Skip to content

Support the new ECOD distribution format #1141

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
josemduarte merged 3 commits into from
Aug 26, 2026
+767 −51
Merged

Support the new ECOD distribution format #1141

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6cb9633
Support the new ECOD distribution format
aalhossary Aug 17, 2026
2ad8e09
Test every ECOD layout offline
aalhossary Aug 17, 2026
cbab39b
Merge upstream master into aa/ecod-new-format
aalhossary Aug 26, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 40 additions & 0 deletions ...egrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodInstallationTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,12 @@

import static org.junit.Assert.*;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.Reader;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
Expand All @@ -47,6 +51,7 @@
import org.biojava.nbio.structure.ecod.EcodDomain;
import org.biojava.nbio.structure.ecod.EcodFactory;
import org.biojava.nbio.structure.ecod.EcodInstallation;
import org.biojava.nbio.structure.ecod.EcodInstallation.EcodParser;
import org.junit.Ignore;
import org.junit.Rule;
import org.junit.Test;
Expand Down Expand Up @@ -277,12 +282,47 @@ public void testFilterByHierarchy() throws IOException {
assertEquals(expected,actual);
}

/**
* Checks that the current release can still be read.
* <p>
* The version is read from the file's header without parsing the domains, so this
* additionally parses the first few thousand lines of the same file. That is enough to
* notice a column change — which is what ECOD did at v294.1, unnoticed for months —
* without building the three million domains the whole file now holds.
*/
@Test
public void testVersion() throws IOException {
EcodDatabase ecod3 = EcodFactory.getEcodDatabase("latest");
String version = ecod3.getVersion();
assertNotNull(version);
assertNotEquals("latest", version);
System.out.println("latest version of ECOD is "+version);

File domainsFile = new File(((EcodInstallation) ecod3).getCacheLocation(),
"ecod.latest.domains.txt");
assertTrue("No local copy of the domains file at "+domainsFile, domainsFile.exists());

EcodParser parser = new EcodParser(firstLines(domainsFile, 5000));
assertEquals(version, parser.getVersion());
assertFalse("No domains parsed from ECOD "+version
+ "; the distribution format has probably changed",
parser.getDomains().isEmpty());
}

/**
* @return a reader over the first {@code maxLines} lines of the file
*/
private static Reader firstLines(File f, int maxLines) throws IOException {
StringBuilder head = new StringBuilder();
try (BufferedReader in = new BufferedReader(new FileReader(f))) {
String line;
int n = 0;
while (n < maxLines && (line = in.readLine()) != null) {
head.append(line).append('\n');
n++;
}
}
return new StringReader(head.toString());
}

/**
Expand Down
Loading
Loading