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Cleaning up handling of communication problems in some methods that q…
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…uery Getty TGN, throwing source authority exceptions, more cleanup of handling source authorities with exceptions. Adding a stub for tdwg/bdq#287.
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@chicoreus
chicoreus committed Aug 27, 2024
1 parent fc785f7 commit efb9018
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189 changes: 125 additions & 64 deletions src/main/java/org/filteredpush/qc/georeference/DwCGeoRefDQ.java
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Original file line number Diff line number Diff line change
Expand Up @@ -185,63 +185,70 @@ public static DQResponse<ComplianceValue> validationCountryFound(
sourceAuthority = GettyLookup.GETTY_TGN;
}

if (GEOUtil.isEmpty(country)) {
result.addComment("dwc:country is empty");
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
} else {
if (sourceAuthority.equalsIgnoreCase(GettyLookup.GETTY_TGN)) {
Boolean cached = GeoUtilSingleton.getInstance().getTgnCountriesEntry(country);
if (cached!=null) {
if (cached) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a nation in the Getty Thesaurus of Geographic Names (TGN).");
try {
GeoRefSourceAuthority foo = new GeoRefSourceAuthority(sourceAuthority);
if (GEOUtil.isEmpty(country)) {
result.addComment("dwc:country is empty");
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
} else {
if (sourceAuthority.equalsIgnoreCase(GettyLookup.GETTY_TGN)) {
Boolean cached = GeoUtilSingleton.getInstance().getTgnCountriesEntry(country);
if (cached!=null) {
if (cached) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
} else {
GettyLookup lookup = new GettyLookup();
if (lookup.lookupCountry(country)==null) {
result.addComment("Error looking up country in " + sourceAuthority);
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
} else if (lookup.lookupCountry(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
GeoUtilSingleton.getInstance().addTgnCountry(country, true);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
GeoUtilSingleton.getInstance().addTgnCountry(country, false);
}
}
} else if (sourceAuthority.equalsIgnoreCase("NaturalEarth")) {
// ne_10m_admin_0_countries
if (GEOUtil.isCountryKnown(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a country name in the NaturalEarth admin regions.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.addComment("the value provided for dwc:country [" + country + "] is not a country name in the NaturalEarth admin regions.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
} else {
GettyLookup lookup = new GettyLookup();
if (lookup.lookupCountry(country)==null) {
result.addComment("Error looking up country in " + sourceAuthority);
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
} else if (lookup.lookupCountry(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a nation in the Getty Thesaurus of Geographic Names (TGN).");
} else if (sourceAuthority.equalsIgnoreCase("datahub.io")) {
if (CountryLookup.countryExistsHasCode(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a country name in the datahub.io list of countries.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
GeoUtilSingleton.getInstance().addTgnCountry(country, true);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a nation in the Getty Thesaurus of Geographic Names (TGN).");
result.addComment("the value provided for dwc:country [" + country + "] is not a country name in the datahub.io list of countries.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
GeoUtilSingleton.getInstance().addTgnCountry(country, false);
}
}
} else if (sourceAuthority.equalsIgnoreCase("NaturalEarth")) {
if (GEOUtil.isCountryKnown(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a country name in the NaturalEarth admin regions.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a country name in the NaturalEarth admin regions.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
} else if (sourceAuthority.equalsIgnoreCase("datahub.io")) {
if (CountryLookup.countryExistsHasCode(country)) {
result.addComment("the value provided for dwc:country [" + country + "] exists as a country name in the datahub.io list of countries.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} else {
result.addComment("the value provided for dwc:country [" + country + "] is not a country name in the datahub.io list of countries.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
result.addComment("Unknown bdq:sourceAuthority");
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
} else {
result.addComment("Unknown bdq:sourceAuthority");
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
} catch (SourceAuthorityException e) {
result.addComment("Error with bdq:sourceAuthority: " + e.getMessage());
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
return result;
}
Expand Down Expand Up @@ -3691,27 +3698,81 @@ public static DQResponse<AmendmentValue> amendmentCoordinatesTransposed(

