

18
org.hl7.fhir.dstu2/src/main/java/org/hl7/fhir/dstu2/utils/ProfileUtilities.java
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@ -1010,6 +1010,24 @@ public class ProfileUtilities {
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
// todo: what to do about conditions?
// condition : id 0..*

18
org.hl7.fhir.dstu2016may/src/main/java/org/hl7/fhir/dstu2016may/utils/ProfileUtilities.java
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@ -1011,6 +1011,24 @@ public class ProfileUtilities {
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
// todo: what to do about conditions?
// condition : id 0..*

18
org.hl7.fhir.dstu3/src/main/java/org/hl7/fhir/dstu3/conformance/ProfileUtilities.java
View File

@ -1337,6 +1337,24 @@ public class ProfileUtilities extends TranslatingUtilities {
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
// todo: what to do about conditions?
// condition : id 0..*

18
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/conformance/ProfileUtilities.java
View File

@ -1841,6 +1841,24 @@ public class ProfileUtilities extends TranslatingUtilities {
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
// todo: what to do about conditions?
// condition : id 0..*

18
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/conformance/ProfileUtilities.java
View File

@ -2827,6 +2827,24 @@ public class ProfileUtilities extends TranslatingUtilities {
derived.getMaxLengthElement().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMaxValue()) {
if (!Base.compareDeep(derived.getMaxValue(), base.getMaxValue(), false))
base.setMaxValue(derived.getMaxValue().copy());
else if (trimDifferential)
derived.setMaxValue(null);
else
derived.getMaxValue().setUserData(DERIVATION_EQUALS, true);
}
if (derived.hasMinValue()) {
if (!Base.compareDeep(derived.getMinValue(), base.getMinValue(), false))
base.setMinValue(derived.getMinValue().copy());
else if (trimDifferential)
derived.setMinValue(null);
else
derived.getMinValue().setUserData(DERIVATION_EQUALS, true);
}
// todo: what to do about conditions?
// condition : id 0..*

239
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/ProfileUtilitiesTests.java
View File

