Switch ftp.ebi.ac.uk URLs to use HTTP.

sbliven · josemduarte · commit 2b66631970fe · 2018-07-13T11:53:19.000-07:00
Travis blocks FTP so we're avoiding it.
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
@@ -688,7 +688,7 @@ public static String getServerName() {
 			name = DEFAULT_PDB_FILE_SERVER;
 			logger.debug("Using default PDB file server {}",name);
 		} else {
-			if (!name.startsWith("http://") && !name.startsWith("ftp://")) {
+			if (!name.startsWith("http://") && !name.startsWith("ftp://") && !name.startsWith("https://")) {
 				logger.warn("Server name {} read from system property {} does not have a leading protocol string. Adding http:// to it", name, PDB_FILE_SERVER_PROPERTY);
 				name = "http://"+name;
 			}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
@@ -66,7 +66,7 @@ public class SiftsChainToUniprotMapping {
 
 	static {
 		try {
-			DEFAULT_URL = new URL("ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/pdb_chain_uniprot.tsv.gz");
+			DEFAULT_URL = new URL("http://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/pdb_chain_uniprot.tsv.gz");
 		} catch (MalformedURLException e) {
 			throw new RuntimeException(e);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
@@ -41,7 +41,7 @@ public class SiftsMappingProvider {
 	private final static Logger logger = LoggerFactory.getLogger(SiftsMappingProvider.class);
 
 
-	private static final String EBI_SIFTS_FILE_LOCATION = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/%s.xml.gz";
+	private static final String EBI_SIFTS_FILE_LOCATION = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/%s.xml.gz";
 
 	private static String fileLoc = EBI_SIFTS_FILE_LOCATION;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java
@@ -33,7 +33,7 @@
 public class RCSBUpdates {
 
 	// The URL for acquiring the data
-	public static final String baseURL = "ftp://ftp.rcsb.org/pub/pdb/data/status/latest/";
+	public static final String baseURL = "http://ftp.rcsb.org/pub/pdb/data/status/latest/";
 
 	/**
 	 *

Original file line number	Diff line number	Diff line change
`@@ -688,7 +688,7 @@ public static String getServerName() {`
`688`	`688`	`name = DEFAULT_PDB_FILE_SERVER;`
`689`	`689`	`logger.debug("Using default PDB file server {}",name);`
`690`	`690`	`} else {`
`691`		`- if (!name.startsWith("http://") && !name.startsWith("ftp://")) {`
	`691`	`+ if (!name.startsWith("http://") && !name.startsWith("ftp://") && !name.startsWith("https://")) {`
`692`	`692`	`logger.warn("Server name {} read from system property {} does not have a leading protocol string. Adding http:// to it", name, PDB_FILE_SERVER_PROPERTY);`
`693`	`693`	`name = "http://"+name;`
`694`	`694`	`}`
Original file line number	Diff line number	Diff line change
`@@ -66,7 +66,7 @@ public class SiftsChainToUniprotMapping {`
`66`	`66`
`67`	`67`	`static {`
`68`	`68`	`try {`
`69`		`- DEFAULT_URL = new URL("ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/pdb_chain_uniprot.tsv.gz");`
	`69`	`+ DEFAULT_URL = new URL("http://ftp.ebi.ac.uk/pub/databases/msd/sifts/flatfiles/tsv/pdb_chain_uniprot.tsv.gz");`
`70`	`70`	`} catch (MalformedURLException e) {`
`71`	`71`	`throw new RuntimeException(e);`
`72`	`72`	`}`
Original file line number	Diff line number	Diff line change
`@@ -33,7 +33,7 @@`
`33`	`33`	`public class RCSBUpdates {`
`34`	`34`
`35`	`35`	`// The URL for acquiring the data`
`36`		`- public static final String baseURL = "ftp://ftp.rcsb.org/pub/pdb/data/status/latest/";`
	`36`	`+ public static final String baseURL = "http://ftp.rcsb.org/pub/pdb/data/status/latest/";`
`37`	`37`
`38`	`38`	`/**`
`39`	`39`	`*`