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andreasprlicandreasprlic
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Merge pull request #546 from josemduarte/fix544
Fix for issue 544
2 parents 12f4e07 + 5a583e7 commit 4201bcd

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2 files changed

+70
-51
lines changed

2 files changed

+70
-51
lines changed

‎biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -35,11 +35,12 @@
3535
*/
3636
public class CathFactory {
3737

38-
public static final String VERSION_3_5_0 = "3.5.0";
39-
public static final String VERSION_4_0_0 = "4.0.0";
40-
public static final String LATEST_VERSION = VERSION_4_0_0;
38+
public static final String VERSION_3_5_0 = "3_5_0";
39+
public static final String VERSION_4_0_0 = "4_0_0";
40+
public static final String VERSION_4_1_0 = "4_1_0";
41+
public static final String LATEST_VERSION = VERSION_4_1_0;
4142

42-
public static String DEFAULT_VERSION = LATEST_VERSION;
43+
public static final String DEFAULT_VERSION = LATEST_VERSION;
4344

4445
private static CathDatabase cath;
4546

‎biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java‎

Lines changed: 65 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,8 @@
2525

2626
import org.biojava.nbio.structure.align.util.UserConfiguration;
2727
import org.biojava.nbio.structure.io.util.FileDownloadUtils;
28+
import org.slf4j.Logger;
29+
import org.slf4j.LoggerFactory;
2830
import org.biojava.nbio.core.util.InputStreamProvider;
2931

3032
import java.io.*;
@@ -41,41 +43,43 @@
4143
*/
4244
public class CathInstallation implements CathDatabase{
4345

46+
private static final Logger LOGGER = LoggerFactory.getLogger(CathInstallation.class);
47+
4448
public static final String DEFAULT_VERSION = CathFactory.DEFAULT_VERSION;
4549

46-
String cathVersion;
47-
48-
public static final String domainListFileName = "CathDomainList";
50+
public static final String domainListFileName = "cath-domain-list-v%s.txt";
51+
// TODO I don't know what are the new file nams for domainDescriptionFileName and nodeListFileName in the new CATH 4.1.0 servers, must find out! - JD 2016-07-28
4952
public static final String domainDescriptionFileName = "CathDomainDescriptionFile";
5053
public static final String nodeListFileName = "CathNames";
51-
public static final String domallFileName = "CathDomall";
52-
53-
public static final String CATH_DOWNLOAD = "http://release.cathdb.info/";
54+
public static final String domallFileName = "cath-domain-boundaries-v%s.txt";
55+
56+
public static final String CATH_DOWNLOAD_URL = "http://download.cathdb.info/cath/releases/";
57+
public static final String CATH_DOWNLOAD_LATEST_RELEASE_DIR = "latest-release";
58+
public static final String CATH_DOWNLOAD_PREV_RELEASE_DIR = "previous-releases";
59+
public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR = "cath-classification-data";
5460

55-
String cathDownloadUrl;
61+
public static final String NEWLINE = System.getProperty("line.separator");;
62+
public static final String FILESPLIT = System.getProperty("file.separator");;
5663

57-
public static final String NEWLINE;
58-
public static final String FILESPLIT ;
59-
60-
static {
61-
NEWLINE = System.getProperty("line.separator");
62-
FILESPLIT = System.getProperty("file.separator");
63-
}
64+
65+
private String cathVersion;
6466

67+
private String cathDownloadUrl;
68+
6569
private String cacheLocation ;
6670

67-
AtomicBoolean installedDomainList;
68-
AtomicBoolean installedDomainDescription;
69-
AtomicBoolean installedNodeList;
70-
AtomicBoolean installedDomall;
71+
private AtomicBoolean installedDomainList;
72+
private AtomicBoolean installedDomainDescription;
73+
private AtomicBoolean installedNodeList;
74+
private AtomicBoolean installedDomall;
7175

72-
final boolean useCathDomainDescriptionFile;
73-
final boolean parseCathFragments;
76+
private final boolean useCathDomainDescriptionFile;
77+
private final boolean parseCathFragments;
7478

