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Fix #703: Recover from empty structure files in PDB_CACHE_DIR #774

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Merged
sbliven merged 11 commits into from
Jun 18, 2018
Merged

Fix #703: Recover from empty structure files in PDB_CACHE_DIR #774

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5c1a335
Improving CathInstallation logging
sbliven Jun 4, 2018
4785d57
Add test for #703
sbliven Jun 4, 2018
c3cec91
Support initial comments in MMCif files (e.g. those generated by PyMOL)
sbliven Jun 8, 2018
b207d34
Make tests for #703 fail with an assertion
sbliven Jun 8, 2018
6ea9ae7
Re-download empty structure or chemical component structures
sbliven Sep 4, 2017
62fb2a4
Set and restore the ChemCompGroupFactory singleton
sbliven Jun 8, 2018
f5b325f
Incorporating suggestions from @josemduarte
sbliven Jun 12, 2018
13f267c
Add GlobalsHelper class to manage our global state
sbliven Jun 14, 2018
c1c3c30
Fix NullPointer when restoring global state
sbliven Jun 14, 2018
0c10a2e
Fix test failure due to PDB change
sbliven Jun 15, 2018
08ab3e1
Revert fix for mmcif files without auth_seq_id column
sbliven Jun 18, 2018
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Add test for #703
  • Loading branch information
@sbliven
sbliven committed Jun 4, 2018
commit 4785d57be7839ace552328c1097fa4595f41a3da
47 changes: 44 additions & 3 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/util/FileDownloadUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,6 @@
*/
package org.biojava.nbio.structure.io.util;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
Expand All @@ -36,6 +33,15 @@
import java.nio.channels.Channels;
import java.nio.channels.FileChannel;
import java.nio.channels.ReadableByteChannel;
import java.nio.file.FileVisitResult;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.SimpleFileVisitor;
import java.nio.file.attribute.BasicFileAttributes;

import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class FileDownloadUtils {

Expand Down Expand Up @@ -240,6 +246,41 @@ public static URLConnection prepareURLConnection(String url, int timeout) throws
connection.setConnectTimeout(timeout);
return connection;
}

/**
* Recursively delete a folder & contents
*
* @param dir directory to delete
*/
public static void deleteDirectory(Path dir) throws IOException {
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@sbliven sbliven Jun 8, 2018

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Surprisingly this isn't an nio method and I couldn't find one in BioJava

if(dir == null || !Files.exists(dir))
return;
Files.walkFileTree(dir, new SimpleFileVisitor<Path>() {
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException {
Files.delete(file);
return FileVisitResult.CONTINUE;
}

@Override
public FileVisitResult postVisitDirectory(Path dir, IOException e) throws IOException {
if (e != null) {
throw e;
}
Files.delete(dir);
return FileVisitResult.CONTINUE;
}
});
}
/**
* Recursively delete a folder & contents
*
* @param dir directory to delete
*/
public static void deleteDirectory(String dir) throws IOException {
deleteDirectory(Paths.get(dir));
}


public static void main(String[] args) {
String url;
Expand Down
130 changes: 118 additions & 12 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/align/util/AtomCacheTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -20,26 +20,48 @@
*/
package org.biojava.nbio.structure.align.util;

import org.biojava.nbio.structure.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.attribute.FileAttribute;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale;
import java.util.zip.GZIPOutputStream;

import org.biojava.nbio.structure.AtomPositionMap;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.ResidueRangeAndLength;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIO;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.StructureTools;
import org.biojava.nbio.structure.SubstructureIdentifier;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
import org.biojava.nbio.structure.io.LocalPDBDirectory.ObsoleteBehavior;
import org.biojava.nbio.structure.io.util.FileDownloadUtils;
import org.biojava.nbio.structure.io.MMCIFFileReader;
import org.biojava.nbio.structure.scop.ScopDatabase;
import org.biojava.nbio.structure.scop.ScopFactory;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;

import java.io.File;
import java.io.IOException;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import java.util.List;
import java.util.Locale;

import static org.junit.Assert.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;


