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ISSUE: MCZ redmine 867 PURPOSE: Update taxon tests to current TG2 spe…
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…cifications. DESCRIPTION: Updating tdwg/bdq#120 VALIDATION_TAXONID_NOTEMPTY to current specification.  Adding an implementation of tdwg/bdq#121 VALIDATION_TAXONID_COMPLETE with notes about needing to update the specification.  Adding supporting RFC8141URN and LSID classes to help in identifying and parsing URNs and LSIDs to support tdwg/bdq#121.  Initial work in progress on implementation of AMENDMENT_SCIENTIFICNAME_FROM_TAXONID.
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@chicoreus
chicoreus committed Jun 8, 2022
1 parent 82960f4 commit 4261a4a
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187 changes: 159 additions & 28 deletions src/main/java/org/filteredpush/qc/sciname/DwCSciNameDQ.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
package org.filteredpush.qc.sciname;

import java.io.IOException;
import java.net.URI;
import java.net.URISyntaxException;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
Expand All @@ -43,6 +45,7 @@
* Implementation of the TDWG TG2 NAME (scientific name) related data quality tests.
*
* #82 VALIDATION_SCIENTIFICNAME_NOTEMPTY 7c4b9498-a8d9-4ebb-85f1-9f200c788595
* #120 VALIDATION_TAXONID_NOTEMPTY 401bf207-9a55-4dff-88a5-abcd58ad97fa
*
* #81 VALIDATION_KINGDOM_FOUND 125b5493-052d-4a0d-a3e1-ed5bf792689e
* #22 VALIDATION_PHYLUM_FOUND eaad41c5-1d46-4917-a08b-4fd1d7ff5c0f
Expand Down Expand Up @@ -76,11 +79,13 @@ public static DQResponse<ComplianceValue> validationPhylumFound(@ActedUpon("dwc:
* Provides: #22 VALIDATION_PHYLUM_FOUND
*
* @param phylum the provided dwc:phylum to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_PHYLUM_FOUND", description="Does the value of dwc:phylum occur at rank of Phylum in bdq:sourceAuthority?")
@Provides("eaad41c5-1d46-4917-a08b-4fd1d7ff5c0f")
public static DQResponse<ComplianceValue> validationPhylumFound(@ActedUpon("dwc:phylum") String phylum, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationPhylumFound(@ActedUpon("dwc:phylum") String phylum,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -115,11 +120,13 @@ public static DQResponse<ComplianceValue> validationFamilyFound(@ActedUpon("dwc:
* Provides: #28 VALIDATION_FAMILY_FOUND
*
* @param family the provided dwc:family to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_FAMILY_FOUND", description="Does the value of dwc:family occur at rank of Family in bdq:sourceAuthority?")
@Provides("3667556d-d8f5-454c-922b-af8af38f613c")
public static DQResponse<ComplianceValue> validationFamilyFound(@ActedUpon("dwc:family") String family, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationFamilyFound(@ActedUpon("dwc:family") String family,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -536,32 +543,67 @@ public DQResponse<ComplianceValue> validationTaxonAmbiguous(@ActedUpon("dwc:clas

return result;
}

public static DQResponse<AmendmentValue> amendmentScientificnameFromTaxonid(
@Consulted("dwc:taxonID") String taxonID,
@ActedUpon("dwc:scientificName") String scientificName
) {
return amendmentScientificnameFromTaxonid(taxonID, scientificName, null);
}

