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Adding missing tests for invalid source authority in amendments. Addi…
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…ng implementation for tdwg/bdq#278 AMENDMENT_PATHWAY_STANDARDIZED along with default method and unit test.
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@chicoreus
chicoreus committed Jul 27, 2024
1 parent 29be3f3 commit 287a6ff
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Showing 3 changed files with 125 additions and 5 deletions.
60 changes: 55 additions & 5 deletions src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQ.java
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Original file line number Diff line number Diff line change
Expand Up @@ -77,6 +77,7 @@
* #75 96667a0a-ae59-446a-bbb0-b7f2b0ca6cf5 AMENDMENT_OCCURRENCESTATUS_ASSUMEDDEFAULT
* #115 f8f3a093-042c-47a3-971a-a482aaaf3b75 AMENDMENT_OCCURRENCESTATUS_STANDARDIZED
* #277 5424e933-bee7-4125-839e-d8743ea69f93 VALIDATION_PATHWAY_STANDARD
* #278 f9205977-f145-44f5-8cb9-e3e2e35ce908 AMENDMENT_PATHWAY_STANDARDIZED
* #285 4833a522-12eb-4fe0-b4cf-7f7a337a6048 VALIDATION_TYPESTATUS_STANDARD
* #283 88d8598b-3318-483d-9475-a5acf9887404 VALIDATION_SEX_STANDARD
* #284 33c45ae1-e2db-462a-a59e-7169bb01c5d6 AMENDMENT_SEX_STANDARDIZED
Expand Down Expand Up @@ -1392,6 +1393,9 @@ public static DQResponse<AmendmentValue> amendmentDegreeofestablishmentStandardi
}
try {
MetadataSourceAuthority sourceAuthorityObject = new MetadataSourceAuthority(sourceAuthority);
if (sourceAuthorityObject.getAuthority().equals(EnumMetadataSourceAuthority.INVALID)) {
throw new SourceAuthorityException("Invalid Source Authority.");
}
if (!MetadataSingleton.getInstance().isLoaded()) {
result.addComment("Error accessing sourceAuthority: " + MetadataSingleton.getInstance().getLoadError() );
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
Expand All @@ -1407,8 +1411,8 @@ public static DQResponse<AmendmentValue> amendmentDegreeofestablishmentStandardi
if (degreeOfEstablishment.trim().toLowerCase().equals("widespreadinvasive")) {
degreeOfEstablishment = "widespreadInvasive";
}
if (MetadataSingleton.getInstance().getDegreeOfEstablishmentValues().containsKey(degreeOfEstablishment.trim())) {
String match = MetadataSingleton.getInstance().getDegreeOfEstablishmentValues().get(degreeOfEstablishment.trim());
if (MetadataSingleton.getInstance().getDegreeOfEstablishmentValues().containsKey(degreeOfEstablishment.trim().toLowerCase())) {
String match = MetadataSingleton.getInstance().getDegreeOfEstablishmentValues().get(degreeOfEstablishment.trim().toLowerCase());
result.setResultState(ResultState.AMENDED);
Map<String, String> values = new HashMap<>();
values.put("dwc:degreeOfEstablishment", match) ;
Expand Down Expand Up @@ -1501,18 +1505,20 @@ public static DQResponse<ComplianceValue> validationPathwayStandard(
/**
* Propose amendment to the value of dwc:pathway using bdq:sourceAuthority.
*
* Provides: AMENDMENT_PATHWAY_STANDARDIZED
* Provides: 278 AMENDMENT_PATHWAY_STANDARDIZED
* Version: 2024-02-09
*
* @param pathway the provided dwc:pathway to evaluate as ActedUpon.
* @param sourceAuthority the bdq:sourceAuthority to consult.
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_PATHWAY_STANDARDIZED", description="Propose amendment to the value of dwc:pathway using bdq:sourceAuthority.")
@Provides("f9205977-f145-44f5-8cb9-e3e2e35ce908")
@ProvidesVersion("https://rs.tdwg.org/bdq/terms/f9205977-f145-44f5-8cb9-e3e2e35ce908/2024-02-09")
@Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:pathway is EMPTY; AMENDED the value of dwc:pathway if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED bdq:sourceAuthority default = 'Darwin Core pathway' {[https://dwc.tdwg.org/list/#dwc_pathway]} {dwc:pathway vocabulary API [https://api.gbif.org/v1/vocabularies/Pathway/concepts]}")
public DQResponse<AmendmentValue> amendmentPathwayStandardized(
@ActedUpon("dwc:pathway") String pathway
public static DQResponse<AmendmentValue> amendmentPathwayStandardized(
@ActedUpon("dwc:pathway") String pathway,
@Parameter(name="bdq:sourceAuthority") String sourceAuthority
) {
DQResponse<AmendmentValue> result = new DQResponse<AmendmentValue>();