/**
Expand All @@ -49,22 +71,30 @@
*/
public class AtomCacheTest {

private static Logger logger = LoggerFactory.getLogger(AtomCacheTest.class);
private AtomCache cache;
private String previousPDB_DIR;
private String previousPDB_CACHE_DIR;
private AtomCache cleanCache = new AtomCache();

@Before
public void setUp() {
previousPDB_DIR = System.getProperty(UserConfiguration.PDB_DIR, null);
previousPDB_CACHE_DIR = System.getProperty(UserConfiguration.PDB_CACHE_DIR, null);
cache = new AtomCache();
cache.setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
StructureIO.setAtomCache(cache);
// Use a fixed SCOP version for stability
ScopFactory.setScopDatabase(ScopFactory.VERSION_1_75B);
}

@After
public void tearDown() {
if (previousPDB_DIR != null)
if (previousPDB_DIR != null) {
System.setProperty(UserConfiguration.PDB_DIR, previousPDB_DIR);
System.setProperty(UserConfiguration.PDB_CACHE_DIR, previousPDB_CACHE_DIR);
}
StructureIO.setAtomCache(cleanCache);
}

/**
Expand Down Expand Up @@ -312,4 +342,80 @@ public void testSeqRes() throws StructureException, IOException {

}

/**
* Test for #703 - Chemical component cache poisoning
*
* Handle empty CIF files
* @throws IOException
* @throws StructureException
*/
@Test
public void testEmptyChemComp() throws IOException, StructureException {
Path tmpCache = Paths.get(System.getProperty("java.io.tmpdir"),"BIOJAVA_TEST_CACHE");
logger.info("Testing AtomCache at {}", tmpCache.toString());
System.setProperty(UserConfiguration.PDB_DIR, tmpCache.toString());
System.setProperty(UserConfiguration.PDB_CACHE_DIR, tmpCache.toString());

FileDownloadUtils.deleteDirectory(tmpCache);
Files.createDirectory(tmpCache);
try {
cache.setPath(tmpCache.toString());
cache.setCachePath(tmpCache.toString());
cache.setUseMmCif(true);

// Create an empty chemcomp
Path sub = tmpCache.resolve(Paths.get("chemcomp", "ALA.cif.gz"));
Files.createDirectories(sub.getParent());
Files.createFile(sub);
assertTrue(Files.exists(sub));
assertEquals(0, Files.size(sub));

Structure s = cache.getStructure("1A4W");

assertNotNull(s);
} finally {
FileDownloadUtils.deleteDirectory(tmpCache);
}
}

/**
* Test for #703 - Chemical component cache poisoning
*
* Handle empty CIF files
* @throws IOException
* @throws StructureException
*/
@Test
public void testEmptyGZChemComp() throws IOException, StructureException {
Path tmpCache = Paths.get(System.getProperty("java.io.tmpdir"),"BIOJAVA_TEST_CACHE");
logger.info("Testing AtomCache at {}", tmpCache.toString());
System.setProperty(UserConfiguration.PDB_DIR, tmpCache.toString());
System.setProperty(UserConfiguration.PDB_CACHE_DIR, tmpCache.toString());

FileDownloadUtils.deleteDirectory(tmpCache);
Files.createDirectory(tmpCache);
try {
cache.setPath(tmpCache.toString());
cache.setCachePath(tmpCache.toString());
cache.setUseMmCif(true);

// Create an empty chemcomp
Path sub = tmpCache.resolve(Paths.get("chemcomp", "ALA.cif.gz"));
Files.createDirectories(sub.getParent());
try(GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(sub.toFile()))) {
// don't write anything
out.flush();
}
assertTrue(Files.exists(sub));
assertTrue(0 < Files.size(sub));

Structure s = cache.getStructure("1A4W");

assertNotNull(s);

} finally {
FileDownloadUtils.deleteDirectory(tmpCache);
}
}

}