Corrected use of Terms and Values maps for validations and amendments…

…, added to unit tests. Added implementations for core tests tdwg/bdq#284 tdwg/bdq#275 and tdwg/bdq#276 along with default methods and unit tests.
FilteredPush · Jul 27, 2024 · 29be3f3 · 29be3f3
1 parent 815e2d7
commit 29be3f3
Show file tree

Hide file tree

Showing 7 changed files with 560 additions and 49 deletions.
diff --git a/src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQ.java b/src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQ.java
diff --git a/src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQDefaults.java b/src/main/java/org/filteredpush/qc/metadata/DwCMetadataDQDefaults.java
@@ -164,4 +164,63 @@ public static DQResponse<ComplianceValue> validationSexStandard(
     ) {
     	return validationSexStandard(sex, null);
     }
+
+    /**
+    * Propose amendment to the value of dwc:sex using bdq:sourceAuthority.
+    * Uses the default source authority
+    *
+    * Provides: 284 AMENDMENT_SEX_STANDARDIZED
+    * Version: 2024-03-25
+    *
+    * @param sex the provided dwc:sex to evaluate as ActedUpon.
+    * @return DQResponse the response of type AmendmentValue to return
+    */
+    @Amendment(label="AMENDMENT_SEX_STANDARDIZED", description="Propose amendment to the value of dwc:sex using bdq:sourceAuthority.")
+    @Provides("33c45ae1-e2db-462a-a59e-7169bb01c5d6")
+    @ProvidesVersion("https://rs.tdwg.org/bdq/terms/33c45ae1-e2db-462a-a59e-7169bb01c5d6/2024-03-25")
+    @Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:sex is EMPTY; AMENDED the value of dwc:sex if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED")
+    public static DQResponse<AmendmentValue> amendmentSexStandardized(
+        @ActedUpon("dwc:sex") String sex
+    ) {
+    	return amendmentSexStandardized(sex, null);
+    }
+
+    /**
+    * Does the value of dwc:degreeOfEstablishment occur in bdq:sourceAuthority?
+    * Uses the default source authority
+    *
+    * Provides: 275 VALIDATION_DEGREEOFESTABLISHMENT_STANDARD
+    * Version: 2024-02-09
+    *
+    * @param degreeOfEstablishment the provided dwc:degreeOfEstablishment to evaluate as ActedUpon.
+    * @return DQResponse the response of type ComplianceValue  to return
+    */
+    @Validation(label="VALIDATION_DEGREEOFESTABLISHMENT_STANDARD", description="Does the value of dwc:degreeOfEstablishment occur in bdq:sourceAuthority?")
+    @Provides("060e7734-607d-4737-8b2c-bfa17788bf1a")
+    @ProvidesVersion("https://rs.tdwg.org/bdq/terms/060e7734-607d-4737-8b2c-bfa17788bf1a/2024-02-09")
+    @Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL_PREREQUISITES_NOT_MET if dwc:degreeOfEstablishment is EMPTY; COMPLIANT if the value of dwc:degreeOfEstablishment is in the bdq:sourceAuthority; otherwise NOT_COMPLIANT.")
+    public static DQResponse<ComplianceValue> validationDegreeofestablishmentStandard(
+        @ActedUpon("dwc:degreeOfEstablishment") String degreeOfEstablishment
+    ) {
+    	return validationDegreeofestablishmentStandard(degreeOfEstablishment, null);
+    }
+
+    /**
+    * Propose amendment to the value of dwc:degreeOfEstablishment using the default bdq:sourceAuthority.
+    *
+    * Provides: 276 AMENDMENT_DEGREEOFESTABLISHMENT_STANDARDIZED
+    * Version: 2024-02-09
+    *
+    * @param degreeOfEstablishment the provided dwc:degreeOfEstablishment to evaluate as ActedUpon.
+    * @return DQResponse the response of type AmendmentValue to return
+    */
+    @Amendment(label="AMENDMENT_DEGREEOFESTABLISHMENT_STANDARDIZED", description="Propose amendment to the value of dwc:degreeOfEstablishment using bdq:sourceAuthority.")
+    @Provides("74ef1034-e289-4596-b5b0-cde73796697d")
+    @ProvidesVersion("https://rs.tdwg.org/bdq/terms/74ef1034-e289-4596-b5b0-cde73796697d/2024-02-09")
+    @Specification("EXTERNAL_PREREQUISITES_NOT_MET if the bdq:sourceAuthority is not available; INTERNAL PREREQUISITES_NOT_MET if dwc:degreeOfEstablishment is EMPTY; AMENDED the value of dwc:degreeOfEstablishment if it can be unambiguously matched to a term in bdq:sourceAuthority; otherwise NOT_AMENDED bdq:sourceAuthority default = 'Darwin Core degreeOfEstablishment' {[https://dwc.tdwg.org/list/#dwc_degreeOfEstablishment]} {dwc:degreeOfEstablishment vocabulary API [https://api.gbif.org/v1/vocabularies/DegreeOfEstablishment/concepts]}")
+    public static DQResponse<AmendmentValue> amendmentDegreeofestablishmentStandardized(
+        @ActedUpon("dwc:degreeOfEstablishment") String degreeOfEstablishment
+    ) {
+    	return amendmentDegreeofestablishmentStandardized(degreeOfEstablishment, null);
+    }
 }
diff --git a/src/main/java/org/filteredpush/qc/metadata/EnumMetadataSourceAuthority.java b/src/main/java/org/filteredpush/qc/metadata/EnumMetadataSourceAuthority.java
@@ -40,6 +40,10 @@ public enum EnumMetadataSourceAuthority {
 	 * GBIF Sex vocabulary
 	 */
 	GBIF_SEX,
+	/**
+	 * GBIF Degree of Establishment Vocabulary
+	 */
+	GBIF_DEGREEOFESTABLISHMENT,
 	/**
 	 * Darwin Core Class Names
 	 */

