update APIs

[korseby]

There are several APIs that needs to be updated. They perform queries to online web services and were outdated. I fixed a bunch 3 months ago. These were the cs_inchikey_inchi-like function calls of the package webchem. They are now aggregated in one large function called cs_convert. It took me a while to discover that as the calls have been deprecated in the package without mentioning... An example is here in the latest commit:

https://github.com/korseby/RMassBank_mFam/blob/d29742edfd676dd1452aae774eb05d68cf9eb94c/galaxy/msp2massbank.r#L127

I suggest to take the version from one year ago as a reference as this is the version that has been known to work underlying the Docker image on dockerhub.

https://github.com/korseby/RMassBank_mFam/blob/93580571e7958175b955adf7efe13d7f0acb0c9b/galaxy/msp2massbank.r

https://hub.docker.com/r/korseby/msp2massbank

If you have questions, please mention me directly at github so I can help.

[sneumann]

Minimum version of webchem needed has to be newer than 04.08.2020,
an issue was closed in ropensci/webchem#275.
And the R code in this repo needs to be newer than bab7818

[sneumann]

Currently this fails with

Fetching structures and PubChem CIDs...pre...to inchi...Error in cs_check_key() : 
  no API key stored for ChemSpider.  See ?cs_check_key() for details
Calls: preprocessContributorToMassBankWorkflow ... tryCatchOne -> doTryCatch -> <Anonymous> -> cs_check_key

since a ChemSpider token needs to be provided. The above is used in
inchiKeyToInchi and smilesToInchi in

RMassBank_mFam/galaxy/msp2massbank.r

Line 128 in be16fc7

inchiKeyToInchi <- sapply(X = inchiKeys, FUN = function(inchiKey){ tryCatch({webchem::cs_convert(inchiKey, from="inchiKey", to="inchi", verbose = FALSE)}, warning = function(w) {ifelse(test = w$message=="inchikey not found... Returning NA.", yes = NA, no = warning(w))}) })

=> I suggest to use a non-web service to convert that.
Yours,
Steffen

[korseby]

I tested the cs_convert function and it now works when defining a chemspider token in the R environment. I think, convert functions can be found in rcdk.