Add support for recent versions of MySQL.jl

[khughitt]

Greetings!

I tried using BioMedQuery.jl for the first time today. Installation went smoothly, however, when I attempt to load the package, I run into an error during the pre-compilation step:

julia> using BioMedQuery
[ Info: Precompiling BioMedQuery [e96904bf-1073-5077-9b57-b0ce0ff5555a]
ERROR: LoadError: LoadError: LoadError: UndefVarError: MySQLHandle not defined
Stacktrace:
 [1] top-level scope at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/DBUtils/mysql_db_utils.jl:55
 [2] include(::String) at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/BioMedQuery.jl:4
 [3] top-level scope at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/DBUtils/DBUtils.jl:4
 [4] include(::String) at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/BioMedQuery.jl:4
 [5] top-level scope at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/BioMedQuery.jl:21
 [6] top-level scope at none:2
 [7] eval at ./boot.jl:331 [inlined]
in expression starting at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/DBUtils/mysql_db_utils.jl:55
in expression starting at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/DBUtils/DBUtils.jl:4
in expression starting at /home/keith/.julia/packages/BioMedQuery/Ps32f/src/BioMedQuery.jl:21
ERROR: Failed to precompile BioMedQuery [e96904bf-1073-5077-9b57-b0ce0ff5555a] to /home/keith/.julia/compiled/v1.4/BioMedQuery/I7mWp_L3y04.ji.

Looking at the code for src/DBUtils/mysql_db_utils.jl, I noticed that the function db_query() is attempting to call MySQL.query(), which doesn't appear to be in the current API for MySQL.jl.

I'm guessing that the MySQL.jl API has changed in some recent version, and that BioMedQuery.jl is still referring to the old interface? It's also possible that I am just misunderstanding something..

As a side note, I also noticed that init_mysql_database() function that gets automatically called during the initial attempt to load BioMedQuery.jl attempts to look for the "test" database. Since it is common to remove the test db after installation, it might be good to avoid this, if possible.

Thanks!

System Info

• Arch Linux 5.6.14 (64-bit)
• Julia 1.4.2
• MariaDB 10.4.13

Package versions:

• [39abe10b] MySQL v1.0.4
• [e96904bf] BioMedQuery v0.6.6 #master (https://github.com/JuliaHealth/BioMedQuery.jl.git)

[DilumAluthge]

Happy to accept pull requests. Unfortunately this package does not have an active maintainer.

[DilumAluthge]

But if people want to make pull requests, I can merge them.

[timholy]

This is a cross-post from https://julialang.zulipchat.com/#narrow/stream/232791-sciences/topic/PubChemCrawler/near/216013362. If I were to create a package to search PubChem,

• is this something I should attempt to integrate with, or is it better to make it standalone? Or base it on some other package?
• Should I host it at JuliaHealth or elwhere?

[DilumAluthge]

• Should I host it at JuliaHealth or elwhere?

I think JuliaHealth would be a great place to host it!

• is this something I should attempt to integrate with, or is it better to make it standalone? Or base it on some other package?

This question is trickier. The problem is that BioMedQuery.jl currently doesn't have a maintainer. Additionally, I'm not sure if the package is currently functional.

@timholy If you want, you are welcome to take over as maintainer of BioMedQuery.jl. But that might entail some work, e.g. to get CI passing again.

Alternatively, it will probably be easier to develop the PubChem package as a separate package, e.g. something like JuliaHealth/PubChemAPI.jl or something like that.

I would probably recommend the latter approach. Using HTTP.jl and JSON3.jl, it's pretty quick to get a working REST client.

[timholy]

Sounds good. I'll do the standalone but plan to host it here at JuliaHealth. Thanks for the input!