veg / hivclustering

Infer molecular transmission networks from pairwise distance files (part of HIV-TRACE)
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Add new "delimiter" argument #15

Closed stevenweaver closed 1 year ago

stevenweaver commented 6 years ago

Because regex is difficult to sanitize when used as an argument in web applications, we should add a new argument, --delimiter, to be used instead of --parser.

spond commented 6 years ago

Dear @stevenweaver,

The current implementation relies on the ability to extract subexpressions. It may be difficult to replicate with delimiters only. Is there a specific use-case you had in mind? Are you worried about malicious argument crafting?

Please elaborate.

Best, Sergei

stevenweaver commented 6 years ago

Dear @spond,

I am worried about malicious argument crafting. Specifically, within the context of a web application. Currently, the galaxy tool will omit this argument.

Best, Steven

spond commented 6 years ago

Dear @stevenweaver,

That's fine. We can implement a limited subset of functionality via a new "delimiter" argument, specifically for web applications, and keep the regex for command line use.

Best, Sergei