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fix failing tests

This commit is contained in:
Grahame Grieve 2020-03-02 09:00:57 +11:00
parent ebdac16263
commit bc9ad8d608
1 changed files with 51 additions and 50 deletions
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101
org.hl7.fhir.validation/src/test/java/org/hl7/fhir/validation/tests/ValidationTestSuite.java
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@ -75,6 +75,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
private String name; private String name;
private JsonObject content; private JsonObject content;
private String version;
public ValidationTestSuite(String name, JsonObject content) { public ValidationTestSuite(String name, JsonObject content) {
this.name = name; this.name = name;
@ -95,33 +96,33 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
if (content.has("txLog")) { if (content.has("txLog")) {
txLog = content.get("txLog").getAsString(); txLog = content.get("txLog").getAsString();
} }
String v = "5.0"; version = "5.0";
List<ValidationMessage> messages = new ArrayList<ValidationMessage>(); List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
if (content.has("version")) { if (content.has("version")) {
v = content.get("version").getAsString(); version = content.get("version").getAsString();
} }
v = VersionUtilities.getMajMin(v); version = VersionUtilities.getMajMin(version);
if (!ve.containsKey(v)) { if (!ve.containsKey(version)) {
if (v.startsWith("5.0")) if (version.startsWith("5.0"))
ve.put(v, new ValidationEngine("hl7.fhir.r5.core#current", DEF_TX, txLog, FhirPublication.R5, true)); ve.put(version, new ValidationEngine("hl7.fhir.r5.core#current", DEF_TX, txLog, FhirPublication.R5, true));
else if (v.startsWith("3.0")) else if (version.startsWith("3.0"))
ve.put(v, new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, txLog, FhirPublication.STU3, true)); ve.put(version, new ValidationEngine("hl7.fhir.r3.core#3.0.2", DEF_TX, txLog, FhirPublication.STU3, true));
else if (v.startsWith("4.0")) else if (version.startsWith("4.0"))
ve.put(v, new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, txLog, FhirPublication.R4, true)); ve.put(version, new ValidationEngine("hl7.fhir.r4.core#4.0.1", DEF_TX, txLog, FhirPublication.R4, true));
else if (v.startsWith("1.0")) else if (version.startsWith("1.0"))
ve.put(v, new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, txLog, FhirPublication.DSTU2, true)); ve.put(version, new ValidationEngine("hl7.fhir.r2.core#1.0.2", DEF_TX, txLog, FhirPublication.DSTU2, true));
else if (v.startsWith("1.4")) else if (version.startsWith("1.4"))
ve.put(v, new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, txLog, FhirPublication.DSTU2016May, true)); ve.put(version, new ValidationEngine("hl7.fhir.r2b.core#1.4.0", DEF_TX, txLog, FhirPublication.DSTU2016May, true));
else else
throw new Exception("unknown version "+v); throw new Exception("unknown version "+version);
} }
vCurr = ve.get(v); vCurr = ve.get(version);
vCurr.setFetcher(this); vCurr.setFetcher(this);
if (TestingUtilities.fcontexts == null) { if (TestingUtilities.fcontexts == null) {
TestingUtilities.fcontexts = new HashMap<>(); TestingUtilities.fcontexts = new HashMap<>();
} }
TestingUtilities.fcontexts.put(v, vCurr.getContext()); TestingUtilities.fcontexts.put(version, vCurr.getContext());
if (content.has("use-test") && !content.get("use-test").getAsBoolean()) if (content.has("use-test") && !content.get("use-test").getAsBoolean())
return; return;
@ -143,13 +144,13 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
if (content.has("questionnaire")) { if (content.has("questionnaire")) {
String filename = content.get("questionnaire").getAsString(); String filename = content.get("questionnaire").getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
vCurr.getContext().cacheResource(loadResource(filename, contents, v)); vCurr.getContext().cacheResource(loadResource(filename, contents));
} }
if (content.has("codesystems")) { if (content.has("codesystems")) {
for (JsonElement je : content.getAsJsonArray("codesystems")) { for (JsonElement je : content.getAsJsonArray("codesystems")) {
String filename = je.getAsString(); String filename = je.getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
CodeSystem sd = (CodeSystem) loadResource(filename, contents, v); CodeSystem sd = (CodeSystem) loadResource(filename, contents);
val.getContext().cacheResource(sd); val.getContext().cacheResource(sd);
} }
} }
@ -157,7 +158,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
for (JsonElement je : content.getAsJsonArray("valuesets")) { for (JsonElement je : content.getAsJsonArray("valuesets")) {
