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CancerRegistryOfNorway / nordcancore

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Trim down user-defined paths #14

Closed CotterpinDoozer closed 2 years ago

CotterpinDoozer commented 3 years ago

Joonas writes: quite many paths are now defined manually in nordcan.R by the user. any way to trim them down?

We will look at this task for the autumn version.

HuidongTian commented 3 years ago

By discussing with Joonas, we will use the structure in this fall, like: The user should have "my/path/nordcan/nordcan_archive/", "my/path/nordcan/nordcan_2018", "my/path/nordcan/nordcan_2019", etc.

CotterpinDoozer commented 3 years ago

Please look also at this comment from Joonas from him running the R-modules for production:

  • the defaults / examples

    directory for saving the output of NORDCAN processing.

    dir_result <- "path/to/nordcan2019/"

    directory for holding the archived (.zip) result.

    dir_archive <- "path/to/nordcan2019/"

    should not be the same. I found it confusing. better to instead have e.g.

    directory for saving the output of NORDCAN processing.

    dir_result <- "path/to/nordcan2019/"

    directory for holding the archived (.zip) result.

    dir_archive <- "path/to/nordcan_archive/"

  • what's the difference between path_nordcan and dir_results?

Can you make sure this is also handled and that the last question is answered (if you have not already talked to Joonas about this).

CotterpinDoozer commented 2 years ago

Huidong will look more into this issue and check communication with Joonas in Slack.

HuidongTian commented 2 years ago

I recommend users have their NORDCAN project structure like: -nordcan_archive -nordcan_2018 -nordcan_2019

Folder "nordcan_archive" contains previously calculated results in .zip format. Folder "nordcan_20**" contains user instruction, cancer related data, iarccrgtools, calculated result, etc.