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refactoring for API updates #27

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refactoring for API updates #27

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1 change: 1 addition & 0 deletions validator-cli/src/main/java/org/phenopackets/validator/cli/ValidatorApplication.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
import org.phenopackets.validator.core.except.PhenopacketValidatorRuntimeException;
import org.phenopackets.validator.jsonschema.JsonSchemaValidators;
import org.phenopackets.validator.jsonschema.JsonSchemaValidator;
import org.phenopackets.validator.ontology.HpoValidator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import picocli.CommandLine;
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6 changes: 3 additions & 3 deletions validator-core/src/main/java/org/phenopackets/validator/core/PhenopacketValidator.java
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Expand Up @@ -18,7 +18,7 @@ public interface PhenopacketValidator {

ValidatorInfo info();

List<ValidationItem> validate(InputStream inputStream);
List<ValidationItem> validate(String content); ;

// -----------------------------------------------------------------------------------------------------------------

Expand All @@ -29,8 +29,8 @@ default List<ValidationItem> validate(File phenopacket) throws IOException {
}
}

default List<ValidationItem> validate(String content) {
return validate(new ByteArrayInputStream(content.getBytes(StandardCharsets.UTF_8)));
default List<ValidationItem> validate(byte[] bytes){
return validate(new String(bytes));
}

}
4 changes: 2 additions & 2 deletions ...r-jsonschema/src/main/java/org/phenopackets/validator/jsonschema/JsonSchemaValidator.java
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Expand Up @@ -79,10 +79,10 @@ public ValidatorInfo info() {
* @return List of {@link ValidationItem} objects (empty list if there were no errors)
*/
@Override
public List<ValidationItem> validate(InputStream inputStream) {
public List<ValidationItem> validate(String jsonString) {
List<ValidationItem> errors = new ArrayList<>();
try {
JsonNode json = objectMapper.readTree(inputStream);
JsonNode json = objectMapper.readTree(jsonString);
jsonSchema.validate(json)
.forEach(e -> errors.add(ValidationItem.of(validatorInfo, stringToErrorType(e.getType()), e.getMessage())));

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7 changes: 3 additions & 4 deletions validator-ontology/src/main/java/org/phenopackets/validator/ontology/HpoValidator.java
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Expand Up @@ -43,8 +43,7 @@ public HpoValidator(Ontology hpoOntology) {
super(hpoOntology, ValidatorInfo.of(ONTOLOGY_VALIDATOR, "Human Phenotype Ontology"));
}

private static Phenopacket readPhenopacket(InputStream inputStream) throws IOException {
String phenopacketJsonString = new String(inputStream.readAllBytes(), StandardCharsets.UTF_8);
private static Phenopacket readPhenopacket(String phenopacketJsonString) throws IOException {
Phenopacket.Builder phenoPacketBuilder = Phenopacket.newBuilder();
JsonFormat.parser().merge(phenopacketJsonString, phenoPacketBuilder);
return phenoPacketBuilder.build();
Expand All @@ -56,10 +55,10 @@ public ValidatorInfo info() {
}

@Override
public List<ValidationItem> validate(InputStream inputStream) {
public List<ValidationItem> validate(String jsonString) {
Phenopacket phenopacket;
try {
phenopacket = readPhenopacket(inputStream);
phenopacket = readPhenopacket(jsonString);
} catch (IOException e) {
LOGGER.warn("Error while validating: {}", e.getMessage(), e);
return List.of(ValidationItem.of(validatorInfo, ValidationItemTypes.syntaxError(), e.getMessage()));
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39 changes: 14 additions & 25 deletions validator-ontology/src/test/java/org/phenopackets/validator/ontology/HpoValidatorTest.java
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Expand Up @@ -29,11 +29,11 @@ public class HpoValidatorTest {

public HpoValidator validator;

