update vulnerable dependency: com.thoughtworks.xstream:xstream

[JavaEcosystemStudy]

Hi! We spot a vulnerable dependency in your project, which might threaten your software. We also found another project that uses the same vulnerable dependency in a similar way as you did, and they have upgraded the dependency. We, thus, believe that your project is highly possible to be affected by this vulnerability similarly. The following shows the detailed information.

Vulnerability description

• CVE: CVE-2021-43859
• Vulnerable dependency: com.thoughtworks.xstream:xstream
• Vulnerable function: com.thoughtworks.xstream.XStream:unmarshal(com.thoughtworks.xstream.io.HierarchicalStreamReader,java.lang.Object,com.thoughtworks.xstream.converters.DataHolder)
• Invocation Path:

  gate.creole.annic.lucene.LuceneIndexer:readParametersFromDisk(java.net.URL)
  ⬇️ 
  com.thoughtworks.xstream.XStream:fromXML(java.io.Reader)
  ⬇️ 
  ...
  ⬇️ 
  com.thoughtworks.xstream.XStream:unmarshal(com.thoughtworks.xstream.io.HierarchicalStreamReader,java.lang.Object,com.thoughtworks.xstream.converters.DataHolder)

Upgrade example

Another project also used the same dependency with a similar invocation path, and they have taken actions to resolve this issue.

• Project: https://github.com/sbmlteam/jsbml
• Action commit:https://github.com/sbmlteam/jsbml/commit/9902c3bb2e64d5e4b8e6b0a51cde6e2c1b7c6106
• Invocation Path:

  org.sbml.jsbml.validator.SBMLValidator:checkConsistency(java.lang.String)
  ⬇️ 
  com.thoughtworks.xstream.XStream:fromXML(java.io.Reader)
  ⬇️ 
  ...
  ⬇️ 
  com.thoughtworks.xstream.XStream:unmarshal(com.thoughtworks.xstream.io.HierarchicalStreamReader,java.lang.Object,com.thoughtworks.xstream.converters.DataHolder)

Therefore, you might also need to upgrade this dependency. Hope this can help you! 😄

[greenwoodma]

I'm closing this PR for now because

1. the issue occurs in the ANNIC indexer component so is only likely to affect the GUI, and hence the only machine you could affect would be your own
2. we currently use version 1.4.17 of XStream (albeit mostly configured with our own security settings). This instance however relies on the default blacklist approach (i.e. doesn't configure security) so upgrading to 1.4.19 would cause the code highlighted to fail completely

At some point we'll update ANNIC to have a whitelist (limited number of params should make this possible) and upgrade XStream, but separate to this PR which would cause more problems than it aims to fix.