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Switch ftp.ebi.ac.uk URLs to use HTTP. #783

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Merged
josemduarte merged 1 commit into from
Jul 13, 2018
Merged

Switch ftp.ebi.ac.uk URLs to use HTTP. #783

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2 changes: 1 addition & 1 deletion 2 biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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;
}
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2 changes: 1 addition & 1 deletion 2 ...ructure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsChainToUniprotMapping.java
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Expand Up @@ -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);
}
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2 changes: 1 addition & 1 deletion 2 ...ava-structure/src/main/java/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.java
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Expand Up @@ -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;

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2 changes: 1 addition & 1 deletion 2 biojava-structure/src/main/java/org/biojava/nbio/structure/rcsb/RCSBUpdates.java
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Expand Up @@ -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/";

/**
*
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