/**
* #71 Amendment SingleRecord Completeness: scientificname from taxonid
* Propose an amendment to the value of dwc:scientificName using the taxonID value from bdq:sourceAuthority.
*
* Provides: AMENDMENT_SCIENTIFICNAME_FROM_TAXONID
* Provides: #71 AMENDMENT_SCIENTIFICNAME_FROM_TAXONID
*
* @param taxonID the provided dwc:taxonID to evaluate
* @param scientificName the provided dwc:scientificName to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type AmendmentValue to return
*/
@Amendment(label="AMENDMENT_SCIENTIFICNAME_FROM_TAXONID", description="Propose an amendment to the value of dwc:scientificName using the taxonID value from bdq:sourceAuthority.")
@Provides("f01fb3f9-2f7e-418b-9f51-adf50f202aea")
public DQResponse<AmendmentValue> amendmentScientificnameFromTaxonid(@ActedUpon("dwc:taxonID") String taxonID, @ActedUpon("dwc:scientificName") String scientificName) {
public static DQResponse<AmendmentValue> amendmentScientificnameFromTaxonid(
@Consulted("dwc:taxonID") String taxonID,
@ActedUpon("dwc:scientificName") String scientificName,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority
) {

DQResponse<AmendmentValue> result = new DQResponse<AmendmentValue>();

//TODO: Implement specification
// EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority
// service was not available; INTERNAL_PREREQUISITES_NOT_MET
// if dwc:taxonID is EMPTY, the value of dwc:taxonID is ambiguous
// or dwc:scientificName was not EMPTY; AMENDED if dwc:scientificName
// was added from a successful lookup of dwc:taxonID in the
//bdq:sourceAuthority; otherwise NOT_AMENDED
// is not available; INTERNAL_PREREQUISITES_NOT_MET if dwc:taxonID
// is EMPTY, the value of dwc:taxonID is ambiguous or dwc:scientificName
// was not EMPTY; FILLED_IN the value of dwc:scientificName
// if the value of dwc:taxonID could be unambiguously interpreted
// as a value in bdq:sourceAuthority; otherwise NOT_AMENDED
// bdq:sourceAuthority default = "GBIF Backbone Taxonomy" [https://doi.org/10.15468/39omei],
// "API endpoint" [https://api.gbif.org/v1/species?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c&name=]
//

//TODO: Parameters. This test is defined as parameterized.
// bdq:sourceAuthority
// bdq:sourceAuthority default="GBIF Backbone Taxonomy"

if (sourceAuthority==null) {
try {
sourceAuthority = new SciNameSourceAuthority(EnumSciNameSourceAuthority.GBIF_BACKBONE_TAXONOMY);
} catch (SourceAuthorityException e) {
logger.error(e.getMessage(),e);
}
}
if (SciNameUtils.isEmpty(taxonID)) {
result.addComment("dwc:taxonID does not contains a value.");
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
} else if (!SciNameUtils.isEmpty(scientificName)) {
result.addComment("dwc:scientificName already contains a value ["+ scientificName +"].");
result.setResultState(ResultState.INTERNAL_PREREQUISITES_NOT_MET);
} else {

}

return result;

}

public static DQResponse<ComplianceValue> validationClassFound(@ActedUpon("dwc:class") String taxonomic_class) {
Expand All @@ -574,11 +616,14 @@ public static DQResponse<ComplianceValue> validationClassFound(@ActedUpon("dwc:c
* Provides: #77 VALIDATION_CLASS_FOUND
*
* @param taxonomic_class the provided dwc:class to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_CLASS_FOUND", description="Does the value of dwc:class occur at rank of Class in bdq:sourceAuthority?")
@Provides("2cd6884e-3d14-4476-94f7-1191cfff309b")
public static DQResponse<ComplianceValue> validationClassFound(@ActedUpon("dwc:class") String taxonomic_class, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationClassFound(
@ActedUpon("dwc:class") String taxonomic_class,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -614,11 +659,13 @@ public static DQResponse<ComplianceValue> validationKingdomFound(@ActedUpon("dwc
* Provides: #81 VALIDATION_KINGDOM_FOUND
*
* @param kingdom the provided dwc:kingdom to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_KINGDOM_FOUND", description="Does the value of dwc:kingdom occur at rank of Kingdom in bdq:sourceAuthority?")
@Provides("125b5493-052d-4a0d-a3e1-ed5bf792689e")
public static DQResponse<ComplianceValue> validationKingdomFound(@ActedUpon("dwc:kingdom") String kingdom, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationKingdomFound(@ActedUpon("dwc:kingdom") String kingdom,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -682,11 +729,13 @@ public static DQResponse<ComplianceValue> validationOrderFound(@ActedUpon("dwc:o
* Provides: #83 VALIDATION_ORDER_FOUND
*
* @param order the provided dwc:order to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_ORDER_FOUND", description="Does the value of dwc:order occur at rank of Order in bdq:sourceAuthority?")
@Provides("81cc974d-43cc-4c0f-a5e0-afa23b455aa3")
public static DQResponse<ComplianceValue> validationOrderFound(@ActedUpon("dwc:order") String order, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationOrderFound(@ActedUpon("dwc:order") String order,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -889,17 +938,19 @@ public static DQResponse<ComplianceValue> validationTaxonEmpty(
}