return result;
}

/**
* Are the supplied geographic coordinates within a defined buffer of the center of the country?
*
* Provides: 287 ISSUE_COORDINATES_CENTEROFCOUNTRY
* Version: 2023-09-17
*
* @param decimalLatitude the provided dwc:decimalLatitude to evaluate as ActedUpon.
* @param decimalLongitude the provided dwc:decimalLongitude to evaluate as ActedUpon.
* @param countryCode the provided dwc:countryCode to evaluate as Consulted.
* @return DQResponse the response of type AmendmentValue to return
* @param sourceAuthority a {@link java.lang.String} object.
*/
@Amendment(label="ISSUE_COORDINATES_CENTEROFCOUNTRY", description="Are the supplied geographic coordinates within a defined buffer of the center of the country?")
@Provides("256e51b3-1e08-4349-bb7e-5186631c3f8e")
@ProvidesVersion("https://rs.tdwg.org/bdqcore/terms/256e51b3-1e08-4349-bb7e-5186631c3f8e/2024-08-20")
@Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL_PREREQUISITES_NOT_MET if any of dwc:countryCode, dwc:decimalLatitude, dwc:decimalLongitude are EMPTY; POTENTIAL_ISSUE if the geographic coordinates are within the distance given by bdq:spatialBufferInMeters from the center (or one of the centers), of the bdq:sourceAuthority provides more than one per country code of the supplied dwc:countryCode as represented in the bdq:sourceAuthority; otherwise NOT_ISSUE.")
public static DQResponse<AmendmentValue> issueCoordinatesCenterofcountry(
@ActedUpon("dwc:decimalLatitude") String decimalLatitude,
@ActedUpon("dwc:decimalLongitude") String decimalLongitude,
@Consulted("dwc:countryCode") String countryCode,
@Parameter(name="bdq:spatialBufferInMeters") String spatialBufferInMeters,
@Parameter(name="bdq:sourceAuthority") String sourceAuthority
) {
DQResponse<AmendmentValue> result = new DQResponse<AmendmentValue>();

// TODO: Specification
// EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available;
// INTERNAL_PREREQUISITES_NOT_MET if any of dwc:countryCode,
// dwc:decimalLatitude, dwc:decimalLongitude are EMPTY; POTENTIAL_ISSUE if the
// geographic coordinates are within the distance given by
// bdq:spatialBufferInMeters from the center (or one of the centers), of the
// bdq:sourceAuthority provides more than one per country code of the supplied
// dwc:countryCode as represented in the bdq:sourceAuthority; otherwise
// NOT_ISSUE.

// Parameters
// bdq:spatialBufferInMeters default = "5000"
// bdq:sourceAuthority default = "GBIF Catalogue of Country Centroides"
// {[https://raw.githubusercontent.com/jhnwllr/catalogue-of-centroids/master/PCLI.tsv]}

if (GEOUtil.isEmpty(sourceAuthority)) {
sourceAuthority = "GBIF Catalogue of Country Centroides";
}
if (GEOUtil.isEmpty(spatialBufferInMeters)) {
sourceAuthority = "3000";
}

try {
GeoRefSourceAuthority sourceAuthorityObject = new GeoRefSourceAuthority(sourceAuthority);
if (sourceAuthorityObject.getAuthority().equals(EnumGeoRefSourceAuthority.INVALID)) {
throw new SourceAuthorityException("Invalid Source Authority");
}

if (GEOUtil.isEmpty(decimalLatitude)) {
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
result.addComment("The value provided for dwc:decimalLatitude is empty");
} else if (GEOUtil.isEmpty(decimalLongitude)) {
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
result.addComment("The value provided for dwc:decimalLongitude is empty");
} else if (GEOUtil.isEmpty(countryCode)) {
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
result.addComment("The value provided for dwc:countryCode is empty");
} else {
// TODO: Implementation


}
} catch (SourceAuthorityException e) {
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
result.addComment("Error with specified Source Authority: " + e.getMessage());
}

