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Travis config to cache pdb dirs across builds #781

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3bc0710
Travis config to cache pdb dirs across builds
josemduarte Jul 2, 2018
84109a6
Trying to fix travis env definitions
josemduarte Jul 2, 2018
bef2fe2
Switch ftp.ebi.ac.uk URLs to use HTTP.
sbliven Jul 11, 2018
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3 changes: 3 additions & 0 deletions .travis.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ sudo: required
cache:
directories:
- "$HOME/.m2"
- "$HOME/pdb_cache"
before_install:
- if [ ! -z "$GPG_SECRET_KEYS" ]; then echo $GPG_SECRET_KEYS | base64 --decode | $GPG_EXECUTABLE --import; fi
- if [ ! -z "$GPG_OWNERTRUST" ]; then echo $GPG_OWNERTRUST | base64 --decode | $GPG_EXECUTABLE --import-ownertrust; fi
Expand All @@ -14,3 +15,5 @@ env:
global:
- secure: MkIoyU3GmlgDRhO0n1lDKvZ/k0myVY3IsFTRNUFjaBBpohLyOBrs5L8gYmfnHYHB/LvJsP6EWA6i0wCchy8hU/2pn66T12K1+WZHyqCe7RRz2kgcvVgMXTsHgvVyZ3dERcBfEDeZENzEYCYADaysT+A73ofWdJemOqfa7IFEb80=
- secure: it5av1icAvJn/6UI0aWS23m+En0ij1hCiPKw1QIbDLCE3oJOE4nHR8qINcnontH4XUQYTkmekStDkXj0WVVgp08zArj9o018XBtadYY+15h2QZBBAIpYb3UdlJoQfkcAx8yCv59BMd/u6DhMtcKSTHptVWvsLAS7YGW5hR6ZNYA=
- PDB_DIR=$HOME/pdb_cache
- PDB_CACHE_DIR=$HOME/pdb_cache
2 changes: 1 addition & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
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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 ...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 ...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 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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