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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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Re-download empty structure or chemical component structures 
Files less than 40 bytes are deleted to allow for gzip headers.

This addresses #703
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@sbliven
sbliven committed Jun 8, 2018
commit 6ea9ae762946efe87998e4ccca16f70b738087ce
11 changes: 11 additions & 0 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/io/LocalPDBDirectory.java
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Expand Up @@ -127,6 +127,9 @@ public static enum FetchBehavior {

protected static final String lineSplit = System.getProperty("file.separator");

/** Minimum size for a valid file, in bytes */
public static final long MIN_PDB_FILE_SIZE = 40;

private File path;
private List<String> extensions;

Expand Down Expand Up @@ -687,6 +690,14 @@ public File getLocalFile(String pdbId) {
for(String ex : getExtensions() ){
File f = new File(searchdir,prefix + pdbId.toLowerCase() + ex) ;
if ( f.exists()) {
// delete files that are too short to have contents
if( f.length() < MIN_PDB_FILE_SIZE ) {
boolean success = f.delete();
if( ! success) {
return null;
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@josemduarte josemduarte Jun 8, 2018

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Shouldn't this rather throw an exception (perhaps IOException)? I don't see how can this null be handled if file can't be deleted.

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@sbliven sbliven Jun 15, 2018

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switched to Files.delete which throws the exception

}
assert(!f.exists());
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@josemduarte josemduarte Jun 8, 2018

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I'd rather log a warning here. Assert is going to be ignored in normal situations

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@sbliven sbliven Jun 12, 2018

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That's intended. If the delete was successful then the file will not exist. This is just a sanity check during development to make sure delete() wasn't asynchronous or something.

}
return f;
}
}
Expand Down
7 changes: 7 additions & 0 deletions ...structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
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Expand Up @@ -42,6 +42,7 @@
import org.biojava.nbio.core.util.InputStreamProvider;
import org.biojava.nbio.structure.align.util.HTTPConnectionTools;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import org.biojava.nbio.structure.io.LocalPDBDirectory;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -344,6 +345,12 @@ private static boolean fileExists(String recordName){

File f = new File(fileName);

// delete files that are too short to have contents
if( f.length() < LocalPDBDirectory.MIN_PDB_FILE_SIZE ) {
f.delete();
return false;
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@josemduarte josemduarte Jun 8, 2018

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If the file fails to be deleted, this won't work as expected. I think the fail to delete case should throw an IOException

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@sbliven sbliven Jun 12, 2018

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I don't check the status because the delete isn't really necessary here. If this method returns false then we re-download the file and move it on top of the old one. I just added the delete defensively.

}

return f.exists();

}
Expand Down