Skip to content

Commit

Permalink
ISSUE: tdwg/bdq#163 PURPOSE: Implementation of Amendment taxonRank St…
Browse files Browse the repository at this point in the history 
…andardized. DESCRIPTION: Minimal implmementation using hardcoded copy of current values able to match on differences in case and a few alternative text forms. Needs lookup and cache implementation and darwin cloud implementation. Working minimal implementation including unit test.
  • Loading branch information
@chicoreus
chicoreus committed Aug 19, 2022
1 parent 6dacf32 commit edab269
Show file tree
Hide file tree
Showing 4 changed files with 166 additions and 29 deletions.
134 changes: 133 additions & 1 deletion src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -70,6 +70,7 @@
*
* #57 AMENDMENT_TAXONID_FROM_TAXON 431467d6-9b4b-48fa-a197-cd5379f5e889
* #71 AMENDMENT_SCIENTIFICNAME_FROM_TAXONID f01fb3f9-2f7e-418b-9f51-adf50f202aea
* #163 AMENDMENT_TAXONRANK_STANDARDIZED e39098df-ef46-464c-9aef-bcdeee2a88cb
*
* Also, with amendmentTaxonidFromTaxon(taxon, sourceAuthority, replaceExisting) provides
* a variant of #57 that allows existing taxonID values to be conformed to a specified sourceAuthority
Expand Down Expand Up @@ -1860,8 +1861,139 @@ public static DQResponse<ComplianceValue> validationTaxonrankStandard(

return result;
}


/**
* Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.
*
* Provides: AMENDMENT_TAXONRANK_STANDARDIZED
*
* @param taxonRank the provided dwc:taxonRank to evaluate
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_TAXONRANK_STANDARDIZED", description="Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.")
@Provides("e39098df-ef46-464c-9aef-bcdeee2a88cb")
public static DQResponse<AmendmentValue> amendmentTaxonrankStandardized(
@ActedUpon("dwc:taxonRank") String taxonRank,
@Parameter(name="bdq:sourceAuthority") String sourceAuthority
){
DQResponse<AmendmentValue> result = new DQResponse<AmendmentValue>();

// Specification
// EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority
// is not available; AMENDED the value of dwc:taxonRank if
// it could be unambiguously interpreted as a value in bdq:sourceAuthority;
// otherwise NOT_AMENDED bdq:sourceAuthority default = "Taxonomic
// Rank GBIF Vocabulary" [https://rs.gbif.org/vocabulary/gbif/rank.xml]

// Parameters. This test is defined as parameterized.
// bdq:sourceAuthority default="Taxonomic Rank GBIF Vocabulary"
if (sourceAuthority==null) {
sourceAuthority = "https://rs.gbif.org/vocabulary/gbif/rank.xml";
}
if (SciNameUtils.isEmpty(taxonRank)) {
result.addComment("No value provided value for taxonRank");
result.setResultState(ResultState.NOT_AMENDED);
} else {
try {
if (sourceAuthority.equals("https://rs.gbif.org/vocabulary/gbif/rank.xml") || sourceAuthority.equals("Taxonomic Rank GBIF Vocabulary")) {
// TODO: Lookup and cache file
HashSet<String> values = new HashSet<String>();
values.add("domain");
values.add("kingdom");
values.add("subkingdom");
values.add("superphylum");
values.add("phylum");
values.add("subphylum");
values.add("superclass");
values.add("class");
values.add("subclass");
values.add("supercohort");
values.add("cohort");
values.add("subcohort");
values.add("superorder");
values.add("order");
values.add("suborder");
values.add("infraorder");
values.add("superfamily");
values.add("family");
values.add("subfamily");
values.add("tribe");
values.add("subtribe");
values.add("genus");
values.add("subgenus");
values.add("section");
values.add("subsection");
values.add("series");
values.add("subseries");
values.add("speciesAggregate");
values.add("species");
values.add("subspecificAggregate");
values.add("subspecies");
values.add("variety");
values.add("subvariety");
values.add("form");
values.add("subform");
values.add("cultivarGroup");
values.add("cultivar");
values.add("strain");

if (values.contains(taxonRank)) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] found in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.NOT_AMENDED);
} else {
if (values.contains(taxonRank.trim().toLowerCase())) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", taxonRank.toLowerCase());
AmendmentValue amendment = new AmendmentValue(keyValue);
result.setValue(amendment);
} else if (taxonRank.trim().equals("var.")) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", "variety");
AmendmentValue amendment = new AmendmentValue(keyValue);
} else if (taxonRank.trim().toLowerCase().equals("forma")) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", "form");
AmendmentValue amendment = new AmendmentValue(keyValue);
} else if (taxonRank.trim().toLowerCase().equals("cultivar group")) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", "cultivarGroup");
AmendmentValue amendment = new AmendmentValue(keyValue);
} else if (taxonRank.trim().toLowerCase().equals("species aggregate")) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", "speciesAggregate");
AmendmentValue amendment = new AmendmentValue(keyValue);
} else if (taxonRank.trim().toLowerCase().equals("subspecific aggregate") || taxonRank.trim().toLowerCase().equals("subspecies aggregate")) {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] matched to value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.AMENDED);
Map<String,String> keyValue = new HashMap<String,String>();
keyValue.put("dwc:taxonRank", "subspecificAggregate");
AmendmentValue amendment = new AmendmentValue(keyValue);
} else {
result.addComment("Provided value for taxonRank ["+ taxonRank+"] not matched to a value in the GBIF taxon rank vocabulary.");
result.setResultState(ResultState.NOT_AMENDED);
}
}
} else {
throw new UnsupportedSourceAuthorityException("Specified bdq:sourceAuthority not supported");
}
} catch (UnsupportedSourceAuthorityException e) {
result.addComment("Unable to process:" + e.getMessage());
result.setResultState(ResultState.EXTERNAL_PREREQUISITES_NOT_MET);
}
}

