Fix modDate

aalhossary · aalhossary · commit b7074de841a1 · 2021-11-24T02:08:21.000+08:00
In case there is only one revision (release), set the modDate to that
value.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -2877,7 +2877,7 @@ private void triggerEndFileChecks(){
 
 			if (! depositionDate.equals(modDate)){
 				// depDate is 0000-00-00
-				pdbHeader.setDepDate(depositionDate);
+				pdbHeader.setModDate(depositionDate);
 			}
 
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -614,17 +614,21 @@ private Date convert(LocalDate localDate) {
     public void consumeDatabasePDBRev(DatabasePDBRev databasePDBrev) {
         logger.debug("got a database revision:" + databasePDBrev);
 
+        Date modDate = null;
         for (int rowIndex = 0; rowIndex < databasePDBrev.getRowCount(); rowIndex++) {
             if (databasePDBrev.getNum().get(rowIndex) == 1) {
                 String dateOriginal = databasePDBrev.getDateOriginal().get(rowIndex);
                 pdbHeader.setDepDate(convert(LocalDate.parse(dateOriginal, DATE_FORMAT)));
 
                 String date = databasePDBrev.getDate().get(rowIndex);
-                pdbHeader.setRelDate(convert(LocalDate.parse(date, DATE_FORMAT)));
+                final Date relDate = convert(LocalDate.parse(date, DATE_FORMAT));
+				pdbHeader.setRelDate(relDate);
+				modDate = relDate;
             } else {
                 String dbrev = databasePDBrev.getDate().get(rowIndex);
-                pdbHeader.setModDate(convert(LocalDate.parse(dbrev, DATE_FORMAT)));
+                modDate = convert(LocalDate.parse(dbrev, DATE_FORMAT));
             }
+            pdbHeader.setModDate(modDate);
         }
     }
 
@@ -733,18 +737,21 @@ public void consumeExptl(Exptl exptl) {
 
     @Override
     public void consumePdbxAuditRevisionHistory(PdbxAuditRevisionHistory pdbxAuditRevisionHistory) {
+    	Date date = null;
         for (int rowIndex = 0; rowIndex < pdbxAuditRevisionHistory.getRowCount(); rowIndex++) {
             // first entry in revision history is the release date
             if (pdbxAuditRevisionHistory.getOrdinal().get(rowIndex) == 1) {
                 String release = pdbxAuditRevisionHistory.getRevisionDate().get(rowIndex);
-                pdbHeader.setRelDate(convert(LocalDate.parse(release, DATE_FORMAT)));
+                date = convert(LocalDate.parse(release, DATE_FORMAT));
+				pdbHeader.setRelDate(date);
             } else {
                 // all other dates are revision dates;
                 // since this method may be called multiple times,
                 // the last revision date will "stick"
                 String revision = pdbxAuditRevisionHistory.getRevisionDate().get(rowIndex);
-                pdbHeader.setModDate(convert(LocalDate.parse(revision, DATE_FORMAT)));
+                date = convert(LocalDate.parse(revision, DATE_FORMAT));
             }
+            pdbHeader.setModDate(date);
         }
     }
 

Original file line number	Diff line number	Diff line change
`@@ -2877,7 +2877,7 @@ private void triggerEndFileChecks(){`
`2877`	`2877`
`2878`	`2878`	`if (! depositionDate.equals(modDate)){`
`2879`	`2879`	`// depDate is 0000-00-00`
`2880`		`- pdbHeader.setDepDate(depositionDate);`
	`2880`	`+ pdbHeader.setModDate(depositionDate);`
`2881`	`2881`	`}`
`2882`	`2882`
`2883`	`2883`	`}`