/**
* #120 Validation SingleRecord Completeness: taxonid empty
* Is there a value in dwc:taxonID?
*
* Provides: VALIDATION_TAXONID_EMPTY
* Provides: #120 VALIDATION_TAXONID_NOTEMPTY
*
* @param taxonID the provided dwc:taxonID to evaluate
* @return DQResponse the response of type ComplianceValue to return
*/
@Provides("urn:uuid:401bf207-9a55-4dff-88a5-abcd58ad97fa")
public static DQResponse<ComplianceValue> validationTaxonidEmpty(@ActedUpon("dwc:taxonID") String taxonID) {
@Validation(label="VALIDATION_TAXONID_NOTEMPTY", description="Is there a value in dwc:taxonID?")
@Provides("401bf207-9a55-4dff-88a5-abcd58ad97fa")
public static DQResponse<ComplianceValue> validationTaxonidNotempty(@ActedUpon("dwc:taxonID") String taxonID) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
// COMPLIANT if dwc:taxonID is not EMPTY; otherwise NOT_COMPLIANT
//

Expand All @@ -916,28 +967,105 @@ public static DQResponse<ComplianceValue> validationTaxonidEmpty(@ActedUpon("dwc
}

/**
* #121 Validation SingleRecord Conformance: taxonid ambiguous
* Does the value of dwc:taxonID contain both a URI and namespace indicator?
*
* Provides: VALIDATION_TAXONID_AMBIGUOUS
* Provides: #121 VALIDATION_TAXONID_COMPLETE
*
* @param taxonID the provided dwc:taxonID to evaluate
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_TAXONID_COMPLETE", description="Does the value of dwc:taxonID contain both a URI and namespace indicator?")
@Provides("a82c7e3a-3a50-4438-906c-6d0fefa9e984")
public DQResponse<ComplianceValue> validationTaxonidAmbiguous(@ActedUpon("dwc:taxonID") String taxonID) {
public static DQResponse<ComplianceValue> validationTaxonidComplete(@ActedUpon("dwc:taxonID") String taxonID) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

//TODO: Specification needs work.
// something like COMPLIANT if taxonID is a validly formed LSID, or taxonID
// is a validly formed URN with at least NID and NSS, or taxonID is a
// validly formed URI with host and path where path consists of
// more than just "/", and if host is www.gbif.org and path begins with
// "/species/", the path contains additional trailing characters, otherwise
// NOT_COMPLIANT

//TODO: Implement specification
// EXTERNAL_PREREQUISITES_NOT_MET if the GBIF backbone taxonomy
// service was not available; INTERNAL_PREREQUISITES_NOT_MET
// if dwc:taxonID is EMPTY or does not include the resolving
// authority; COMPLIANT if the value of dwc:taxonID is resolvable;
//otherwise NOT_COMPLIANT
// INTERNAL_PREREQUISITES_NOT_MET if dwc:taxonID is EMPTY;
// COMPLIANT if dwc:taxonID contains both a URI and a namespace
// indicator; otherwise NOT_COMPLIANT


