galaxyproject/galaxy: technical due diligence, read from its repository

The median source file here is 92 lines. 81 files exceed 1,000 lines, the largest being 13,686. Size is not a defect on its own — some problems genuinely live in one place — but these are where merge conflicts, review fatigue and single-owner knowledge concentrate, and they are the first thing that slows an inheriting engineer down.

586 product files are in the new language and 148 are still in the old one, 48 months after the first new file appeared. The new language's share of the lines rose from 0% to 95%, and moved 2 percentage points in the last year. Two languages for one job doubles what an engineer has to know, and the unmoved half is usually what nobody wants to touch. Ask whether finishing it is planned, and what it costs.

15 third-party CI actions are referenced by a tag or branch rather than a commit, so they run whatever that tag points to on the day. Tags have been moved to malicious commits in real supply-chain attacks, and a piped script is whatever the server returns that minute. Pinning to a commit is the fix, and it is small.

21 HTTP calls use a client with no timeout (Python `requests` without `timeout=`, or Go's default client). When a dependency slows down, each one holds a worker until the connection gives up, and enough of them take the service down with the dependency.

9 places run a command through a shell (`shell=True`, `os.system`, `exec` with a template) rather than passing arguments. Where any part comes from outside, it is command injection. Ask where each one's input comes from.

2 places read data with a deserialiser that executes what it reads (`yaml.load` without a safe loader). That is safe on data the system wrote itself and remote code execution on anything else. Ask where each one's input comes from.

1 workload manifests set no CPU or memory limits. One pod that leaks memory or spins can starve everything else on its node, and the scheduler cannot plan capacity for what it cannot see.

12 places set HTML from a value that is neither a literal nor passed through a sanitiser. Where the value can come from a user, that is stored cross-site scripting, and it is the first thing a buyer's security review looks for in a frontend.

Third-party code is committed into this repository without any statement of the terms it arrived under. Unknown terms are harder to deal with than inconvenient ones: an awkward licence can be complied with, an absent one cannot. Each of these needs its origin established before the code changes hands.

1 deployments set `replicas: 1`, and nothing (an autoscaler, a disruption budget) adds more. Every deploy and every node drain is downtime, and the availability the buyer inherits has a ceiling.