Expand All @@ -1529,6 +1535,47 @@ public DQResponse<AmendmentValue> amendmentPathwayStandardized(
//TODO: Parameters. This test is defined as parameterized.
// bdq:sourceAuthority

if (MetadataUtils.isEmpty(pathway)) {
result.addComment("No Value provided for dwc:pathway");
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
} else {
if (MetadataUtils.isEmpty(sourceAuthority)) {
sourceAuthority = "GBIF Pathway Vocabulary";
}
try {
MetadataSourceAuthority sourceAuthorityObject = new MetadataSourceAuthority(sourceAuthority);
if (sourceAuthorityObject.getAuthority().equals(EnumMetadataSourceAuthority.INVALID)) {
throw new SourceAuthorityException("Invalid Source Authority.");
}
if (!MetadataSingleton.getInstance().isLoaded()) {
result.addComment("Error accessing sourceAuthority: " + MetadataSingleton.getInstance().getLoadError() );
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
} else {
if (MetadataSingleton.getInstance().getPathwayTerms().containsKey(pathway)) {
result.addComment("Provided value of dwc:pathway found in the sourceAuthority");
result.setResultState(ResultState.NOT_AMENDED);
} else {
if (MetadataSingleton.getInstance().getPathwayValues().containsKey(pathway.trim().toLowerCase())) {
String match = MetadataSingleton.getInstance().getPathwayValues().get(pathway.trim().toLowerCase());
result.setResultState(ResultState.AMENDED);
Map<String, String> values = new HashMap<>();
values.put("dwc:pathway", match) ;
result.setValue(new AmendmentValue(values));
} else {
result.addComment("Provided value of dwc:pathway [" + pathway + "] unable to be conformed to the the sourceAuthority");
result.setResultState(ResultState.NOT_AMENDED);
}
}
}
} catch (SourceAuthorityException e) {
result.addComment("Error with specified bdq:sourceAuthority ["+ sourceAuthority +"]: " + e.getMessage());
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
} catch (Exception e) {
result.addComment("Error evaluating dwc:pathway: " + e.getMessage());
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
}

return result;
}

Expand Down Expand Up @@ -1670,6 +1717,9 @@ public static DQResponse<AmendmentValue> amendmentSexStandardized(
}
try {
MetadataSourceAuthority sourceAuthorityObject = new MetadataSourceAuthority(sourceAuthority);
if (sourceAuthorityObject.getAuthority().equals(EnumMetadataSourceAuthority.INVALID)) {
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
if (!MetadataSingleton.getInstance().isLoaded()) {
result.addComment("Error accessing sourceAuthority: " + MetadataSingleton.getInstance().getLoadError() );
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
Expand Down
19 changes: 19 additions & 0 deletions src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQDefaults.java
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Original file line number Diff line number Diff line change
Expand Up @@ -223,4 +223,23 @@ public static DQResponse<AmendmentValue> amendmentDegreeofestablishmentStandardi
) {
return amendmentDegreeofestablishmentStandardized(degreeOfEstablishment, null);
}

