Allow the use of a custom datafiles in db_load_* functions

[arendsee]

Description

This commit adds a "path" keyword argument to the db_download_* files that allows the user to bypass the taxonomy database download step and use a custom local file.

Related Issue

Fixes #71, or at least provides a workaround.

Example

# This command will
#  1. download the NCBI taxonomy dump as "taxdmp.zip" using curl and a hard-coded URL
#  2. unzip the file and build the sqlite database
db_download_ncbi()

# This command bypasses the first download step. This allows
# the user to retrieve the data from a different source, modify it,
# or use a different tool to retrieve it (e.g., wget, rsync, or whatever).
db_download_ncbi(path="taxdmp.zip")

[arendsee]

The issue reported in #71 about curl timing out is happening in the tests here. It appears to be unrelated to my new code.

On my personal Linux machine this works:

> db_url <- 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip'
> db_path_file = "z.zip"
> curl::curl_download(db_url, db_path_file, quiet = TRUE)

This also works:

> taxizedb::db_download_ncbi()

Using libcurl 8.5.0, OpenSSL/3.2.0, R 4.3.2, and curl_5.2.0

On my server at work I encountered the same time out problem as the check here and @bergalu in #71.

[stitam]

Thanks @arendsee for opening this PR. I thought about the issue some more and suggested an alternative solution that does not require an additional argument. Just a thought, I'm okay with your implementation as well.

If you want to go with your version, then I think overwrite rules should be more explicit for file.copy(). Let me know what you think.

[stitam]

Thanks @arendsee for this. I am wondering if it is possible to implement a solution that does not require an extra argument. How do you feel about something like this?

if (!file.exists(db_path_file) | overwrite) {
  # download data
  mssg(verbose, 'downloading...')
  curl::curl_download(db_url, db_path_file, quiet = TRUE)
}

This approach is more complex for users because it requires them to copy the manually downloaded file to the right location and rename it (we could rename db_path_file in line 50 to taxdmp.zip to eliminate the need to rename). On the other hand it resolves the issue without changing/complicating the user interface. Maybe we could add a note/guide in the documentation for those who want to use their own, manually downloaded database. What do you think of this alternative?

[stitam]

If there is already a taxdump.zip in the cache directory, then file.copy() will not do anything because the default behaviour of the function is overwrite = FALSE. However if we call db_download_ncbi() with overwrite = TRUE and a manually downloaded taxdump.zip, we might expect to overwrite the old cache file with the new, manually downloaded file. Maybe the overwrite argument should be called explicitly?

file.copy(path, db_path_file, overwrite = overwrite)

This way if db_download_ncbi() is called with overwrite = TRUE then the manually downloaded taxdump.zip will overwrite matching files in the cache directory.