geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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In some environments, the xrefs page (Xrefs.pm) fails with a server error #688

Closed kltm closed 1 year ago

kltm commented 1 year ago

xrefs pages are now failing is several server instance with errors like:

[Fri Jun 16 13:17:53.570182 2023] [cgi:error] [pid 10780] [client ::1:52446] AH01215: Experimental keys on scalar is now forbidden at /home/bbop/local/src/git/amigo/perl/lib/AmiGO/WebApp/Xrefs.pm line 69.: /home/bbop/local/src/git/amigo/perl/bin/xrefs
[Fri Jun 16 13:17:53.570433 2023] [cgi:error] [pid 10780] [client ::1:52446] AH01215: Type of arg 1 to keys must be hash or array (not private variable) at /home/bbop/local/src/git/amigo/perl/lib/AmiGO/WebApp/Xrefs.pm line 69, near "$all)": /home/bbop/local/src/git/amigo/perl/bin/xrefs
[Fri Jun 16 13:17:53.570548 2023] [cgi:error] [pid 10780] [client ::1:52446] AH01215: Compilation failed in require at /home/bbop/local/src/git/amigo/perl/bin/xrefs line 9.: /home/bbop/local/src/git/amigo/perl/bin/xrefs
[Fri Jun 16 13:17:53.570667 2023] [cgi:error] [pid 10780] [client ::1:52446] AH01215: BEGIN failed--compilation aborted at /home/bbop/local/src/git/amigo/perl/bin/xrefs line 9.: /home/bbop/local/src/git/amigo/perl/bin/xrefs
[Fri Jun 16 13:17:53.573147 2023] [cgi:error] [pid 10780] [client ::1:52446] End of script output before headers: xrefs
[Fri Jun 16 13:17:53.702889 2023] [authz_core:error] [pid 10788] [client ::1:52448] AH01630: client denied by server configuration: /home/bbop/local/src/git/amigo/favicon.ico, referer: https://amigo-staging.geneontology.io/xrefs

The key here is Experimental keys on scalar is now forbidden; see: https://www.perlmonks.org/?node_id=1214264 Basically, we've been background updated to a new perl version (likely for security reasons) that is more strict than the original code (see references that this started coming in at 5.14).

kltm commented 1 year ago

Fix now in production.