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Automatically re-download ECOD if the cache is >2weeks old #481

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Merged
sbliven merged 1 commit into from
May 13, 2016
Merged

Automatically re-download ECOD if the cache is >2weeks old #481

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26 changes: 19 additions & 7 deletions ...egrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@
import org.biojava.nbio.structure.ecod.EcodDomain;
import org.biojava.nbio.structure.ecod.EcodFactory;
import org.biojava.nbio.structure.ecod.EcodInstallation;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.TemporaryFolder;
Expand All @@ -60,13 +61,13 @@
public class EcodInstallationTest {

private static final Logger logger = LoggerFactory.getLogger(EcodInstallationTest.class);
private static final String VERSION = "develop124"; // Should be updated periodically
private static final String VERSION = "develop133"; // Should be updated periodically

// Info about known versions, for testing
private static final int DEVELOP_FIRST_VERSION = 45;
private static final int DEVELOP_LATEST_VERSTION = 124; // Should be updated periodically
private static final int DEVELOP_FIRST_VERSION = 124;
private static final int DEVELOP_LATEST_VERSTION = 136; // Should be updated periodically
//versions known to be unreleased
private static final List<Integer> DEVELOP_VERSIONS_BLACKLIST = Arrays.asList( 85, 107, 113 );
private static final List<Integer> DEVELOP_VERSIONS_BLACKLIST = Arrays.asList( 85, 107, 113, 125, 128, 131 );

static {
//System.setProperty("Log4jContextSelector", "org.apache.logging.log4j.core.async.AsyncLoggerContextSelector");
Expand Down Expand Up @@ -106,6 +107,18 @@ public void testAllDomains() throws IOException {
case "develop124":
expected = 468680; //version124
break;
case "develop133":
expected = 479738; //version133
break;
case "develop134":
expected = 483056; //version134 (stats file)
break;
case "develop135":
expected = 483812; //version135 (stats file)
break;
case "develop136":
expected = 484847; //version136 (stats file)
break;
default:
fail("Unrecognized version "+VERSION);
return;
Expand Down Expand Up @@ -154,10 +167,9 @@ public void testParsing() throws IOException {
// String chainName, String range, String seqId, String architectureName,
".", "A:3-97,B:106-346", "A:3-97,B:1-241", "beta barrels",
// String xGroupName, String hGroupName, String tGroupName,
"cradle loop barrel", "RIFT-related",
"NO_T_NAME",// should be "acid protease" except for bug in develop124
"cradle loop barrel", "RIFT-related","acid protease",
// String fGroupName, Boolean isAssembly, List<String> ligands
"EF00710",//"UNK_F_TYPE",
"EF00710",
20669l, Collections.singleton("EPE")
);
assertEquals(ecodId,expected,domain);
Expand Down
46 changes: 45 additions & 1 deletion biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodInstallation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.LinkedHashSet;
import java.util.LinkedList;
Expand Down Expand Up @@ -86,6 +88,9 @@ public class EcodInstallation implements EcodDatabase {

private String url;

// Frequency of ECOD updates, in days. If non-null, redownloads "latest" if older than this.
private Integer updateFrequency = 14;

/**
* Use EcodFactory to create instances. The instantiation of multiple
* installations at the same path can lead to race conditions when downloading
Expand Down Expand Up @@ -359,7 +364,25 @@ private boolean domainsAvailable() {
try {
File f = getDomainFile();

return f.exists() && f.length()>0;
if (!f.exists() || f.length() <= 0 )
return false;

// Re-download old copies of "latest"
if(updateFrequency != null && requestedVersion == DEFAULT_VERSION ) {
long mod = f.lastModified();
// Time of last update
Date lastUpdate = new Date();
Calendar cal = Calendar.getInstance();
cal.setTime(lastUpdate);
cal.add(Calendar.DAY_OF_WEEK, -updateFrequency);
long updateTime = cal.getTimeInMillis();
// Check if file predates last update
if( mod < updateTime ) {
logger.info("{} is out of date.",f);
return false;
}
}
return true;
} finally {
logger.trace("UNLOCK readlock");
domainsFileLock.readLock().unlock();
Expand Down Expand Up @@ -403,6 +426,27 @@ private File getDomainFile() {
return new File(getCacheLocation(),getDomainFilename());
}

/**
* The expected ECOD update frequency determines whether the version
* "latest" should be re-downloaded
* @return the expected ECOD update frequency, in days
*/
public Integer getUpdateFrequency() {
return updateFrequency;
}

/**
* The "latest" version will be re-downloaded if it is older than
* {@link #getUpdateFrequency()} days. Setting this to null disables
* re-downloading (delete $PDB_CACHE_DIR/ecod.latest.domains.txt manually
* to force updating). Setting to 0 will force downloading for every
* program execution.
* @param updateFrequency the updateFrequency to set
*/
public void setUpdateFrequency(Integer updateFrequency) {
this.updateFrequency = updateFrequency;
}

/**
* Parses the domains from the local file
* @throws IOException
Expand Down