diff --git a/src/main/java/org/filteredpush/qc/metadata/MetadataSourceAuthority.java b/src/main/java/org/filteredpush/qc/metadata/MetadataSourceAuthority.java
@@ -88,6 +88,14 @@ public MetadataSourceAuthority(String authorityString) throws SourceAuthorityExc
 	    } else if (authorityString.equals("https://api.gbif.org/v1/vocabularies/Sex")) { 
 	    	this.authority = EnumMetadataSourceAuthority.GBIF_SEX;		
 
+	    } else if (authorityString.toUpperCase().equals("GBIF DEGREEOFESTABLISHMENT VOCABULARY")) { 
+	    	this.authority = EnumMetadataSourceAuthority.GBIF_DEGREEOFESTABLISHMENT;	
+	    } else if (authorityString.equals("https://api.gbif.org/v1/vocabularies/DegreeOfEstablishment")) { 
+	    	this.authority = EnumMetadataSourceAuthority.GBIF_DEGREEOFESTABLISHMENT;	
+	    } else if (authorityString.toUpperCase().equals("DEGREE OF ESTABLISHMENT CONTROLLED VOCABULARY LIST OF TERMS")) { 
+	    	// TODO: This should point at the TDWG vocabulary
+	    	this.authority = EnumMetadataSourceAuthority.GBIF_DEGREEOFESTABLISHMENT;	
+
 	    } else if (authorityString.toUpperCase().startsWith("HTTPS://INVALID/")) { 
 	    	this.authority = EnumMetadataSourceAuthority.INVALID;	
 	    } else { 

diff --git a/src/main/java/org/filteredpush/qc/metadata/services/GbifService.java b/src/main/java/org/filteredpush/qc/metadata/services/GbifService.java
@@ -112,18 +112,33 @@ public Map<String,List<String>> loadVocabulary(String vocabulary) {
 						String name = item.get("name").toString();
 						ArrayList<String> list = new ArrayList<String>();
 						list.add(name);
+						if (!name.equals(name.toLowerCase())) { 
+							list.add(name.toLowerCase());
+						}
 						logger.debug(name);
 						// label[0].value
 						JSONArray labels = (JSONArray) item.get("label");
 						for (int j=0; j<labels.size(); j++) { 
 							String label = ((JSONObject)labels.get(j)).get("value").toString();
 							list.add(label);
+							if (!label.equals(label.toLowerCase())) { 
+								list.add(label.toLowerCase());
+							}
+							if (!label.equals(label.toUpperCase())) { 
+								list.add(label.toUpperCase());
+							}
 						}
 						// externalDefinitions[0]
 						JSONArray terms = (JSONArray) item.get("externalDefinitions");
 						for (int j=0; j<terms.size(); j++) { 
 							String externalDefinition = terms.get(j).toString();
 							list.add(externalDefinition);
+							if (!externalDefinition.equals(externalDefinition.toLowerCase())) { 
+								list.add(externalDefinition.toLowerCase());
+							}
+							if (!externalDefinition.equals(externalDefinition.toUpperCase())) { 
+								list.add(externalDefinition.toUpperCase());
+							}
 						}
 						result.put(name,list);
 					}

diff --git a/src/main/java/org/filteredpush/qc/metadata/util/MetadataSingleton.java b/src/main/java/org/filteredpush/qc/metadata/util/MetadataSingleton.java
@@ -55,6 +55,9 @@ public class MetadataSingleton {
 	private Map<String,List<String>> sexTerms = new HashMap<String,List<String>>();
 	private Map<String,String> sexValues = new HashMap<String,String>();
 
