Fix date parsing from NCBI gene info file

Properly parse modification date in NCBI gene info using SimpleDateFormat.
PavlidisLab · Jul 3, 2020 · 3afd5bb · 3afd5bb
1 parent 59e7ad5
commit 3afd5bb
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/src/main/java/ubc/pavlab/rdp/model/Gene.java b/src/main/java/ubc/pavlab/rdp/model/Gene.java
@@ -4,10 +4,7 @@
 import lombok.*;
 
 import javax.persistence.*;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.*;
 
 /**
  * Created by mjacobson on 17/01/18.
@@ -37,8 +34,9 @@ public class Gene {
     @Column(name = "synonyms", columnDefinition = "TEXT")
     private String aliases;
 
+    @Temporal(TemporalType.DATE)
     @Column(name = "modification_date")
-    private int modificationDate;
+    private Date modificationDate;
 
     @Transient
     @JsonIgnore

diff --git a/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java b/src/main/java/ubc/pavlab/rdp/util/GeneInfoParser.java
@@ -10,7 +10,10 @@
 
 import java.io.*;
 import java.net.URL;
+import java.sql.Date;
+import java.text.MessageFormat;
 import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.Set;
 import java.util.stream.Collectors;
 import java.util.zip.GZIPInputStream;
@@ -94,7 +97,12 @@ private static Set<Gene> parse( Taxon taxon, InputStream input ) throws ParseExc
                 gene.setSymbol( values[2] );
                 gene.setAliases( values[4] );
                 gene.setName( values[8] );
-                gene.setModificationDate( Integer.valueOf( values[14] ) );
+                SimpleDateFormat ncbiDateFormat = new SimpleDateFormat("YYYYMMDD");
+                try {
+                    gene.setModificationDate( ncbiDateFormat.parse( values[14] ) );
+                } catch ( ParseException e ) {
+                    log.warn( MessageFormat.format("Could not parse date {0} for gene {1}.", values[14], values[1]), e);
+                }
                 return gene;
             } ).collect( Collectors.toSet() );
         } catch (IOException e) {