sjoerdk / pimsclient Goto Github PK

• pimsclient version: 0.5.2

For debugging server interactions it is often useful to output the full content of post requests done with pimsclient, including full json content.

As far as I have found you can get the requests lib to output a lot of http debug info (https://stackoverflow.com/questions/16337511/log-all-requests-from-the-python-requests-module/57325050#57325050), but not the json content sent. I think this should be added in pimsclient code.

• pimsclient version: 0.5.2
• Python version: 3

Description

The PIMS API endpoint
api/Keyfiles/{keyfile_id}/Files/Deidentify
is the main way of setting pseudonyms via pims API. (see ​https://github.com/sjoerdk/pimsclient/issues/159)

It turned out in #10042 that in case identifiers already exist with a different pseudonym, PIMS will silently skip these. The call finishes as succesful. However the pseudonyms will not be set.

This is unwanted behavior. PIMS itself needs to be changed to return some kind of warning or error. However, in the mean time, consider having pimsclient check everything manually beforehand to avoid these errors.

• pimsclient version: 1.5.2

For Project.set_keys() there should be an 'ignore errors' flag. Currently an error is thrown if any pseudonym to set already exists. When adding many pseudonyms however, upon hitting any error, often part of the pseudonyms you were setting aready exist. Having to prune these away each time before re-running the script is annoying.

Add 'ignore_errors=False' which will print warnings instead of raise exceptions when trying to set existing pseudonyms

We want to be able to save AccessionNumber pseudonyms in PIMS. Add this as a datatype

pimsclient version: 0.5.1

Currently pimsclient can only send identifiers to PIMS to retrieve a pseudonym, or send in pseudonyms to retrieve identifiers.
This is enough for projects starting clean with PIMS.

For projects with existing data this is not sufficient however. These often require historic pseudonym/identifier pairs to be added to PIMS so that new data for historic patients will be pseudonymized consistently with already acquired data.

For this there needs to be a way to set manual pseudonym/identifier pairs in PIMS.
Special care needs to be taken to handle conflicts:

• If a manual pseudonym is already present in PIMS but linked to a different identifier
• If a manual identifier is already present but linked to a different pseudonym

There is an unwanted schroedingers behaviour in the current PIMS API. By querying whether an identity has a pseudonym, you create that pseudonym.

There should be an API endpoint to get a yes or no answer without creating pseudonym. This is important when doing larger scale operations on legacy archives. You don't always want to create pseudonyms for everything you query.

Hey Sjoerd,

Really nice client, I have been trying to get it to work with our downloading scripts.

Description

Currently, the automatic download for e.g. COVID CT has per patient ID both a pseudonym and another random number, the anonymization salt. This is used to perturb data randomly, e.g. moving dates around etc.

I would therefore like to be able to not only have "PatientID" | "Pseudonym" in PIMS, but actually rows like "PatientID" | "Pseudonym" | "Salt".

What I Did

I tried hacking around the KeyFiles.deidentify method and also tried fiddling around on the swagger UI of PIMS. I think /api/Keyfiles/{KeyfileKey}/Pseudonyms/{PseudonymId}/Data should be suitable, but I get an insufficient rights error.

Do you know if this is already possible with pimsclient now and I am missing something?