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Fix for issue 544 #546

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Merged
andreasprlic merged 2 commits into from
Jul 28, 2016
Merged

Fix for issue 544 #546

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372ea6a
Some work towards fixing #544
josemduarte Jul 28, 2016
5a583e7
Fixing #544 and improving logging
josemduarte Jul 28, 2016
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9 changes: 5 additions & 4 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,11 +35,12 @@
*/
public class CathFactory {

public static final String VERSION_3_5_0 = "3.5.0";
public static final String VERSION_4_0_0 = "4.0.0";
public static final String LATEST_VERSION = VERSION_4_0_0;
public static final String VERSION_3_5_0 = "3_5_0";
public static final String VERSION_4_0_0 = "4_0_0";
public static final String VERSION_4_1_0 = "4_1_0";
public static final String LATEST_VERSION = VERSION_4_1_0;

public static String DEFAULT_VERSION = LATEST_VERSION;
public static final String DEFAULT_VERSION = LATEST_VERSION;

private static CathDatabase cath;

Expand Down
112 changes: 65 additions & 47 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/cath/CathInstallation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,6 +25,8 @@

import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.io.util.FileDownloadUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.biojava.nbio.core.util.InputStreamProvider;

import java.io.*;
Expand All @@ -41,41 +43,43 @@
*/
public class CathInstallation implements CathDatabase{

private static final Logger LOGGER = LoggerFactory.getLogger(CathInstallation.class);

public static final String DEFAULT_VERSION = CathFactory.DEFAULT_VERSION;

String cathVersion;

public static final String domainListFileName = "CathDomainList";
public static final String domainListFileName = "cath-domain-list-v%s.txt";
// 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
public static final String domainDescriptionFileName = "CathDomainDescriptionFile";
public static final String nodeListFileName = "CathNames";
public static final String domallFileName = "CathDomall";

public static final String CATH_DOWNLOAD = "http://release.cathdb.info/";
public static final String domallFileName = "cath-domain-boundaries-v%s.txt";

public static final String CATH_DOWNLOAD_URL = "http://download.cathdb.info/cath/releases/";
public static final String CATH_DOWNLOAD_LATEST_RELEASE_DIR = "latest-release";
public static final String CATH_DOWNLOAD_PREV_RELEASE_DIR = "previous-releases";
public static final String CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR = "cath-classification-data";

String cathDownloadUrl;
public static final String NEWLINE = System.getProperty("line.separator");;
public static final String FILESPLIT = System.getProperty("file.separator");;

public static final String NEWLINE;
public static final String FILESPLIT ;

static {
NEWLINE = System.getProperty("line.separator");
FILESPLIT = System.getProperty("file.separator");
}

private String cathVersion;

private String cathDownloadUrl;

private String cacheLocation ;

AtomicBoolean installedDomainList;
AtomicBoolean installedDomainDescription;
AtomicBoolean installedNodeList;
AtomicBoolean installedDomall;
private AtomicBoolean installedDomainList;
private AtomicBoolean installedDomainDescription;
private AtomicBoolean installedNodeList;
private AtomicBoolean installedDomall;

final boolean useCathDomainDescriptionFile;
final boolean parseCathFragments;
private final boolean useCathDomainDescriptionFile;
private final boolean parseCathFragments;

Map<String, List<CathDomain>> pdbMap;
Map<String, CathDomain> domainMap;
Map<String, CathNode> cathTree;
Map<String, List<CathFragment>> fragmentMap;
private Map<String, List<CathDomain>> pdbMap;
private Map<String, CathDomain> domainMap;
private Map<String, CathNode> cathTree;
private Map<String, List<CathFragment>> fragmentMap;



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

cathVersion = DEFAULT_VERSION;
cathDownloadUrl = CATH_DOWNLOAD;
cathDownloadUrl = CATH_DOWNLOAD_URL;

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

public String getDomainListFileName() {
return cacheLocation + domainListFileName + ".v" + cathVersion;
return cacheLocation + buildFileName(domainListFileName);
}

public String getDomainDescriptionFileName() {
return cacheLocation + domainDescriptionFileName + ".v" + cathVersion;
return cacheLocation + buildFileName(domainDescriptionFileName);
}

public String getNodeListFileName() {
return cacheLocation + nodeListFileName + ".v" + cathVersion;
return cacheLocation + buildFileName(nodeListFileName);
}

public String getDomallFileName() {
return cacheLocation + domallFileName + ".v" + cathVersion;
return cacheLocation + buildFileName(domallFileName);
}

private String buildFileName(String fileNameTemplate) {
return String.format(fileNameTemplate, cathVersion);
}

private String buildUrl(String remoteFileName) {
String remoteFileNameWithVer = buildFileName(remoteFileName);
String releasesDir = CATH_DOWNLOAD_LATEST_RELEASE_DIR;
if (!cathVersion.equals(CathFactory.LATEST_VERSION)) {
releasesDir = CATH_DOWNLOAD_PREV_RELEASE_DIR;
}
return cathDownloadUrl + releasesDir + "/v" + cathVersion + "/" + CATH_DOWNLOAD_CLASSIFICATION_DATA_DIR + "/" + remoteFileNameWithVer;
}

