allow for schema column type [path.kingdom.name] to populate value ev…

…en though no path ids are available; related to #177
globalbioticinteractions · Jun 14, 2024 · 3fd3a56 · 3fd3a56
1 parent 0e13e60
commit 3fd3a56
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/nomer/src/main/java/org/globalbioticinteractions/nomer/util/AppenderUtil.java b/nomer/src/main/java/org/globalbioticinteractions/nomer/util/AppenderUtil.java
@@ -59,21 +59,19 @@ public static String valueForTaxonProperty(Taxon taxon,
         } else if (StringUtils.equalsIgnoreCase(taxonPropertyName, "path.authorship")) {
             colValue = taxon.getPathAuthorships();
         } else if (StringUtils.startsWith(taxonPropertyName, "path.")
-                && ranks.size() > 0
-                && ranks.size() == ids.size()
-                && names.size() == ids.size()) {
+                && ranks.size() > 0) {
             String[] split = StringUtils.split(taxonPropertyName, '.');
             if (split != null && split.length > 1) {
                 String rank = split[1];
                 int i1 = ranks.indexOf(rank);
                 if (i1 > -1) {
                     if (split.length > 2) {
                         String propertyName = split[2];
-                        if ("id".equalsIgnoreCase(propertyName)) {
+                        if ("id".equalsIgnoreCase(propertyName) && ranks.size() == ids.size()) {
                             colValue = ids.get(i1);
-                        } else if ("name".equalsIgnoreCase(propertyName)) {
+                        } else if ("name".equalsIgnoreCase(propertyName) && ranks.size() == names.size()) {
                             colValue = names.get(i1);
-                        } else if ("authorship".equalsIgnoreCase(propertyName)) {
+                        } else if ("authorship".equalsIgnoreCase(propertyName) && ranks.size() == authorships.size()) {
                             colValue = authorships.get(i1);
                         }
                     } else {

diff --git a/nomer/src/test/java/org/globalbioticinteractions/nomer/util/AppenderUtilTest.java b/nomer/src/test/java/org/globalbioticinteractions/nomer/util/AppenderUtilTest.java
@@ -22,6 +22,18 @@ public void getKingdomFromPath() {
         assertThat(kingdomName, is("someKingdom"));
     }
 
+    @Test
+    public void getKingdomFromPath2() {
+        TaxonImpl taxon = new TaxonImpl("someName", "someId");
+        taxon.setPath("Animalia | Arthropoda | Insecta | Hymenoptera | Apidae | Apinae | Apini | None | Apis | Apis | Apis mellifera");
+        taxon.setPathNames("kingdom | phylum | class | order | family | subfamily | tribe | subtribe | genus | subgenus | species");
+        String kingdomName = AppenderUtil.valueForTaxonProperty(
+                taxon,
+                "path.kingdom.name");
+
+        assertThat(kingdomName, is("Animalia"));
+    }
+
     @Test
     public void getUnknownKingdomFromPath() {
         TaxonImpl taxon = new TaxonImpl("someName", "someId");