return result;
}
/**
* Provides internals for validationKingdomNotFound etc.
*
Expand Down
16 changes: 16 additions & 0 deletions src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQDefaults.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -467,6 +467,7 @@ public static DQResponse<ComplianceValue> validationTaxonrankNotempty(@ActedUpon

/**
* Does the value of dwc:taxonRank occur in bdq:sourceAuthority?
* where bdq:sourceAuthority is the default GBIF taxon rank vocabulary.
*
* Provides: VALIDATION_TAXONRANK_STANDARD
*
Expand All @@ -479,6 +480,21 @@ public DQResponse<ComplianceValue> validationTaxonrankStandard(@ActedUpon("dwc:t
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();
return DwCSciNameDQ.validationTaxonrankStandard(taxonRank, null);
}

/**
* Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.
* where bdq:sourceAuthority is the default GBIF taxon rank vocabulary.
*
* Provides: AMENDMENT_TAXONRANK_STANDARDIZED
*
* @param taxonRank the provided dwc:taxonRank to evaluate
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_TAXONRANK_STANDARDIZED", description="Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.")
@Provides("e39098df-ef46-464c-9aef-bcdeee2a88cb")
public DQResponse<AmendmentValue> amendmentTaxonrankStandardized(@ActedUpon("dwc:taxonRank") String taxonRank) {
return DwCSciNameDQ.amendmentTaxonrankStandardized(taxonRank, null);
}

/**
* Can the combination of higher classification taxonomic terms be unambiguously resolved using bdq:sourceAuthority?
Expand Down
27 changes: 0 additions & 27 deletions src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ_stubs.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,31 +47,4 @@ public DQResponse<ComplianceValue> validationClassificationUnambiguous(@ActedUpo
}


/**
* Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.
*
* Provides: AMENDMENT_TAXONRANK_STANDARDIZED
*
* @param taxonRank the provided dwc:taxonRank to evaluate
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_TAXONRANK_STANDARDIZED", description="Propose amendment to the value of dwc:taxonRank using bdq:sourceAuthority.")
@Provides("e39098df-ef46-464c-9aef-bcdeee2a88cb")
public DQResponse<AmendmentValue> amendmentTaxonrankStandardized(@ActedUpon("dwc:taxonRank") String taxonRank) {
DQResponse<AmendmentValue> result = new DQResponse<AmendmentValue>();

//TODO: Implement specification
// EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority
// is not available; AMENDED the value of dwc:taxonRank if
// it could be unambiguously interpreted as a value in bdq:sourceAuthority;
// otherwise NOT_AMENDED bdq:sourceAuthority default = "Taxonomic
// Rank GBIF Vocabulary" [https://rs.gbif.org/vocabulary/gbif/rank.xml]
//

//TODO: Parameters. This test is defined as parameterized.
// bdq:sourceAuthority default="Taxonomic Rank GBIF Vocabulary"

return result;
}

}
18 changes: 17 additions & 1 deletion src/test/java/org/filteredpush/qc/sciname/TestDwCSciNameDQ.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -437,7 +437,23 @@ public void testValidationTaxonrankNotstandard() {
*/
@Test
public void testAmendmentTaxonrankStandardized() {
// TODO: fail("Not yet implemented");
String taxonRank = "species";
DQResponse<AmendmentValue> response = DwCSciNameDQ.amendmentTaxonrankStandardized(taxonRank, null);
logger.debug(response.getComment());
assertEquals(ResultState.NOT_AMENDED.getLabel(), response.getResultState().getLabel());
assertNull(response.getValue());

taxonRank = "Species";
response = DwCSciNameDQ.amendmentTaxonrankStandardized(taxonRank, null);
logger.debug(response.getComment());
assertEquals(ResultState.AMENDED.getLabel(), response.getResultState().getLabel());
assertEquals("species",response.getValue().getObject().get("dwc:taxonRank"));

taxonRank = "kingdom";
response = DwCSciNameDQ.amendmentTaxonrankStandardized(taxonRank, "https://www.example.com/example");
logger.debug(response.getComment());
assertEquals(ResultState.EXTERNAL_PREREQUISITES_NOT_MET.getLabel(), response.getResultState().getLabel());

}

}

0 comments on commit edab269

Please sign in to comment.