Add image_math tool

[kostrykin]

For the contributor:

• - I have read the CONTRIBUTING.md document.
• - License permits unrestricted use (educational + commercial).
• - This PR adds or updates a tool or tool collection.
  • - This PR adds a new tool or tool collection.
  • - This PR updates an existing tool or tool collection.
  • - Tools added/updated by this PR comply with the Naming and Annotation Conventions for Tools in the Image Community in Galaxy (or explain why they do not).
• - This PR does something else (explain below).

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Add tool for processing images using arithmetic expressions.

In particular, this tool can be used to negate images (this is what is meant by image inversion in #105 according to the Java source code). An example is given in the help section of the tool.

[bgruening]

I'm a little bit worried about the security of this tool.

Can you please look at this tool https://github.com/galaxyproject/tools-iuc/blob/main/tools/column_maker/column_maker.xml#L5

And see if you can get some inspirations on how to avoid arbitrary code executions.

For example we could also just allow a few operations abs/sqr etc ... and add more if there is a real need.
The linked tool above also adds the allowed tools to the help, so people know what they can use.

Am I overly careful here?

[kostrykin]

I understand your concerns, I was also a bit concerned at first. However, there also are Jupyter notebooks running on Galaxy, which also permit arbitrary code execution, right? Or are these apples and oranges, somehow?

[bgruening]

Apple and Organes, Jupyter is running only in Docker and is locked down. We also do not allow to run Jupyter 100 times with a lot of resources etc ...

[kostrykin]

Ok, makes sense. Then I will look for some other solution which avoids eval.

[kostrykin]

I have purged the eval-based implementation and replaced it by a custom implementation using abstract syntax trees in 080ffe7. I think this should be safe, because only a small set of operators is permitted, only integer and float literals, and only variables passed in via --input.

And the only allowed function calls are abs and sqrt. I have updated the help section in 01eaf51. The help section now lists all supported operators and functions:

• Addition, subtraction, multiplication, and division (+, -, *, /)
• Integer division (e.g., input // 2)
• Power (e.g., input ** 2)
• Negation (e.g., -input)
• Absolute values (e.g., abs(input))
• Square root (e.g., sqrt(input))
• Combinations of the above (also using parentheses)

If you prefer that, I think we could leave out Integer division, Power, Absolute values, and Square root for the moment, but I don't think that including these is an issue.

[bgruening]

Please add all functions you like, I was just anxious about arbitrary eval() executions. My abs/sqr was just a stupid example.

Thanks a lot for changing the implementation so fast.

[bgruening]

The tool looks great to me. Please decide on your own when you want to merge or add new function.

Thanks!