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Master Build fails: SonarCloud returns HTTP 403 for SONAR_TOKEN

Status: Open.

#1140 In biojava/biojava;

· aalhossary opened on Aug 17, 2026

ECOD changed its distribution format: neither the version header nor the column layout is recognised

Status: Open.

#1139 In biojava/biojava;

· aalhossary opened on Aug 17, 2026

CathInstallation downloads over http, which now redirects to https, and the redirect body is cached as classification data

Status: Open.

#1138 In biojava/biojava;

· aalhossary opened on Aug 17, 2026

CI red on all PRs since 2025-12: three independent causes (tracking)

Status: Open.

#1135 In biojava/biojava;

· aalhossary opened on Aug 15, 2026

UniProt XML module code contribution

Status: Open.

#1112 In biojava/biojava;

· heuermh opened on Mar 19, 2025

Unable to find entrez (e -utilities) NCBI

Status: Open.

#1090 In biojava/biojava;

· kshitijgarg2609 opened on Apr 12, 2024

Quality: Sonar RSPEC-1940 "Boolean checks should not be inverted"

Status: Open.

#1074 In biojava/biojava;

· jlerbsc opened on Dec 12, 2023

Suggestion: Sonar S2129 Constructors should not be used to instantiate "String", "BigInteger", "BigDecimal" and primitive-wrapper classes

Status: Open.

#1066 In biojava/biojava;

· jlerbsc opened on Jun 25, 2023

Suggestion: Sonar S1130 "throws" declarations should not be superfluous

Status: Open.

#1061 In biojava/biojava;

· jlerbsc opened on May 10, 2023

Test Smell: it is not a good test practice to use the loop in the test

Status: Open.

#1038 In biojava/biojava;

· TestSmell opened on Aug 17, 2022

NCBIQBlastService.sendAlignmentRequest | Always throws ArrayIndexOutOfBoundsException

Status: Open.

#1033 In biojava/biojava;

· FC123321 opened on Jun 30, 2022

Harmonize Profile and LightweightProfile

Status: Open.

#1018 In biojava/biojava;

· sbliven opened on Jan 27, 2022

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6.1.0