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yufree / xMSannotator

fork from https://sourceforge.net/projects/xmsannotator/
https://sourceforge.net/projects/xmsannotator/
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ChemSpider SOAP APIs are now retired #4

Open sharped-rsc opened 5 years ago

sharped-rsc commented 5 years ago

The ChemSpider SOAP APIs are now retired, which means that the look-up based upon ChemSpider can no-longer be used. There is a new replacement API which is described at https://developer.rsc.org, which could be used to provide the same functionality.

yufree commented 5 years ago

Thanks for your reminder! I think the new API totally changed chspider.batch.annotation.child.R

If @kuppal2 plan to re-write this function, I could update when the svn repo is updated. Otherwise I might add warnings when someone use this function. The 1000 compounds per day of free API plan might not be enough for metabolomics studies while enough for targeted analysis.

sharped-rsc commented 5 years ago

Thanks for your response. The 1000 calls per day is only a restriction on the default account. Higher usage allowances are available upon request - at no charge for non-commercial users.

sharped-rsc commented 5 years ago

Hi @yufree, have you heard anything from @kuppal2. If not I would be willing to help with updating the code to use the new APIs but I'm not that familiar with R so I would need to work with you on that.

yufree commented 5 years ago

I add you and @kuppal2 as collaborators of this repo and you could directly modify the code now. I could help to explain the R code. The major function is chspider.batch.annotation.child.R. The former function pastes the request via SOAP and now you use REST. Here is the related code https://github.com/yufree/xMSannotator/blob/cf9e5994bf0a74a26401a6acfd8ef4977e8e5712/R/chspider.batch.annotation.child.R#L71-L240