Packages no longer supported

[dometto]

I noticed interactive tools on new Galaxy cloud deployments no longer worked. It seems like the gx-it-proxy app is no longer functional due to deprecated packages:

$ nvm use v20.18.1
Now using node v20.18.1 (npm v10.8.2)
$ npx -v
10.8.2

$ npx gx-it-proxy --version
Need to install the following packages:
[email protected]
Ok to proceed? (y) y

npm warn deprecated @npmcli/[email protected]: This functionality has been moved to @npmcli/fs
npm warn deprecated [email protected]: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.
npm warn deprecated [email protected]: This package is no longer supported.
npm warn deprecated [email protected]: This package is no longer supported.
npm warn deprecated [email protected]: Rimraf versions prior to v4 are no longer supported
npm warn deprecated [email protected]: This package is no longer supported.
npm warn deprecated [email protected]: This package is no longer supported.
npm warn deprecated [email protected]: Glob versions prior to v9 are no longer supported
npm warn deprecated [email protected]: This package is no longer supported.
npm warn deprecated [email protected]: This package is no longer supported.

I get the same result with Node v14/npx 6.14.4.

[bgruening]

@dometto thanks a lot for reporting. @dannon has already started to work on this.

[dometto]

Thanks to @dannon for the fix in #26! However, I think installation of gx-it-proxy via Gravity is still broken, as it pulls in the highest possible version from npm, which is still 0.1.0. Can we expect a new release on npm anytime soon?

And in general: thanks so much for all of your work on Galaxy, and for the responsiveness!

[dannon]

@dometto Sorry for the trouble -- 0.2.0 should be available (https://www.npmjs.com/package/gx-it-proxy) since yesterday, let me check into what Gravity is doing.

[dometto]

Ah, I see it is indeed pulling 0.2.0 now, but there is still a deprecation error for npm itself. When I run the command for galaxy-gx-it-proxy.service I get this:

$ /srv/galaxy/venv/bin/galaxyctl --config-file /srv/galaxy/config/galaxy.yml exec _default_ gx-it-proxy
Working directory: /srv/galaxy/server
Executing: npm_config_yes=true VIRTUAL_ENV=/srv/galaxy/venv PATH=/srv/galaxy/venv/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin /srv/galaxy/venv/bin/npx gx-it-proxy@>=0.0.6 --ip localhost --port 8001 --sessions /srv/galaxy/datadir/interactivetools_map.sqlite --verbose    --proxyPathPrefix /interactivetool/ep
npm WARN deprecated @npmcli/[email protected]: This functionality has been moved to @npmcli/fs
npm WARN deprecated [email protected]: This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.
npm WARN deprecated [email protected]: This package is no longer supported.
npm WARN deprecated [email protected]: Rimraf versions prior to v4 are no longer supported
npm WARN deprecated [email protected]: This package is no longer supported.
npm WARN deprecated [email protected]: Glob versions prior to v9 are no longer supported
npm WARN deprecated [email protected]: This package is no longer supported.
npm notice 
npm notice New major version of npm available! 8.19.2 -> 11.0.0
npm notice Changelog: https://github.com/npm/cli/releases/tag/v11.0.0
npm notice Run npm install -g [email protected] to update!
npm notice 

Looks like its trying to use an old version of node that is installed in the galaxy venv. Should I open a bug for gravity?

[dannon]

Ahh, yeah, it's not respecting the 'overrides' block there as expected. That's a relief at least that it's pulling 0.2.0.

No need on a new issue for the galaxy base node version -- we actually have an open PR for bumping that to 20 that I need to follow up on and just go straight to the 22 LTS in.

If you use a more modern node, you're not seeing the deprecations, correct?