gut non schema files and reorganize #100
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I really like this! Thanks for cleaning this out! I'm curious, though, what we do about the |
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I'm going to suggest this is a medium change. I approve but I don't have the historical knowledge of Chado to know 100% sure if something was removed that shouldn't be. So, while it looks good to me I think we need more eyes on this one. |
My vision of how it would work (agreed it should be sorted in isolation from this general task of cleaning up the repo) Diff files: no. There will no longer be version-to-version diff files. We will keep the existing ones, perhaps in a "legacy" folder. Diff file functionality is covered by flyway now. Schemas: Yes. We will create full schema definitions of |
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I would suggest changing the name of the possibly_useful_old_stuff directory to preflyway_archive? 😜 Otherwise this looks good to me 👍
Testing: Checked out the branch and checked the schema files I expected were still there and dug through the other remaining files (all of which I would also keep). 🤷♀️
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This is a beast of a pull request, though I commented a few times in the issue that I support doing it. Since https://github.com/GMOD/chado_tools looks good (it contains all the stuff being removed from this repo), I feel pretty good about going forward with this.
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One other thing: I am reasonably sure looking at the "files affected" that this will not clash with the best practices pull request (https://github.com/GMOD/Chado/pull/92/files) that will place a file in chado/docs/best_practices.rst |
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I would dump the possibly_useful_old_stuff directory altogether.
It appears to be mostly code related to and relying on the Data::Stag and DBIx::DBStag perl modules that are no longer maintained (@scottcain can you confirm this?). Some of which is now obsolete with the native XML support in PostgreSQL as well. In addition, it is coupled with the Chado schema in a way that requires it to be manually maintained as the schema changes. It will continue to degrade over time unless someone takes this on.
I see little reason to keep it around.
Other than this, everything looks great and I've verified with Pinglei that the XORT code can be dumped. Thanks for all the work that went into this PR!
This commit removed old code that used the DBIx::DBStag perl module to interact with a Chado database. It also removed old and outdated install and chado module metadata docs.
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Yay!!! 🎉 |
implements #79 . The new Chado repo will ONLY be the SQL schema and its documentation. Perl tools for building hte diffs, for loading data, etc, will now live in the Chado Tools repository. There are some files that i am keeping in a "junk drawer" since i think we'll want to adopt them into the documentation, see some of my comments in #79.
I also reorganized the repo so that everything sits at the root instead of
chado/