/**
* Propose amendment to the value of dwc:pathway using the default bdq:sourceAuthority.
*
* Provides: AMENDMENT_PATHWAY_STANDARDIZED
* Version: 2024-02-09
*
* @param pathway the provided dwc:pathway to evaluate as ActedUpon.
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_PATHWAY_STANDARDIZED", description="Propose amendment to the value of dwc:pathway using bdq:sourceAuthority.")
@Provides("f9205977-f145-44f5-8cb9-e3e2e35ce908")
@ProvidesVersion("https://rs.tdwg.org/bdq/terms/f9205977-f145-44f5-8cb9-e3e2e35ce908/2024-02-09")
@Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:pathway is EMPTY; AMENDED the value of dwc:pathway if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED bdq:sourceAuthority default = 'Darwin Core pathway' {[https://dwc.tdwg.org/list/#dwc_pathway]} {dwc:pathway vocabulary API [https://api.gbif.org/v1/vocabularies/Pathway/concepts]}")
public static DQResponse<AmendmentValue> amendmentPathwayStandardized(
@ActedUpon("dwc:pathway") String pathway
) {
return amendmentPathwayStandardized(pathway,null);
}
}
51 changes: 51 additions & 0 deletions src/test/java/org/filteredpush/qc/metadata/DwCMetadataDQTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1224,7 +1224,58 @@ public void testValidationPathwayStandard() {

}

/**
* Test method for {@link org.filteredpush.qc.metadata.DwCMetadataDQ#amendmentPathwayStandardized(java.lang.String, java.lang.String)}.
*/
@Test
public void testAmendmentPathwayStandardized() {

String pathway = "";
DQResponse<AmendmentValue> result = DwCMetadataDQ.amendmentPathwayStandardized(pathway, null);
logger.debug(result.getComment());
assertEquals(ResultState.INTERNAL_PREREQUISITES_NOT_MET.getLabel(), result.getResultState().getLabel());
assertNull(result.getValue());
assertNotNull(result.getComment());

pathway = "foo";
result = DwCMetadataDQ.amendmentPathwayStandardized(pathway, "https://invalid/invalidauthority");
logger.debug(result.getComment());
assertEquals(ResultState.EXTERNAL_PREREQUISITES_NOT_MET.getLabel(), result.getResultState().getLabel());
assertNull(result.getValue());
assertNotNull(result.getComment());

Map<String, String> vocabulary = MetadataSingleton.getInstance().getPathwayValues();
Set<String> keys = vocabulary.keySet();
Iterator<String> i = keys.iterator();
while (i.hasNext()){
pathway=i.next();
if (MetadataSingleton.getInstance().getPathwayTerms().containsKey(pathway)) {
result = DwCMetadataDQ.amendmentPathwayStandardized(pathway, null);
logger.debug(result.getComment());
assertEquals(ResultState.NOT_AMENDED.getLabel(), result.getResultState().getLabel());
assertNull(result.getValue());
assertNotNull(result.getComment());
} else {
String match = MetadataSingleton.getInstance().getPathwayValues().get(pathway);
result = DwCMetadataDQ.amendmentPathwayStandardized(pathway, null);
logger.debug(result.getComment());
assertEquals(ResultState.AMENDED.getLabel(), result.getResultState().getLabel());
assertEquals(match,result.getValue().getObject().get("dwc:pathway"));
assertNotNull(result.getComment());

if (pathway.equals(pathway.toLowerCase())) {
pathway = pathway.toUpperCase();
} else {
pathway = " " + pathway.toLowerCase();
}
result = DwCMetadataDQ.amendmentPathwayStandardized(pathway, null);
logger.debug(result.getComment());
assertEquals(ResultState.AMENDED.getLabel(), result.getResultState().getLabel());
assertEquals(match,result.getValue().getObject().get("dwc:pathway"));
assertNotNull(result.getComment());
}
}
}

/**
* Test method for {@link org.filteredpush.qc.metadata.DwCMetadataDQ#validationOccurrenceidStandard(java.lang.String)}.
Expand Down

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