public String getCathDownloadUrl() {
Expand Down Expand Up @@ -418,7 +435,7 @@ private void parseCathDomainDescriptionFile(BufferedReader bufferedReader) throw
try {
cathDescription.setDate( dateFormat.parse( line.substring(10) ) );
} catch (ParseException e) {
e.printStackTrace();
LOGGER.error(e.getMessage(), e);
}
} else if ( line.startsWith("NAME") ) {
name.append( line.substring(10) );
Expand Down Expand Up @@ -622,7 +639,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{
}
}

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

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

private boolean domainDescriptionFileAvailable(){
Expand All @@ -680,33 +697,33 @@ private boolean domallFileAvailable() {
return f.exists();
}

protected void downloadDomainListFile() throws FileNotFoundException, IOException{
protected void downloadDomainListFile() throws IOException{
String remoteFilename = domainListFileName;
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
URL url = new URL(buildUrl(remoteFilename));
String localFileName = getDomainListFileName();
File localFile = new File(localFileName);
downloadFileFromRemote(url, localFile);
}

protected void downloadDomainDescriptionFile() throws FileNotFoundException, IOException{
protected void downloadDomainDescriptionFile() throws IOException{
String remoteFilename = domainDescriptionFileName;
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
URL url = new URL(buildUrl(remoteFilename));
String localFileName = getDomainDescriptionFileName();
File localFile = new File(localFileName);
downloadFileFromRemote(url, localFile);
}

protected void downloadNodeListFile() throws FileNotFoundException, IOException{
protected void downloadNodeListFile() throws IOException{
String remoteFilename = nodeListFileName;
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFilename);
URL url = new URL(buildUrl(remoteFilename));
String localFileName = getNodeListFileName();
File localFile = new File(localFileName);
downloadFileFromRemote(url, localFile);
}

protected void downloadDomallFile() throws IOException {
String remoteFileName = domallFileName;
URL url = new URL(cathDownloadUrl + "v" + cathVersion + "/" + remoteFileName);
URL url = new URL(buildUrl(remoteFileName));
String localFileName = getDomallFileName();
File localFile = new File(localFileName);
downloadFileFromRemote(url, localFile);
Expand All @@ -719,7 +736,7 @@ public void ensureDomainListInstalled(){
try {
downloadDomainListFile();
} catch (Exception e){
e.printStackTrace();
LOGGER.error("Could not download CATH domain list file. Error: {}", e.getMessage());
installedDomainList.set(false);
return;
}
Expand All @@ -728,7 +745,7 @@ public void ensureDomainListInstalled(){
try {
parseCathDomainList();
} catch (Exception e){
e.printStackTrace();
LOGGER.error(e.getMessage(), e);
installedDomainList.set(false);
return;
}
Expand All @@ -742,7 +759,7 @@ public void ensureDomainDescriptionInstalled(){
try {
downloadDomainDescriptionFile();
} catch (Exception e){
e.printStackTrace();
LOGGER.error("Could not download CATH domain description file. Error: {}", e.getMessage());
installedDomainDescription.set(false);
return;
}
Expand All @@ -751,7 +768,7 @@ public void ensureDomainDescriptionInstalled(){
try {
parseCathDomainDescriptionFile();
} catch (Exception e){
e.printStackTrace();
LOGGER.error(e.getMessage(), e);
installedDomainDescription.set(false);
return;
}
Expand All @@ -765,7 +782,7 @@ public void ensureNodeListInstalled(){
try {
downloadNodeListFile();
} catch (Exception e){
e.printStackTrace();
LOGGER.error("Could not download CATH node list file. Error: {}", e.getMessage());
installedNodeList.set(false);
return;
}
Expand All @@ -774,7 +791,7 @@ public void ensureNodeListInstalled(){
try {
parseCathNames();
} catch (Exception e){
e.printStackTrace();
LOGGER.error(e.getMessage(), e);
installedNodeList.set(false);
return;
}
Expand All @@ -795,7 +812,7 @@ public void ensureDomallInstalled() {
try {
downloadDomallFile();
} catch (Exception e) {
e.printStackTrace();
LOGGER.error("Could not download CATH domain all file. Error: {}", e.getMessage());
installedDomall.set(false);
return;
}
Expand All @@ -804,7 +821,7 @@ public void ensureDomallInstalled() {
try {
parseCathDomall();
} catch (Exception e) {
e.printStackTrace();
LOGGER.error(e.getMessage(), e);
installedDomall.set(false);
return;
}
Expand All @@ -814,5 +831,6 @@ public void ensureDomallInstalled() {
public void setCathVersion(String cathVersion) {
this.cathVersion = cathVersion;
}


}