75-
Map<String, List<CathDomain>> pdbMap;
76-
Map<String, CathDomain> domainMap;
77-
Map<String, CathNode> cathTree;
78-
Map<String, List<CathFragment>> fragmentMap;
79+
private Map<String, List<CathDomain>> pdbMap;
80+
private Map<String, CathDomain> domainMap;
81+
private Map<String, CathNode> cathTree;
82+
private Map<String, List<CathFragment>> fragmentMap;
7983

8084

8185

@@ -91,7 +95,7 @@ public CathInstallation(String cacheLocation, boolean usingCDDF, boolean parseCF
9195
installedDomall = new AtomicBoolean(false);
9296

9397
cathVersion = DEFAULT_VERSION;
94-
cathDownloadUrl = CATH_DOWNLOAD;
98+
cathDownloadUrl = CATH_DOWNLOAD_URL;
9599

96100
pdbMap = new HashMap<String, List<CathDomain>>();
97101
domainMap = new HashMap<String ,CathDomain>();
@@ -110,19 +114,32 @@ public CathInstallation() {
110114
}
111115

112116
public String getDomainListFileName() {
113-
return cacheLocation + domainListFileName + ".v" + cathVersion;
117+
return cacheLocation + buildFileName(domainListFileName);
114118
}
115119

116120
public String getDomainDescriptionFileName() {
117-
return cacheLocation + domainDescriptionFileName + ".v" + cathVersion;
121+
return cacheLocation + buildFileName(domainDescriptionFileName);
118122
}
119123

120124
public String getNodeListFileName() {
121-
return cacheLocation + nodeListFileName + ".v" + cathVersion;
125+
return cacheLocation + buildFileName(nodeListFileName);
122126
}
123127

124128
public String getDomallFileName() {
125-
return cacheLocation + domallFileName + ".v" + cathVersion;
129+
return cacheLocation + buildFileName(domallFileName);
130+
}
131+
132+
private String buildFileName(String fileNameTemplate) {
133+
return String.format(fileNameTemplate, cathVersion);
134+
}
135+
136+
private String buildUrl(String remoteFileName) {
137+
String remoteFileNameWithVer = buildFileName(remoteFileName);
138+
String releasesDir = CATH_DOWNLOAD_LATEST_RELEASE_DIR;
139+
if (!cathVersion.equals(CathFactory.LATEST_VERSION)) {
140+
releasesDir = CATH_DOWNLOAD_PREV_RELEASE_DIR;
141+
}
142+
return cathDownloadUrl + releasesDir + "/v" + cathVersion + "/" + CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR + "/" + remoteFileNameWithVer;
126143
}
127144

128145
public String getCathDownloadUrl() {
@@ -418,7 +435,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
418435
try {
419436
cathDescription.setDate( dateFormat.parse( line.substring(10) ) );
420437
} catch (ParseException e) {
421-
e.printStackTrace();
438+
LOGGER.error(e.getMessage(), e);
422439
}
423440
} else if ( line.startsWith("NAME") ) {
424441
name.append( line.substring(10) );
@@ -622,7 +639,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
622639
}
623640
}
624641

625-
protected void downloadFileFromRemote(URL remoteURL, File localFile) throws FileNotFoundException, IOException{
642+
protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
626643
// System.out.println("downloading " + remoteURL + " to: " + localFile);
627644

628645
long timeS = System.currentTimeMillis();
@@ -653,7 +670,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws File
653670
disp = disp / 1024.0;
654671
}
655672
long timeE = System.currentTimeMillis();
656-
System.out.println("downloaded " + String.format("%.1f",disp) + unit + " in " + (timeE - timeS)/1000 + " sec.");
673+
LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
657674
}
658675

659676
private boolean domainDescriptionFileAvailable(){
@@ -680,33 +697,33 @@ private boolean domallFileAvailable() {
680697
return f.exists();
681698
}
682699

683-
protected void downloadDomainListFile() throws FileNotFoundException, IOException{
700+
protected void downloadDomainListFile() throws IOException{
684701
String remoteFilename = domainListFileName;
685-
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
702+
URL url = new URL(buildUrl(remoteFilename));
686703
String localFileName = getDomainListFileName();
687704
File localFile = new File(localFileName);
688705
downloadFileFromRemote(url, localFile);
689706
}
690707