+	private Map<String,List<String>> degreeOfEstablishmentTerms = new HashMap<String,List<String>>();
+	private Map<String,String> degreeOfEstablishmentValues = new HashMap<String,String>();
+
 	private MetadataSingleton() { 
 		init();
 	}
@@ -118,6 +121,16 @@ private void init() {
 				}
 			}
 
+			degreeOfEstablishmentTerms = gbif.loadVocabulary("DegreeOfEstablishment");
+			keys = degreeOfEstablishmentTerms.keySet().iterator();
+			while (keys.hasNext()) { 
+				String key = keys.next();
+				List<String> values = degreeOfEstablishmentTerms.get(key);
+				Iterator<String> i = values.iterator();
+				while (i.hasNext()) { 
+					degreeOfEstablishmentValues.put(i.next(), key);
+				}
+			}
 
 			loaded = true;
 			loadError = "";
@@ -127,39 +140,101 @@ private void init() {
 	}
 
 	/**
-	 * get the lifeStage key:value pairs
+	 * get the lifeStage value:key pairs
+	 * for finding vocabulary values for alternative labels
 	 *  
 	 * @return the map of lifeStage values from the vocabulary
 	 */
 	public Map<String,String> getLifeStageValues() { 
 		return lifeStageValues;
 	}
 	/**
-	 * get the pathway key:value pairs
+	 * get the liifeStage key:list of value pairs 
+	 * for finding values in the vocabulary
+	 * 
+	 * @return the map of lifeStage values from the vocabulary
+	 */
+	public Map<String, List<String>> getLifeStageTerms() { 
+		return lifeStageTerms;
+	}
+
+	/**
+	 * get the pathway value:key pairs
+	 * for finding vocabulary values for alternative labels
 	 * 
 	 * @return the map of pathway values from the vocabulary
 	 */
 	public Map<String,String> getPathwayValues() { 
 		return pathwayValues;
 	}
 	/**
-	 * get the typeStatus key:value pairs
+	 * get the pathway key:list of value pairs 
+	 * for finding values in the vocabulary
+	 * 
+	 * @return the map of pathway values from the vocabulary
+	 */
+	public Map<String, List<String>> getPathwayTerms() { 
+		return pathwayTerms;
+	}
+
+	/**
+	 * get the typeStatus value:key pairs
 	 * 
 	 * @return the map of typeStatus values from the vocabulary
 	 */
 	public Map<String,String> getTypeStatusValues() { 
 		return typeStatusValues;
 	}
+	/**
+	 * get the typeStatus key:list of value pairs 
+	 * for finding values in the vocabulary
+	 * 
+	 * @return the map of typeStatus values from the vocabulary
+	 */
+	public Map<String, List<String>> getTypeStatusTerms() { 
+		return typeStatusTerms;
+	}
 
 	/**
-	 * get the sex key:value pairs
+	 * get the sex value:key pairs
+	 * for finding vocabulary values for alternative labels
 	 * 
 	 * @return the map of sex values from the vocabulary
 	 */
 	public Map<String,String> getSexValues() { 
 		return sexValues;
 	}
 
+	/**
+	 * get the sex key:list of value pairs 
+	 * for finding values in the vocabulary
+	 * 
+	 * @return the map of sex values from the vocabulary
+	 */
+	public Map<String, List<String>> getSexTerms() { 
+		return sexTerms;
+	}
+
+	/**
+	 * get the degreeOfEstablishment value:key pairs
+	 * for finding vocabulary values for alternative labels
+	 * 
+	 * @return the map of degreeOfEstablishment values from the vocabulary
+	 */
+	public Map<String,String> getDegreeOfEstablishmentValues() { 
+		return degreeOfEstablishmentValues;
+	}
+
+	/**
+	 * get the degreeOfEstablishment key:list of value pairs 
+	 * for finding values in the vocabulary
+	 * 
+	 * @return the map of degreeOfEstablishment values from the vocabulary
+	 */
+	public Map<String, List<String>> getDegreeOfEstablishmentTerms() { 
+		return degreeOfEstablishmentTerms;
+	}
+
 	/**
 	 * @return true if vocabularies have been loaded
 	 */