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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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Improving CathInstallation logging 
log slow downloads upon start
  • Loading branch information
@sbliven
sbliven committed Jun 4, 2018
commit 5c1a335d43cf951344bd359e8f2ddec0e88a932e
3 changes: 2 additions & 1 deletion 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 @@ -636,6 +636,7 @@ private void parseCathDomall(BufferedReader bufferedReader) throws IOException{

protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOException{
// System.out.println("downloading " + remoteURL + " to: " + localFile);
LOGGER.info("Downloaded file {} to local file {}", remoteURL, localFile);
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@josemduarte josemduarte Jun 8, 2018

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Shouldn't this be "Downloading"? It isn't downloaded at this point yet

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@sbliven sbliven Jun 15, 2018

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fixed


long timeS = System.currentTimeMillis();
File tempFile = File.createTempFile(FileDownloadUtils.getFilePrefix(localFile), "."+ FileDownloadUtils.getFileExtension(localFile));
Expand Down Expand Up @@ -665,7 +666,7 @@ protected void downloadFileFromRemote(URL remoteURL, File localFile) throws IOEx
disp = disp / 1024.0;
}
long timeE = System.currentTimeMillis();
LOGGER.info("Downloaded file {} ({}) to local file {} in {} sec.", remoteURL, String.format("%.1f",disp) + unit, localFile, (timeE - timeS)/1000);
LOGGER.info("Downloaded {} in {} sec. to {}", String.format("%.1f",disp) + unit, (timeE - timeS)/1000, localFile);
}

private boolean domainDescriptionFileAvailable(){
Expand Down