Integration of US EPA API for data retrieval

MassBank / RMassBank

Playground for experiments on the official http://bioconductor.org/packages/devel/bioc/html/RMassBank.html

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Integration of US EPA API for data retrieval #350

Closed tsufz closed 10 months ago

tsufz commented 10 months ago

The US EPA API is back again. We should add a webinterface to retrieve DTXSID on the fly. However, requires a personal API key. I guess, for public institutions, it should be no problem to retrieve it.

tsufz commented 10 months ago

[x] add basic API interface
[x] add retrieval by InChIKey
[ ] if key failes, fall back to CAS
[x] write to infolist
[x] add key entry to settings

ChemConnector commented 10 months ago

Contact @. and he will Give you a keyOn Aug 14, 2023, at 11:35 PM, Tobias Schulze @.> wrote:

[ ] add basic API interface [ ] add retrieval by InChIKey [ ] if key failes, fall back to CAS [ ] add key entry to settings

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tsufz commented 10 months ago

@ChemConnector, I got a private key. I guess, this is not the purpose of a key to distribute it publicly? I will integrate the function in RMassBank. If the people do not provide a key in the settings, they could add the DTXSID using the batch search.

This is a difference to the validation during the record submission. In this case, we could amend missing DTXSID / rerun old records using an application key, which is kept safely in the Github vault. @meier-rene, what do you think about?

Cheers, Tobi

tsufz commented 10 months ago

Skip the CAS request so far. Let's check the performance and add it later (also name search).

tsufz commented 10 months ago

Solved in https://github.com/MassBank/RMassBank/pull/342/commits/cc4f10208e07fe876822d9ae211d32430fbd0900