@ -1,27 +1,21 @@
package org.hl7.fhir.r5.test;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import org.fhir.ucum.UcumException;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.r5.conformance.ProfileUtilities;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.formats.XmlParser;
import org.hl7.fhir.r5.model.Base;
import org.hl7.fhir.r5.model.ElementDefinition;
import org.hl7.fhir.r5.model.IntegerType;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.model.StructureDefinition.TypeDerivationRule;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.EOperationOutcome;
import org.hl7.fhir.utilities.CSFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.validation.ValidationMessage;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.util.ArrayList;
import java.util.List;
public class ProfileUtilitiesTests {
// /**
@ -32,7 +26,7 @@ public class ProfileUtilitiesTests {
// * @throws EOperationOutcome
// */
@Test
public void testSimple() throws FHIRException, FileNotFoundException, IOException, UcumException {
public void testSimple() throws FHIRException {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
@ -40,7 +34,7 @@ public class ProfileUtilitiesTests {
focus.setBaseDefinition(base.getUrl());
focus.setType("Patient");
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org/test", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
@ -62,11 +56,7 @@ public class ProfileUtilitiesTests {
}
}
if (!ok) {
compareXml(base, focus);
throw new FHIRException("Snap shot generation simple test failed");
} else
System.out.println("Snap shot generation simple test passed");
Assertions.assertTrue(ok);
}
@ -79,13 +69,13 @@ public class ProfileUtilitiesTests {
// * @throws EOperationOutcome
// */
@Test
public void testSimple2() throws EOperationOutcome, Exception {
public void testSimple2() {
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/ValueSet").copy();
StructureDefinition focus = base.copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setSnapshot(null);
focus.setDifferential(null);
List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
@ -111,59 +101,147 @@ public class ProfileUtilitiesTests {
}
}
if (!ok) {
compareXml(base, focus);
System.out.println("Snap shot generation simple test failed");
throw new FHIRException("Snap shot generation simple test failed");
} else
System.out.println("Snap shot generation simple test passed");
Assertions.assertTrue(ok);
}
/**
* Change one cardinality.
*/
@Test
void testCardinalityChange() {
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Patient.identifier");
id.setMin(1);
List<ValidationMessage> messages = new ArrayList<>();
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
else {
if (f.getPath().equals("Patient.identifier")) {
ok = f.getMin() == 1;
if (ok) {
f.setMin(0);
}
}
if (!Base.compareDeep(b, f, true)) {
ok = Base.compareDeep(b, f, true);
}
}
}
}
Assertions.assertTrue(ok);
}
/**
* Change min value
*/
@Test
void testMinValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Appointment.minutesDuration");
id.setMinValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
else {
if (f.getPath().equals("Appointment.minutesDuration")) {
ok = f.getMinValue() instanceof IntegerType && ((IntegerType) f.getMinValue()).getValue() == 1;
if (ok) {
// Can't set minValue to null so change base minValue to IntegerType(1)
b.setMinValue(new IntegerType(1));
}
}
if (!Base.compareDeep(b, f, true)) {
ok = false;
}
}
}
}
Assertions.assertTrue(ok);
}
/**
* Change max value
*/
@Test
void testMaxValueChange() {
// Given
StructureDefinition focus = new StructureDefinition();
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Appointment").copy();
focus.setUrl(Utilities.makeUuidUrn());
focus.setBaseDefinition(base.getUrl());
focus.setType(base.getType());
focus.setDerivation(TypeDerivationRule.CONSTRAINT);
ElementDefinition id = focus.getDifferential().addElement();
id.setPath("Appointment.minutesDuration");
id.setMaxValue(new IntegerType(1));
List<ValidationMessage> messages = new ArrayList<>();
// When
new ProfileUtilities(TestingUtilities.context(), messages, null).generateSnapshot(base, focus, focus.getUrl(), "http://test.org", "Simple Test");
// Then
boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
if (ok) {
ElementDefinition b = base.getSnapshot().getElement().get(i);
ElementDefinition f = focus.getSnapshot().getElement().get(i);
b.setRequirements(null);
f.setRequirements(null);
if (!f.hasBase() || !b.getPath().equals(f.getPath())) {
ok = false;
}
else {
if (f.getPath().equals("Appointment.minutesDuration")) {
ok = f.getMaxValue() instanceof IntegerType && ((IntegerType) f.getMaxValue()).getValue() == 1;
if (ok) {
// Can't set maxValue to null so change base maxValue to IntegerType(1)
b.setMaxValue(new IntegerType(1));
}
}
if (!Base.compareDeep(b, f, true)) {
ok = false;
}
}
}
}
Assertions.assertTrue(ok);
}
// /**
// * Change one cardinality.
// *
// * @param context2
// * @
// * @throws EOperationOutcome
// */
// private void testCardinalityChange() throws EOperationOutcome, Exception {
// StructureDefinition focus = new StructureDefinition();
// StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
// focus.setUrl(Utilities.makeUuidUrn());
// focus.setBaseDefinition(base.getUrl());
// focus.setType(base.getType());
// focus.setDerivation(TypeDerivationRule.CONSTRAINT);
// ElementDefinition id = focus.getDifferential().addElement();
// id.setPath("Patient.identifier");
// id.setMin(1);
// List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
// new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test" );
//
// boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size();
// for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
// if (ok) {
// ElementDefinition b = base.getSnapshot().getElement().get(i);
// ElementDefinition f = focus.getSnapshot().getElement().get(i);
// if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath()))
// ok = false;
// else {
// f.setBase(null);
// if (f.getPath().equals("Patient.identifier")) {
// ok = f.getMin() == 1;
// if (ok)
// f.setMin(0);
// }
// ok = ok && Base.compareDeep(b, f, true);
// }
// }
// }
//
// if (!ok) {
// compareXml(base, focus);
// throw new FHIRException("Snap shot generation chenge cardinality test failed");
// } else
// System.out.println("Snap shot generation chenge cardinality test passed");
// }
//
// /**
// * check that documentation appending is working
@ -794,23 +872,4 @@ public class ProfileUtilitiesTests {
// }
//
private void compareXml(StructureDefinition base, StructureDefinition focus) throws FileNotFoundException, IOException {
base.setText(null);
focus.setText(null);
base.setDifferential(null);
// focus.setDifferential(null);
String f1 = Utilities.path("c:", "temp", "base.xml");
String f2 = Utilities.path("c:", "temp", "derived.xml");
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f1), base);
;
new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(f2), focus);
;
String diff = Utilities.path(System.getenv("ProgramFiles(X86)"), "WinMerge", "WinMergeU.exe");
List<String> command = new ArrayList<String>();
command.add("\"" + diff + "\" \"" + f1 + "\" \"" + f2 + "\"");
ProcessBuilder builder = new ProcessBuilder(command);
builder.directory(new CSFile("c:\\temp"));
builder.start();
}
}