return result;
}


// TODO: Implementation of VALIDATION_COUNTRY_FOUND is not up to date with current version: https://rs.tdwg.org/bdq/terms/69b2efdc-6269-45a4-aecb-4cb99c2ae134/2024-08-19 see line: 155
// TODO: Implementation of AMENDMENT_COORDINATES_FROM_VERBATIM is not up to date with current version: https://rs.tdwg.org/bdq/terms/3c2590c7-af8a-4eb4-af57-5f73ba9d1f8e/2024-08-19 see line: 389
// TODO: Implementation of VALIDATION_COUNTRY_NOTEMPTY is not up to date with current version: https://rs.tdwg.org/bdq/terms/6ce2b2b4-6afe-4d13-82a0-390d31ade01c/2023-09-17 see line: 743
// TODO: Implementation of AMENDMENT_COORDINATES_CONVERTED is not up to date with current version: https://rs.tdwg.org/bdq/terms/620749b9-7d9c-4890-97d2-be3d1cde6da8/2023-09-18 see line: 796
// TODO: Implementation of AMENDMENT_COUNTRYCODE_STANDARDIZED is not up to date with current version: https://rs.tdwg.org/bdq/terms/fec5ffe6-3958-4312-82d9-ebcca0efb350/2023-09-17 see line: 917
// TODO: Implementation of VALIDATION_COORDINATES_COUNTRYCODE_CONSISTENT is not up to date with current version: https://rs.tdwg.org/bdq/terms/adb27d29-9f0d-4d52-b760-a77ba57a69c9/2023-09-17 see line: 1019
// TODO: Implementation of AMENDMENT_MINDEPTH-MAXDEPTH_FROM_VERBATIM is not up to date with current version: https://rs.tdwg.org/bdq/terms/c5658b83-4471-4f57-9d94-bf7d0a96900c/2024-08-03 see line: 1139
// TODO: Implementation of VALIDATION_GEODETICDATUM_STANDARD is not up to date with current version: https://rs.tdwg.org/bdq/terms/7e0c0418-fe16-4a39-98bd-80e19d95b9d1/2023-09-17 see line: 1459
// TODO: Implementation of AMENDMENT_GEODETICDATUM_STANDARDIZED is not up to date with current version: https://rs.tdwg.org/bdq/terms/0345b325-836d-4235-96d0-3b5caf150fc0/2024-08-05 see line: 1518
// TODO: Implementation of VALIDATION_COUNTRY_COUNTRYCODE_CONSISTENT is not up to date with current version: https://rs.tdwg.org/bdq/terms/b23110e7-1be7-444a-a677-cdee0cf4330c/2023-09-18 see line: 1599
// TODO: Implementation of AMENDMENT_MINELEVATION-MAXELEVATION_FROM_VERBATIM is not up to date with current version: https://rs.tdwg.org/bdq/terms/2d638c8b-4c62-44a0-a14d-fa147bf9823d/2024-08-03 see line: 1701
// TODO: Implementation of AMENDMENT_COUNTRYCODE_FROM_COORDINATES is not up to date with current version: https://rs.tdwg.org/bdq/terms/8c5fe9c9-4ba9-49ef-b15a-9ccd0424e6ae/2024-08-18 see line: 1925
// TODO: Implementation of VALIDATION_GEODETICDATUM_NOTEMPTY is not up to date with current version: https://rs.tdwg.org/bdq/terms/239ec40e-a729-4a8e-ba69-e0bf03ac1c44/2023-09-18 see line: 2002
// TODO: Implementation of VALIDATION_DECIMALLONGITUDE_NOTEMPTY is not up to date with current version: https://rs.tdwg.org/bdq/terms/9beb9442-d942-4f42-8b6a-fcea01ee086a/2023-09-18 see line: 2168
// TODO: Implementation of VALIDATION_COUNTRYCODE_NOTEMPTY is not up to date with current version: https://rs.tdwg.org/bdq/terms/853b79a2-b314-44a2-ae46-34a1e7ed85e4/2023-09-18 see line: 2203
// TODO: Implementation of AMENDMENT_GEODETICDATUM_ASSUMEDDEFAULT is not up to date with current version: https://rs.tdwg.org/bdq/terms/7498ca76-c4d4-42e2-8103-acacccbdffa7/2024-08-18 see line: 2244
// TODO: Implementation of VALIDATION_MINDEPTH_INRANGE is not up to date with current version: https://rs.tdwg.org/bdq/terms/04b2c8f3-c71b-4e95-8e43-f70374c5fb92/2023-09-18 see line: 2316
// TODO: Implementation of VALIDATION_MINELEVATION_LESSTHAN_MAXELEVATION is not up to date with current version: https://rs.tdwg.org/bdq/terms/d708526b-6561-438e-aa1a-82cd80b06396/2023-09-18 see line: 2390
// TODO: Implementation of VALIDATION_COORDINATEUNCERTAINTY_INRANGE is not up to date with current version: https://rs.tdwg.org/bdq/terms/c6adf2ea-3051-4498-97f4-4b2f8a105f57/2023-09-18 see line: 2455
// TODO: Implementation of VALIDATION_DECIMALLATITUDE_NOTEMPTY is not up to date with current version: https://rs.tdwg.org/bdq/terms/7d2485d5-1ba7-4f25-90cb-f4480ff1a275/2023-09-18 see line: 2581
// TODO: Implementation of VALIDATION_MAXDEPTH_INRANGE is not up to date with current version: https://rs.tdwg.org/bdq/terms/3f1db29a-bfa5-40db-9fd1-fde020d81939/2023-09-18 see line: 2620
// TODO: Implementation of VALIDATION_STATEPROVINCE_FOUND is not up to date with current version: https://rs.tdwg.org/bdq/terms/4daa7986-d9b0-4dd5-ad17-2d7a771ea71a/2023-09-18 see line: 2693
}
3 changes: 3 additions & 0 deletions src/main/java/org/filteredpush/qc/georeference/EnumGeoRefSourceAuthority.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,9 @@ public enum EnumGeoRefSourceAuthority {
GADM_ADM1,
GETTY_TGN,
INVALID;

