add support for path authorship columns in output schema; related to g…

…lobalbioticinteractions/name-alignment-template#18
globalbioticinteractions · Apr 20, 2024 · 52d6655 · 52d6655
1 parent 3bf7ed0
commit 52d6655
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Showing 5 changed files with 39 additions and 8 deletions.
diff --git a/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdInputSchema.java b/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdInputSchema.java
@@ -2,6 +2,8 @@
 
 import picocli.CommandLine;
 
+import static org.globalbioticinteractions.nomer.cmd.CmdMatcherParams.NOMER_SCHEMA_INPUT;
+
 @CommandLine.Command(
         name = "input-schema",
         description = "Show input schema in JSON."
@@ -10,7 +12,7 @@ public class CmdInputSchema extends CmdProperties {
 
     @Override
     public void run() {
-        String property = getProperties().getProperty("nomer.schema.input");
+        String property = getProperties().getProperty(NOMER_SCHEMA_INPUT);
         System.out.println(property);
     }
 }
diff --git a/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdMatcherParams.java b/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdMatcherParams.java
@@ -18,6 +18,8 @@
 
 public abstract class CmdMatcherParams extends TermMatcherContextCaching implements Runnable {
 
+    public static final String NOMER_SCHEMA_INPUT = "nomer.schema.input";
+    public static final String NOMER_SCHEMA_OUTPUT = "nomer.schema.output";
     @CommandLine.Parameters(description = "[matcher]", arity = "1")
     private List<String> matchers = new ArrayList<>();
 
@@ -34,12 +36,12 @@ public List<String> getMatchers() {
 
     @Override
     public Map<Integer, String> getInputSchema() {
-        return parseSchema(getProperty("nomer.schema.input"));
+        return parseSchema(getProperty(NOMER_SCHEMA_INPUT));
     }
 
     @Override
     public Map<Integer, String> getOutputSchema() {
-        return parseSchema(getProperty("nomer.schema.output"));
+        return parseSchema(getProperty(NOMER_SCHEMA_OUTPUT));
     }
 
     public static Map<Integer, String> parseSchema(String schema) {

diff --git a/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdOutputSchema.java b/nomer/src/main/java/org/globalbioticinteractions/nomer/cmd/CmdOutputSchema.java
@@ -2,11 +2,13 @@
 
 import picocli.CommandLine;
 
+import static org.globalbioticinteractions.nomer.cmd.CmdMatcherParams.NOMER_SCHEMA_OUTPUT;
+
 @CommandLine.Command(name = "output-schema", description = "Show output schema in JSON.")
 public class CmdOutputSchema extends CmdProperties {
 
     @Override
     public void run() {
-        System.out.println(getProperties().getProperty("nomer.schema.output"));
+        System.out.println(getProperties().getProperty(NOMER_SCHEMA_OUTPUT));
     }
 }
diff --git a/nomer/src/main/java/org/globalbioticinteractions/nomer/util/AppenderUtil.java b/nomer/src/main/java/org/globalbioticinteractions/nomer/util/AppenderUtil.java
@@ -40,6 +40,7 @@ public static String valueForTaxonProperty(Taxon taxon,
         List<String> ranks = splitAndTrim(taxon.getPathNames());
         List<String> ids = splitAndTrim(taxon.getPathIds());
         List<String> names = splitAndTrim(taxon.getPath());
+        List<String> authorships = splitAndTrim(taxon.getPathAuthorships());
         String colValue = "";
         if (StringUtils.equalsIgnoreCase(taxonPropertyName, "id")) {
             colValue = taxon.getExternalId();
@@ -67,10 +68,14 @@ public static String valueForTaxonProperty(Taxon taxon,
                 int i1 = ranks.indexOf(rank);
                 if (i1 > -1) {
                     if (split.length > 2) {
-                        boolean shouldUseId = "id".equalsIgnoreCase(split[2]);
-                        colValue = shouldUseId
-                                ? ids.get(i1)
-                                : names.get(i1);
+                        String propertyName = split[2];
+                        if ("id".equalsIgnoreCase(propertyName)) {
+                            colValue = ids.get(i1);
+                        } else if ("name".equalsIgnoreCase(propertyName)) {
+                            colValue = names.get(i1);
+                        } else if ("authorship".equalsIgnoreCase(propertyName)) {
+                            colValue = authorships.get(i1);
+                        }
                     } else {
                         colValue = rank;
                     }

diff --git a/nomer/src/test/java/org/globalbioticinteractions/nomer/util/AppenderUtilTest.java b/nomer/src/test/java/org/globalbioticinteractions/nomer/util/AppenderUtilTest.java
@@ -35,6 +35,26 @@ public void getUnknownKingdomFromPath() {
         assertThat(kingdomName, is(""));
     }
 
+    @Test
+    public void getKnownKingdomFromPath() {
+        TaxonImpl taxon = new TaxonImpl("someName", "someId");
+        taxon.setPathNames("kingdom | genus | species");
+        taxon.setPath("someKingdom | someGenus | someSpecies");
+        taxon.setPathIds("foo:0 | foo:1 | foo:2");
+        taxon.setPathAuthorships("Doe 2013 | Smith 2031 | Johnson 2012");
+        String kingdomName = AppenderUtil.valueForTaxonProperty(
+                taxon,
+                "path.kingdom.name");
+
+        assertThat(kingdomName, is("someKingdom"));
+
+        String authorship = AppenderUtil.valueForTaxonProperty(
+                taxon,
+                "path.kingdom.authorship");
+
+        assertThat(authorship, is("Doe 2013"));
+    }
+
     @Test   
     public void getUnknownAuthorship() {
         TaxonImpl taxon = new TaxonImpl("someName", "someId");