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Fix ArrayIndexOutOfBoundsException and file validation in CathInstallation #1145

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Merged
josemduarte merged 6 commits into from
Aug 27, 2026
Merged

Fix ArrayIndexOutOfBoundsException and file validation in CathInstallation #1145

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72b5ed1
Fix ArrayIndexOutOfBoundsException and file validation in CathInstall…
josemduarte Aug 26, 2026
4b4e91f
Merge branch 'master' into jd/cath-fixes
josemduarte Aug 26, 2026
83fe61a
Safeguard for case of nothing parseable in file
josemduarte Aug 26, 2026
27bb418
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josemduarte Aug 26, 2026
26c03d1
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josemduarte Aug 27, 2026
954d75a
Test fix suggested by AI: test was failing when download was too slow
josemduarte Aug 27, 2026
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Test fix suggested by AI: test was failing when download was too slow
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@josemduarte
josemduarte committed Aug 27, 2026
commit 954d75a9dedf7136ce35c8c85aa6e3a519000cce
3 changes: 3 additions & 0 deletions biojava-structure/src/test/java/org/biojava/nbio/structure/cath/CathInstallationTest.java
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Expand Up @@ -24,6 +24,7 @@
import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.concurrent.atomic.AtomicBoolean;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
Expand All @@ -41,6 +42,8 @@ public void testParseCathDomainListSuccess() throws IOException {
CathInstallation installation = new CathInstallation("");
BufferedReader reader = new BufferedReader(new StringReader(data));
installation.parseCathDomainList(reader);
installation.setInstalledDomainList(new AtomicBoolean(true)); //1
installation.setInstalledDomall(new AtomicBoolean(true)); //2

CathDomain domain = installation.getDomainByCathId("1oaiA00");
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assertNotNull(domain);
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