private static byte[] wrapInPhenopacketAndGetJsonBytes(List<PhenotypicFeature> phenotypicFeatures) throws InvalidProtocolBufferException {
private static String wrapInPhenopacketAndGetJsonString(List<PhenotypicFeature> phenotypicFeatures) throws InvalidProtocolBufferException {
Phenopacket phenopacket = Phenopacket.newBuilder()
.addAllPhenotypicFeatures(phenotypicFeatures)
.build();
return JsonFormat.printer().print(phenopacket).getBytes(StandardCharsets.UTF_8);
return JsonFormat.printer().print(phenopacket);
}

private static PhenotypicFeature makePhenotypicFeature(String termId, boolean excluded) {
Expand Down Expand Up @@ -85,9 +85,9 @@ public void disjointTerms() throws Exception {
List<PhenotypicFeature> phenotypicFeatures = List.of(
makePhenotypicFeature("HP:0000002", false),
makePhenotypicFeature("HP:0000005", false));
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);
String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);

List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));
List<ValidationItem> items = validator.validate(json);

assertThat(items, hasSize(0));
}
Expand All @@ -99,10 +99,8 @@ public void parentIsPresentWhileChildrenAreExcluded() throws Exception {
makePhenotypicFeature("HP:0000004", true),
makePhenotypicFeature("HP:0000005", true)
);
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);

List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));

String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);
List<ValidationItem> items = validator.validate(json);
assertThat(items, hasSize(0));
}

Expand All @@ -114,10 +112,8 @@ public class ValidationFails {
@Test
public void termIdIsAbsentFromOntology() throws Exception {
List<PhenotypicFeature> phenotypicFeatures = List.of(makePhenotypicFeature("HP:9999999", false));
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);

List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));

String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);
List<ValidationItem> items = validator.validate(json);
assertThat(items, hasSize(1));
ValidationItem expected = ValidationItem.of(validator.info(), OntologyValidationItemTypes.ONTOLOGY_INVALID_ID, "Could not find term id: HP:9999999");
assertThat(items.get(0), equalTo(expected));
Expand All @@ -126,13 +122,10 @@ public void termIdIsAbsentFromOntology() throws Exception {
@Test
public void nonPrimaryTermIdIsUsed() throws Exception {
List<PhenotypicFeature> phenotypicFeatures = List.of(makePhenotypicFeature("HP:9999999", false));
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);

String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);
when(ontology.containsTerm(TermId.of("HP:9999999"))).thenReturn(true);
when(ontology.getPrimaryTermId(TermId.of("HP:9999999"))).thenReturn(TermId.of("HP:0000001"));

List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));

List<ValidationItem> items = validator.validate(json);
assertThat(items, hasSize(1));
ValidationItem expected = ValidationItem.of(validator.info(),
OntologyValidationItemTypes.ONTOLOGY_TERM_WITH_ALTERNATE_ID,
Expand All @@ -145,10 +138,8 @@ public void usingTermAlongWithItsAncestor() throws Exception {
List<PhenotypicFeature> phenotypicFeatures = List.of(
makePhenotypicFeature("HP:0000003", false),
makePhenotypicFeature("HP:0000004", false));
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);


List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));
String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);
List<ValidationItem> items = validator.validate(json);

assertThat(items, hasSize(1));
ValidationItem expected = ValidationItem.of(validator.info(),
Expand All @@ -162,10 +153,8 @@ public void usingTermWhileParentTermIsExcluded() throws Exception {
List<PhenotypicFeature> phenotypicFeatures = List.of(
makePhenotypicFeature("HP:0000003", true),
makePhenotypicFeature("HP:0000004", false));
byte[] bytes = wrapInPhenopacketAndGetJsonBytes(phenotypicFeatures);


List<ValidationItem> items = validator.validate(new ByteArrayInputStream(bytes));
String json = wrapInPhenopacketAndGetJsonString(phenotypicFeatures);
List<ValidationItem> items = validator.validate(json);

assertThat(items, hasSize(1));
ValidationItem expected = ValidationItem.of(validator.info(),
Expand Down