// TODO; add datahub.io
// TODO: add ne_10m_admin_0_countries

/**
* <p>getName.</p>
Expand Down
32 changes: 15 additions & 17 deletions src/main/java/org/filteredpush/qc/georeference/util/GettyLookup.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -71,8 +71,9 @@ private void init() {
* @return true if the country is found as a sovereign nation level entity in TGN matching
* any form of the name, false if the country is not found as a sovereign nation lavel entity
* in TGN, null on an exception querying TGN.
* @throws SourceAuthorityException
*/
public Boolean lookupCountry(String country) {
public Boolean lookupCountry(String country) throws SourceAuthorityException {

Boolean retval = null;

Expand Down Expand Up @@ -103,7 +104,6 @@ public Boolean lookupCountry(String country) {
Unmarshaller unmarshaler = jc.createUnmarshaller();
Vocabulary response = (Vocabulary) unmarshaler.unmarshal(is);
System.out.println(response.getCount());
System.out.println(response.getCount());
if (response.getCount().compareTo(BigInteger.ONE)==0) {
// idiom for line above from BigInteger docs: (x.compareTo(y) <op> 0)
// one match
Expand All @@ -129,14 +129,13 @@ public Boolean lookupCountry(String country) {
retval = false;
}
} catch (JAXBException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
throw new SourceAuthorityException("Error interpreting json response returned from Getty TGN:" + e.getMessage());
} catch (MalformedURLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
throw new SourceAuthorityException("Error querying the Getty TGN:" + e.getMessage());
}
}
}
Expand All @@ -150,8 +149,9 @@ public Boolean lookupCountry(String country) {
* @param country preferred name of sovereign nation level entity to look up.
* @return true if the provided country matches a preferred name of a sovereign nation level
* entity in TGN, false if it does not, null on an error querying the TGN service.
* @throws SourceAuthorityException
*/
public Boolean lookupCountryExact(String country) {
public Boolean lookupCountryExact(String country) throws SourceAuthorityException {

Boolean retval = null;

Expand All @@ -178,8 +178,7 @@ public Boolean lookupCountryExact(String country) {
JAXBContext jc = JAXBContext.newInstance(Vocabulary.class);
Unmarshaller unmarshaler = jc.createUnmarshaller();
Vocabulary response = (Vocabulary) unmarshaler.unmarshal(is);
System.out.println(response.getCount());
System.out.println(response.getCount());
logger.debug(response.getCount());
if (response.getCount().compareTo(BigInteger.ONE)==0) {
String preferredTerm = response.getSubject().get(0).getPreferredTerm().getValue();
String cleanedPreferredTerm = preferredTerm.replaceAll("\\([A-Za-z ]+\\)$", "").trim();
Expand All @@ -193,14 +192,13 @@ public Boolean lookupCountryExact(String country) {
retval = false;
}
} catch (JAXBException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
throw new SourceAuthorityException("Error interpreting json response returned from Getty TGN:" + e.getMessage());
} catch (MalformedURLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
logger.error(e.getMessage());
throw new SourceAuthorityException("Error querying the Getty TGN:" + e.getMessage());
}

}
Expand Down

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