if (SciNameUtils.isEmpty(taxonID)) {
result.addComment("No value provided for taxonId.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
} else {
try {
RFC8141URN urn = new RFC8141URN(taxonID);
if (urn.getNid().equalsIgnoreCase("lsid")) {
try {
LSID lsid = new LSID(taxonID);
lsid.getAuthority();
lsid.getNamespace();
lsid.getObjectID();
result.addComment("Provided taxonID recognized as an LSID.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} catch (URNFormatException e2) {
logger.debug(e2.getMessage());
result.addComment("Provided value for taxonID ["+taxonID+"] claims to be an lsid, but is not correctly formatted as such.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
} else {
logger.debug(urn.getNid());
logger.debug(urn.getNss());
if (urn.getNid().length()>0 && urn.getNss().length()>0) {
result.addComment("Provided taxonID recognized as an URN.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
} else {
result.addComment("Provided taxonID appears to be a URN, but doesn't have both NID and NSS");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
}
} catch (URNFormatException e) {
logger.debug(e.getMessage());
try {
URI uri = new URI(taxonID);
logger.debug(uri.getScheme());
logger.debug(uri.getAuthority());
logger.debug(uri.getHost());
logger.debug(uri.getPath());
if (uri.getHost()!=null && uri.getPath()!=null
&& uri.getHost().length()>0 && uri.getPath().length()>0
&& !uri.getPath().equals("/")) {
if (uri.getHost().equalsIgnoreCase("www.gbif.org") && uri.getPath().equals("/species/")) {
result.addComment("Provided taxonID recognized as GBIF species URL, but lacks the ID ["+taxonID+"]");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
} else {
result.addComment("Provided taxonID recognized as an URI with host, and path.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.COMPLIANT);
}
} else {
result.addComment("Provided taxonID may be a URI, but doesn't have host and path ["+taxonID+"]");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
} catch (URISyntaxException e1) {
logger.debug(e1);
result.addComment("Provided value for taxonID ["+taxonID+"] is not a URN or a URI.");
result.setResultState(ResultState.RUN_HAS_RESULT);
result.setValue(ComplianceValue.NOT_COMPLIANT);
}
}

}
return result;
}

public DQResponse<ComplianceValue> validationGenusFound(@ActedUpon("dwc:genus") String genus) {
public static DQResponse<ComplianceValue> validationGenusFound(@ActedUpon("dwc:genus") String genus) {
return validationGenusFound(genus, null);
}

Expand All @@ -947,11 +1075,13 @@ public DQResponse<ComplianceValue> validationGenusFound(@ActedUpon("dwc:genus")
* Provides: #122 VALIDATION_GENUS_FOUND
*
* @param genus the provided dwc:genus to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type ComplianceValue to return
*/
@Validation(label="VALIDATION_GENUS_FOUND", description="Does the value of dwc:genus occur at the rank of Genus in bdq:sourceAuthority?")
@Provides("f2ce7d55-5b1d-426a-b00e-6d4efe3058ec")
public static DQResponse<ComplianceValue> validationGenusFound(@ActedUpon("dwc:genus") String genus, @Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
public static DQResponse<ComplianceValue> validationGenusFound(@ActedUpon("dwc:genus") String genus,
@Parameter(name="bdq:sourceAuthority") SciNameSourceAuthority sourceAuthority) {
DQResponse<ComplianceValue> result = new DQResponse<ComplianceValue>();

// Specification
Expand Down Expand Up @@ -1135,6 +1265,7 @@ public DQResponse<ComplianceValue> validationTaxonrankNotstandard(@ActedUpon("dw
* Provides: AMENDMENT_TAXONRANK_STANDARDIZED
*
* @param taxonRank the provided dwc:taxonRank to evaluate
* @param sourceAuthority the bdq:sourceAuthority to consult, defaults to GBIF Backbone Taxonomy if null
* @return DQResponse the response of type AmendmentValue to return
*/
@Provides("e39098df-ef46-464c-9aef-bcdeee2a88cb")
Expand Down
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