Switching to new DNS name for wwpdb http file server

josemduarte · josemduarte · commit 17a893f1434c · 2022-10-26T09:56:45.000-07:00
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,13 +8,17 @@ BioJava 6.1.0
 * GenBankWriterHelper - method that uses the original locus line rather than creating a new one, preventing loss of information
 * GenBankReader - the ability to successfully parse GenBank files with a LOCUS ID containing white space
 * GenBankReader - the ability to successfully parse GenBank files missing a LOCUS ID
+* Aromaticity calculation in biojava-aa-prop module
 
 ### Fixed
 * GenBankWriter - outputting db_xref feature qualifiers
 * GenBankWriter - outputting the accession version and GI ID
 * GenBankWriter - outputting feature locations containing joins and partial locations
 * GenBankReader - reading locations split over multiple lines
 * GenBankReader - set if feature qualifier values require quotes
+* Local alignment with linear gap penalty was producing an NPE #1036
+* New default server for PDB files
+* Dependency upgrades
 
 BioJava 6.0.5
 ==============================
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
@@ -66,7 +66,7 @@ public abstract class LocalPDBDirectory implements StructureIOFile {
 	 * Note that we don't support file stamp retrieving for ftp protocol, thus some of the
 	 * fetch modes will not work properly with ftp protocol
 	 */
-	public static final String DEFAULT_PDB_FILE_SERVER = "https://ftp.wwpdb.org";
+	public static final String DEFAULT_PDB_FILE_SERVER = "https://files.wwpdb.org";
 	public static final String PDB_FILE_SERVER_PROPERTY = "PDB.FILE.SERVER";
 
 	/**
@@ -123,7 +123,7 @@ public static enum FetchBehavior {
 	 */
 	public static final long LAST_REMEDIATION_DATE ;
 	private static final String LAST_REMEDIATION_DATE_STRING = "2011/07/12";
-	
+
 	static {
 
 		SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd", Locale.US);
@@ -388,7 +388,7 @@ protected InputStream getInputStream(PdbId pdbId) throws IOException{
 	 * @throws IOException
 	 */
 	public void prefetchStructure(String pdbId) throws IOException {
-		
+
 		// Check existing
 		File file = downloadStructure(new PdbId(pdbId));
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/TestURLBasedFileParsing.java
@@ -36,13 +36,10 @@ public class TestURLBasedFileParsing {
 
 	@Test
 	public void testMMcifURL() throws StructureException, IOException{
-
-		String u = "https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/divided/nw/4nwr-assembly1.cif.gz";
+		String u = "https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/divided/nw/4nwr-assembly1.cif.gz";
 
 		Structure s = StructureIO.getStructure(u);
 
 		assertNotNull(s);
-
-
 	}
 }

Original file line number	Diff line number	Diff line change
`@@ -36,13 +36,10 @@ public class TestURLBasedFileParsing {`
`36`	`36`
`37`	`37`	`@Test`
`38`	`38`	`public void testMMcifURL() throws StructureException, IOException{`
`39`		`-`
`40`		`- String u = "https://ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/divided/nw/4nwr-assembly1.cif.gz";`
	`39`	`+ String u = "https://files.wwpdb.org/pub/pdb/data/assemblies/mmCIF/divided/nw/4nwr-assembly1.cif.gz";`
`41`	`40`
`42`	`41`	`Structure s = StructureIO.getStructure(u);`
`43`	`42`
`44`	`43`	`assertNotNull(s);`
`45`		`-`
`46`		`-`
`47`	`44`	`}`
`48`	`45`	`}`