691-
protected void downloadDomainDescriptionFile() throws FileNotFoundException, IOException{
708+
protected void downloadDomainDescriptionFile() throws IOException{
692709
String remoteFilename = domainDescriptionFileName;
693-
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
710+
URL url = new URL(buildUrl(remoteFilename));
694711
String localFileName = getDomainDescriptionFileName();
695712
File localFile = new File(localFileName);
696713
downloadFileFromRemote(url, localFile);
697714
}
698715

699-
protected void downloadNodeListFile() throws FileNotFoundException, IOException{
716+
protected void downloadNodeListFile() throws IOException{
700717
String remoteFilename = nodeListFileName;
701-
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
718+
URL url = new URL(buildUrl(remoteFilename));
702719
String localFileName = getNodeListFileName();
703720
File localFile = new File(localFileName);
704721
downloadFileFromRemote(url, localFile);
705722
}
706723

707724
protected void downloadDomallFile() throws IOException {
708725
String remoteFileName = domallFileName;
709-
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFileName);
726+
URL url = new URL(buildUrl(remoteFileName));
710727
String localFileName = getDomallFileName();
711728
File localFile = new File(localFileName);
712729
downloadFileFromRemote(url, localFile);
@@ -719,7 +736,7 @@ public void ensureDomainListInstalled(){
719736
try {
720737
downloadDomainListFile();
721738
} catch (Exception e){
722-
e.printStackTrace();
739+
LOGGER.error("Could not download CATH domain list file. Error: {}", e.getMessage());
723740
installedDomainList.set(false);
724741
return;
725742
}
@@ -728,7 +745,7 @@ public void ensureDomainListInstalled(){
728745
try {
729746
parseCathDomainList();
730747
} catch (Exception e){
731-
e.printStackTrace();
748+
LOGGER.error(e.getMessage(), e);
732749
installedDomainList.set(false);
733750
return;
734751
}
@@ -742,7 +759,7 @@ public void ensureDomainDescriptionInstalled(){
742759
try {
743760
downloadDomainDescriptionFile();
744761
} catch (Exception e){
745-
e.printStackTrace();
762+
LOGGER.error("Could not download CATH domain description file. Error: {}", e.getMessage());
746763
installedDomainDescription.set(false);
747764
return;
748765
}
@@ -751,7 +768,7 @@ public void ensureDomainDescriptionInstalled(){
751768
try {
752769
parseCathDomainDescriptionFile();
753770
} catch (Exception e){
754-
e.printStackTrace();
771+
LOGGER.error(e.getMessage(), e);
755772
installedDomainDescription.set(false);
756773
return;
757774
}
@@ -765,7 +782,7 @@ public void ensureNodeListInstalled(){
765782
try {
766783
downloadNodeListFile();
767784
} catch (Exception e){
768-
e.printStackTrace();
785+
LOGGER.error("Could not download CATH node list file. Error: {}", e.getMessage());
769786
installedNodeList.set(false);
770787
return;
771788
}
@@ -774,7 +791,7 @@ public void ensureNodeListInstalled(){
774791
try {
775792
parseCathNames();
776793
} catch (Exception e){
777-
e.printStackTrace();
794+
LOGGER.error(e.getMessage(), e);
778795
installedNodeList.set(false);
779796
return;
780797
}
@@ -795,7 +812,7 @@ public void ensureDomallInstalled() {
795812
try {
796813
downloadDomallFile();
797814
} catch (Exception e) {
798-
e.printStackTrace();
815+
LOGGER.error("Could not download CATH domain all file. Error: {}", e.getMessage());
799816
installedDomall.set(false);
800817
return;
801818
}
@@ -804,7 +821,7 @@ public void ensureDomallInstalled() {
804821
try {
805822
parseCathDomall();
806823
} catch (Exception e) {
807-
e.printStackTrace();
824+
LOGGER.error(e.getMessage(), e);
808825
installedDomall.set(false);
809826
return;
810827
}
@@ -814,5 +831,6 @@ public void ensureDomallInstalled() {
814831
public void setCathVersion(String cathVersion) {
815832
this.cathVersion = cathVersion;
816833
}
834+
817835

818836
}

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