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Merge DNA terms with GBIF ones as they share the same namespace #16

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Merge DNA terms with GBIF ones as they share the same namespace #16

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74 changes: 0 additions & 74 deletions src/main/java/org/gbif/dwc/terms/GbifDnaTerm.java
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17 changes: 16 additions & 1 deletion src/main/java/org/gbif/dwc/terms/GbifTerm.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,12 @@ public enum GbifTerm implements Term, AlternativeNames, Serializable {
*/
Distribution(GbifTerm.GROUP_ROW_TYPE),

/**
* The <a href="http://rs.gbif.org/terms/1.0/DNADerivedData">DNA Derived Data</a>
* extension row type.
*/
DNADerivedData(GbifTerm.GROUP_ROW_TYPE),

/**
* The <a href="http://rs.gbif.org/terms/1.0/Identifier">GBIF Alternative Identifiers</a>
* extension row type.
Expand Down Expand Up @@ -347,15 +353,24 @@ public enum GbifTerm implements Term, AlternativeNames, Serializable {
geologicalTime(DwcTerm.GROUP_OCCURRENCE),
lithostratigraphy(DwcTerm.GROUP_OCCURRENCE),
biostratigraphy(DwcTerm.GROUP_OCCURRENCE),

/** DNA Derived Data **/
pcr_primer_forward(GbifTerm.GROUP_DNA_DERIVED_DATA),
pcr_primer_reverse(GbifTerm.GROUP_DNA_DERIVED_DATA),
pcr_primer_name_forward(GbifTerm.GROUP_DNA_DERIVED_DATA),
pcr_primer_name_reverse(GbifTerm.GROUP_DNA_DERIVED_DATA),
pcr_primer_reference(GbifTerm.GROUP_DNA_DERIVED_DATA),
dna_sequence(GbifTerm.GROUP_DNA_DERIVED_DATA),
// not from the DNA extension:
dnaSequenceID(GbifTerm.GROUP_DNA_DERIVED_DATA);

private static final String PREFIX = "gbif";
private static final String NS = "http://rs.gbif.org/terms/1.0/";
private static final URI NS_URI = URI.create(NS);

public static final String GROUP_ROW_TYPE = "RowType";
public static final String GROUP_CRAWLING = "Crawling";
public static final String GROUP_DATASET = "Dataset";
public static final String GROUP_ROW_TYPE = "RowType";
public static final String GROUP_SPECIES_DISTRIBUTION_EXTENSION = "SpeciesDistribution";
public static final String GROUP_SPECIES_PROFILE_EXTENSION = "SpeciesProfile";
public static final String GROUP_VERNACULAR_NAME_EXTENSION = "VernacularName";
Expand Down
1 change: 0 additions & 1 deletion src/main/java/org/gbif/dwc/terms/TermFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,6 @@ private void loadKnownTerms() {

// DWCA extensions
registerTermEnum(ChronoTerm.class);
registerTermEnum(GbifDnaTerm.class);
registerTermEnum(GbifMiqeTerm.class);
registerTermEnum(GermplasmTerm.class);
registerTermEnum(GgbnTerm.class);
Expand Down
34 changes: 0 additions & 34 deletions src/test/java/org/gbif/dwc/terms/GbifDnaTermTest.java
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18 changes: 15 additions & 3 deletions src/test/java/org/gbif/dwc/terms/GbifTermTest.java
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Expand Up @@ -27,7 +27,7 @@
public class GbifTermTest extends TermBaseTest<GbifTerm> {

public GbifTermTest() {
super(GbifTerm.class);
super(GbifTerm.class, new String[]{"-"}, false);
}

@Test
Expand All @@ -43,7 +43,19 @@ public void testTerm() {
public void testIsClass() {
assertTrue(GbifTerm.VernacularName.isClass());
assertTrue(GbifTerm.Distribution.isClass());
assertTrue(GbifTerm.DNADerivedData.isClass());
assertFalse(GbifTerm.datasetKey.isClass());
int counter = 0;
for (GbifTerm term : GbifTerm.values()) {
if (term.isClass()) {
counter++;
assertEquals(GbifTerm.GROUP_ROW_TYPE, term.getGroup());
}
}
for (GbifTerm term : GbifTerm.listByGroup(GbifTerm.GROUP_ROW_TYPE)) {
assertTrue(term.isClass());
}
assertEquals(10, counter);
}

@Test
Expand All @@ -69,8 +81,8 @@ public void testListByGroup() {
assertEquals(9, new HashSet<>(locationTerms).size());

List<GbifTerm> rowTerms = GbifTerm.listByGroup(GbifTerm.GROUP_ROW_TYPE);
assertEquals(9, rowTerms.size());
assertEquals(9, new HashSet<>(rowTerms).size());
assertEquals(10, rowTerms.size());
assertEquals(10, new HashSet<>(rowTerms).size());

List<GbifTerm> distributionTerms = GbifTerm.listByGroup(GbifTerm.GROUP_SPECIES_DISTRIBUTION_EXTENSION);
assertEquals(2, distributionTerms.size());
Expand Down
1 change: 0 additions & 1 deletion src/test/java/org/gbif/dwc/terms/TermFactoryTest.java
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Expand Up @@ -67,7 +67,6 @@ public void testKnownTermUniqueness() {

// Terms for extensions supported in GBIF downloads.
addTerms(names, ChronoTerm.values());
addTerms(names, GbifDnaTerm.values());
addTerms(names, GbifMiqeTerm.values());
addTerms(names, GermplasmTerm.values());
addTerms(names, termsBut(GgbnTerm.values(), GgbnTerm.MaterialSample));
Expand Down