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IntChron parser prototype - #1

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joeroe wants to merge 5 commits into
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intchron
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IntChron parser prototype#1
joeroe wants to merge 5 commits into
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intchron

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@joeroe

@joeroe joeroe commented Oct 19, 2020

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This was an initial prototype of a parser for IntChron. Following discussion in ropensci#115, we decided to leave interacting with IntChron to another package (rintchron https://github.com/joeroe/rintchron) and use this to write separate parsers for each individual database indexed by IntChron.

joeroe and others added 5 commits October 8, 2020 18:21
Some IntChron record names contain spaces.
Recursive function for retrieving all records from a given entry point. Called on <https://intchron.org/host> or <https://intchron.org/record> it grabs the whole database in a rough form.

Relies on extra dependencies tools and purrr, but these should be 'free' as tools is bundled with base and purrr is a dependency of tidyr.
It can now successfully retrieve the whole database, albeit slowly and with much more cleaning to be done.
@joeroe joeroe closed this Oct 19, 2020
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joeroe deleted the intchron branch October 19, 2020 14:29
@dirkseidensticker

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@joeroe do you think we can revitalize this? I stated some crude work on ropensci#147 in order to finally takle ropensci#115 . It would be great to (again) get your view & input in how best to integrate Intchron via your package.

@joeroe

joeroe commented Sep 3, 2021

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Yeah, I was actually planning to work on rintchron again next week in relation to https://github.com/xronos-ch/.

As I recall, the core functionality is there, and the remaining issues relate to adding additional query functions (not really relevant to c14bazAAR), and making the response parsing more robust (probably the problem you are running into in joeroe/rintchron#13!) I'm aiming to submit it to CRAN after those are fixed, at which point I think rintchron can be a reliable dependency for c14bazAAR.

Here you can see how I envisaged a parser for an IntChron database looking: https://github.com/joeroe/c14bazAAR/blob/c2031d41101d12f50a838a5a28817b56778974e6/R/get_oxa.R – simple and almost the same as yours. The only problem is the extreme slowness of getting an entire database from IntChron compared to flat-file databases, the unfortunate tendency of the IntChron server to occasionally fail for no reason. However as I remember @nevrome thought this shouldn't stop us adding it to c14bazAAR.

@dirkseidensticker

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I am looking forward to see a CRAN release of rintchron. And despite some waiting time, I think the databases to be queried are worth that. So many thanks for keeping your package up and us in the loop.

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2 participants