String filename = je.getAsString(); String filename = je.getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
ValueSet vs = (ValueSet) loadResource(filename, contents, v); ValueSet vs = (ValueSet) loadResource(filename, contents);
val.getContext().cacheResource(vs); val.getContext().cacheResource(vs);
} }
} }
@ -165,7 +166,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
for (JsonElement je : content.getAsJsonArray("profiles")) { for (JsonElement je : content.getAsJsonArray("profiles")) {
String filename = je.getAsString(); String filename = je.getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
StructureDefinition sd = loadProfile(filename, contents, v, messages); StructureDefinition sd = loadProfile(filename, contents, messages);
val.getContext().cacheResource(sd); val.getContext().cacheResource(sd);
} }
} }
@ -194,15 +195,15 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
for (JsonElement e : profile.getAsJsonArray("supporting")) { for (JsonElement e : profile.getAsJsonArray("supporting")) {
String filename = e.getAsString(); String filename = e.getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
CanonicalResource mr = (CanonicalResource) loadResource(filename, contents, v); CanonicalResource mr = (CanonicalResource) loadResource(filename, contents);
val.getContext().cacheResource(mr); val.getContext().cacheResource(mr);
} }
} }
String filename = profile.get("source").getAsString(); String filename = profile.get("source").getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
System.out.println("Name: " + name+" - profile : "+profile.get("source").getAsString()); System.out.println("Name: " + name+" - profile : "+profile.get("source").getAsString());
v = content.has("version") ? content.get("version").getAsString() : Constants.VERSION; version = content.has("version") ? content.get("version").getAsString() : Constants.VERSION;
StructureDefinition sd = loadProfile(filename, contents, v, messages); StructureDefinition sd = loadProfile(filename, contents, messages);
val.getContext().cacheResource(sd); val.getContext().cacheResource(sd);
val.setAssumeValidRestReferences(profile.has("assumeValidRestReferences") ? profile.get("assumeValidRestReferences").getAsBoolean() : false); val.setAssumeValidRestReferences(profile.has("assumeValidRestReferences") ? profile.get("assumeValidRestReferences").getAsBoolean() : false);
List<ValidationMessage> errorsProfile = new ArrayList<ValidationMessage>(); List<ValidationMessage> errorsProfile = new ArrayList<ValidationMessage>();
@ -219,7 +220,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
for (JsonElement e : logical.getAsJsonArray("supporting")) { for (JsonElement e : logical.getAsJsonArray("supporting")) {
String filename = e.getAsString(); String filename = e.getAsString();
String contents = TestingUtilities.loadTestResource("validator", filename); String contents = TestingUtilities.loadTestResource("validator", filename);
CanonicalResource mr = (CanonicalResource) loadResource(filename, contents, v); CanonicalResource mr = (CanonicalResource) loadResource(filename, contents);
if (mr instanceof StructureDefinition) { if (mr instanceof StructureDefinition) {
val.getContext().generateSnapshot((StructureDefinition) mr, true); val.getContext().generateSnapshot((StructureDefinition) mr, true);
} }
@ -245,11 +246,11 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
return res; return res;
} }
public StructureDefinition loadProfile(String filename, String contents, String v, List<ValidationMessage> messages) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException { public StructureDefinition loadProfile(String filename, String contents, List<ValidationMessage> messages) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {
StructureDefinition sd = (StructureDefinition) loadResource(filename, contents, v); StructureDefinition sd = (StructureDefinition) loadResource(filename, contents);
ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(), messages, null); ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context(version), messages, null);
if (!sd.hasSnapshot()) { if (!sd.hasSnapshot()) {
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, sd.getBaseDefinition()); StructureDefinition base = TestingUtilities.context(version).fetchResource(StructureDefinition.class, sd.getBaseDefinition());
pu.generateSnapshot(base, sd, sd.getUrl(), null, sd.getTitle()); pu.generateSnapshot(base, sd, sd.getUrl(), null, sd.getTitle());
