detect year pattern in the publication year field to avoid extra char…

…acters like commas. TaxoDros/TaxoDros.github.io#41
bio-guoda · Jul 12, 2024 · 6969e74 · 6969e74
1 parent 00da2b9
commit 6969e74
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Showing 3 changed files with 26 additions and 3 deletions.
diff --git a/preston-taxodros/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java b/preston-taxodros/src/main/java/bio/guoda/preston/cmd/ZenodoMetaUtil.java
@@ -8,6 +8,8 @@
 import org.apache.commons.lang3.StringUtils;
 
 import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Stream;
 
 public class ZenodoMetaUtil {
@@ -116,10 +118,19 @@ public static void setCreators(ObjectNode objectNode, List<String> creatorList)
     }
 
     public static void setPublicationDate(ObjectNode objectNode, String publicationYear) {
-        if (publicationYear.startsWith("2")) {
+        Pattern compile = Pattern.compile(".*(?<year>[12][0-9]{3}).*");
+        Matcher matcher = compile.matcher(publicationYear);
+
+        if (!matcher.matches()) {
+            throw new IllegalArgumentException("cannot parse publication year [" + publicationYear + "]");
+        }
+
+        String year = matcher.group("year");
+        if (StringUtils.startsWith(year, "2")) {
             setRestricted(objectNode);
         }
-        setValue(objectNode, PUBLICATION_DATE, publicationYear);
+
+        setValue(objectNode, PUBLICATION_DATE, year);
     }
 
     private static void setRestricted(ObjectNode objectNode) {

diff --git a/preston-taxodros/src/test/java/bio/guoda/preston/cmd/TaxoDrosFileExtractorTest.java b/preston-taxodros/src/test/java/bio/guoda/preston/cmd/TaxoDrosFileExtractorTest.java
@@ -59,14 +59,25 @@ public void streamTaxoDrosToLineJsonWithDOI() throws IOException {
         assertThat(taxonNode.get("doi").textValue(), is("10.7868/S0016675814060150"));
     }
 
+    @Test
+    public void streamTaxoDrosToLineJsonYear() throws IOException {
+        String[] jsonObjects = getResource("DROS5.TEXT.year.txt");
+        assertThat(jsonObjects.length, is(1));
+
+        JsonNode taxonNode = unwrapMetadata(jsonObjects[0]);
+
+        assertThat(taxonNode.has("doi"), is(true));
+        assertThat(taxonNode.get("doi").textValue(), is("10.11646/zootaxa.4161.2.4"));
+        assertThat(taxonNode.get("publication_date").textValue(), is("2016"));
+    }
+
     @Test
     public void streamTaxoDrosToLineJsonAuthorsWithAmpersand() throws IOException {
         String[] jsonObjects = getResource("DROS5.TEXT.authors.ampersand.txt");
         assertThat(jsonObjects.length, is(1));
 
         JsonNode taxonNode = unwrapMetadata(jsonObjects[0]);
 
-
         assertThat(taxonNode.has("doi"), is(true));
         assertThat(taxonNode.get("doi").textValue(), is("10.1016/j.tpb.2006.05.001"));
 

diff --git a/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/DROS5.TEXT.year.txt b/preston-taxodros/src/test/resources/bio/guoda/preston/cmd/DROS5.TEXT.year.txt
@@ -0,0 +1 @@
+.TEXT;huang & chen, 2016.A Huang, J. & Chen, H.,.J 2016,.S The genus Leucophenga (Diptera, Drosophilidae), part VI:the argentata species group from the East Asia, withmorphological and molecular evidence..Z Zootaxa, 4161(2):207-227..K ocr++ / 5.ix.2016 / DOI:10.11646/zootaxa.4161.2.4.P Huang & Chen, 2016.pdf