Add slidescore server URL and slidescore study ID to slidescore_mapping.txt

[YoniSchirris]

Is your feature request related to a problem? Please describe. Documentation is improved. e.g. /mnt/archive/data/pathology/youngboost_TNBC_HE contains a TNBC subset of slides, but it is unclear where these slides come from. Also, it's unknown how to upload slides from the directory alone.

Describe the solution you'd like

• additionally save study.txt with required info for slidescore to upload annotatations

Describe alternatives you've considered

• manually writing a readme.txt

[YoniSchirris]

From slack:

Jonas: I guess outputting it as json will help right

Yoni: a meta.json with slidescore_server: str, slidescore_study_id: int, slide_mapping: dict ? Certainly

Jonas: Yes all in a file not sure if meta.json is the proper name

[YoniSchirris]

While working on it, I realized that it might happen that users download multiple setudies to a single directory, which would then overwrite the slidescore_url or slidescore_study_id. Hence, I added an additional layer of unique identifiers using thte url and study id, leading to

{
    "https://rhpc.nki.nl/slidescore/": {
        "876": {
            "slidescore_url": "https://rhpc.nki.nl/slidescore/",
            "slidescore_study_id": 876,
            "slide_filename_to_study_image_id_mapping": {
                "PD10010a_HE-2014-12-07_14.37.01.ndpi": 98528,
                "PD10011a_HE-2014-12-07_15.02.40.ndpi": 98337
            }
        }
    }
}

Which may seem a bit redundant. However, I added the slidescore_url and slidescore_study_id keys as a means of "documentation".

The name slide_filename_to_study_image_id_mapping clearly states that the image_id that the filename is mapped to is dependent on the study, hopefully.

[YoniSchirris]

@AjeyPaiK Do you use the old way of saving the ids? I could still save it the old way.

[YoniSchirris]

@jonasteuwen With the current set-up I can't save multiple slidescore slides that have the same filename.

I'd say this is not really supposed to happen, unless there's duplicates which we don't care about. But maybe somehow it could happen. Should we handle this?