// (debugging) new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", sd.getId()+".xml")), sd); // (debugging) new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", sd.getId()+".xml")), sd);
} }
@ -257,7 +258,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
if (r instanceof StructureDefinition) { if (r instanceof StructureDefinition) {
StructureDefinition childSd = (StructureDefinition)r; StructureDefinition childSd = (StructureDefinition)r;
if (!childSd.hasSnapshot()) { if (!childSd.hasSnapshot()) {
StructureDefinition base = TestingUtilities.context().fetchResource(StructureDefinition.class, childSd.getBaseDefinition()); StructureDefinition base = TestingUtilities.context(version).fetchResource(StructureDefinition.class, childSd.getBaseDefinition());
pu.generateSnapshot(base, childSd, childSd.getUrl(), null, childSd.getTitle()); pu.generateSnapshot(base, childSd, childSd.getUrl(), null, childSd.getTitle());
} }
} }
@ -265,34 +266,34 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
return sd; return sd;
} }
public Resource loadResource(String filename, String contents, String v) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException { public Resource loadResource(String filename, String contents) throws IOException, FHIRFormatError, FileNotFoundException, FHIRException, DefinitionException {
try (InputStream inputStream = IOUtils.toInputStream(contents, Charsets.UTF_8)) { try (InputStream inputStream = IOUtils.toInputStream(contents, Charsets.UTF_8)) {
if (filename.contains(".json")) { if (filename.contains(".json")) {
if (Constants.VERSION.equals(v) || "5.0".equals(v)) if (Constants.VERSION.equals(version) || "5.0".equals(version))
return new JsonParser().parse(inputStream); return new JsonParser().parse(inputStream);
else if (org.hl7.fhir.dstu3.model.Constants.VERSION.equals(v) || "3.0".equals(v)) else if (org.hl7.fhir.dstu3.model.Constants.VERSION.equals(version) || "3.0".equals(version))
return VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(inputStream), false); return VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.JsonParser().parse(inputStream), false);
else if (org.hl7.fhir.dstu2016may.model.Constants.VERSION.equals(v) || "1.4".equals(v)) else if (org.hl7.fhir.dstu2016may.model.Constants.VERSION.equals(version) || "1.4".equals(version))
return VersionConvertor_14_50.convertResource(new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(inputStream)); return VersionConvertor_14_50.convertResource(new org.hl7.fhir.dstu2016may.formats.JsonParser().parse(inputStream));
else if (org.hl7.fhir.dstu2.model.Constants.VERSION.equals(v) || "1.0".equals(v)) else if (org.hl7.fhir.dstu2.model.Constants.VERSION.equals(version) || "1.0".equals(version))
return VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.JsonParser().parse(inputStream)); return VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.JsonParser().parse(inputStream));
else if (org.hl7.fhir.r4.model.Constants.VERSION.equals(v) || "4.0".equals(v)) else if (org.hl7.fhir.r4.model.Constants.VERSION.equals(version) || "4.0".equals(version))
return VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(inputStream)); return VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.JsonParser().parse(inputStream));
else else
throw new FHIRException("unknown version "+v); throw new FHIRException("unknown version "+version);
} else { } else {
if (Constants.VERSION.equals(v) || "5.0".equals(v)) if (Constants.VERSION.equals(version) || "5.0".equals(version))
return new XmlParser().parse(inputStream); return new XmlParser().parse(inputStream);
else if (org.hl7.fhir.dstu3.model.Constants.VERSION.equals(v) || "3.0".equals(v)) else if (org.hl7.fhir.dstu3.model.Constants.VERSION.equals(version) || "3.0".equals(version))
return VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.XmlParser().parse(inputStream), false); return VersionConvertor_30_50.convertResource(new org.hl7.fhir.dstu3.formats.XmlParser().parse(inputStream), false);
else if (org.hl7.fhir.dstu2016may.model.Constants.VERSION.equals(v) || "1.4".equals(v)) else if (org.hl7.fhir.dstu2016may.model.Constants.VERSION.equals(version) || "1.4".equals(version))
return VersionConvertor_14_50.convertResource(new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(inputStream)); return VersionConvertor_14_50.convertResource(new org.hl7.fhir.dstu2016may.formats.XmlParser().parse(inputStream));
else if (org.hl7.fhir.dstu2.model.Constants.VERSION.equals(v) || "1.0".equals(v)) else if (org.hl7.fhir.dstu2.model.Constants.VERSION.equals(version) || "1.0".equals(version))
return VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.XmlParser().parse(inputStream)); return VersionConvertor_10_50.convertResource(new org.hl7.fhir.dstu2.formats.XmlParser().parse(inputStream));
else if (org.hl7.fhir.r4.model.Constants.VERSION.equals(v) || "4.0".equals(v)) else if (org.hl7.fhir.r4.model.Constants.VERSION.equals(version) || "4.0".equals(version))
return VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.XmlParser().parse(inputStream)); return VersionConvertor_40_50.convertResource(new org.hl7.fhir.r4.formats.XmlParser().parse(inputStream));
else else
throw new FHIRException("unknown version " + v); throw new FHIRException("unknown version " + version);
} }
} }
} }
@ -320,7 +321,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
} }
} }
} }
if (TestingUtilities.context().isNoTerminologyServer() || !focus.has("tx-dependent")) { if (TestingUtilities.context(version).isNoTerminologyServer() || !focus.has("tx-dependent")) {
Assert.assertEquals("Expected "+Integer.toString(java.get("errorCount").getAsInt())+" errors, but found "+Integer.toString(ec)+".", java.get("errorCount").getAsInt(), ec); Assert.assertEquals("Expected "+Integer.toString(java.get("errorCount").getAsInt())+" errors, but found "+Integer.toString(ec)+".", java.get("errorCount").getAsInt(), ec);
if (java.has("warningCount")) if (java.has("warningCount"))
Assert.assertEquals("Expected "+Integer.toString(java.get("warningCount").getAsInt())+" warnings, but found "+Integer.toString(wc)+".", java.get("warningCount").getAsInt(), wc); Assert.assertEquals("Expected "+Integer.toString(java.get("warningCount").getAsInt())+" warnings, but found "+Integer.toString(wc)+".", java.get("warningCount").getAsInt(), wc);
@ -392,18 +393,18 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException { public Element fetch(Object appContext, String url) throws FHIRFormatError, DefinitionException, IOException, FHIRException {
Element res = null; Element res = null;
if (url.equals("Patient/test")) { if (url.equals("Patient/test")) {
res = new ObjectConverter(TestingUtilities.context()).convert(new Patient()); res = new ObjectConverter(TestingUtilities.context(version)).convert(new Patient());
} else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".json")) { } else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".json")) {
res = Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".json")); res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".json"));
} else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".xml")) { } else if (TestingUtilities.findTestResource("validator", url.replace("/", "-").toLowerCase()+".xml")) {
res = Manager.makeParser(TestingUtilities.context(), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".xml")); res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", url.replace("/", "-").toLowerCase()+".xml"));
} }
if (res == null && url.contains("/")) { if (res == null && url.contains("/")) {
String tail = url.substring(url.indexOf("/")+1); String tail = url.substring(url.indexOf("/")+1);
if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".json")) { if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".json")) {
res = Manager.makeParser(TestingUtilities.context(), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".json")); res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.JSON).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".json"));
} else if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".xml")) { } else if (TestingUtilities.findTestResource("validator", tail.replace("/", "-").toLowerCase()+".xml")) {
res = Manager.makeParser(TestingUtilities.context(), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".xml")); res = Manager.makeParser(TestingUtilities.context(version), FhirFormat.XML).parse(TestingUtilities.loadTestResourceStream("validator", tail.replace("/", "-").toLowerCase()+".xml"));
} }
} }
return res; return res;
@ -424,7 +425,7 @@ public class ValidationTestSuite implements IEvaluationContext, IValidatorResour
@Override @Override
public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException { public boolean conformsToProfile(Object appContext, Base item, String url) throws FHIRException {
IResourceValidator val = TestingUtilities.context().newValidator(); IResourceValidator val = TestingUtilities.context(version).newValidator();
List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>(); List<ValidationMessage> valerrors = new ArrayList<ValidationMessage>();
if (item instanceof Resource) { if (item instanceof Resource) {
val.validate(appContext, valerrors, (Resource) item, url); val.validate(appContext, valerrors, (Resource) item, url);