I have been blocked for multiple API requests ( analyzing lots of cite seq data)

[KikoSchmiko]

Thank you to whomever reads this and can help!

I have been using an API to submit lists of genes, get back lists of pathways, the found entities, as well as PDFs. I ran four requests at a time in parallel with a sys sleep, and I believe I have been blocked instead of rate limited since all of my APIs return the following error:

[1] "Error: 403"
Error in parsed_content$summary :
object of type 'closure' is not subsettable

Worse than that, now I cannot access any reactome website to manually perform the analysis. The websites provide this error:

Forbidden
You don't have permission to access this resource.
Apache/2.4.41 (Ubuntu) Server at reactome.org Port 443

I am not doing anything nefarious, I just have 8 patients of data, each with multiple drug treatments to work through analyzing.

Please help!! Any advice is welcome!

So far I have confirmed I can access everything through my phone VPN but it is too slow to carry the analysis. My computer and my husbands computer are blocked and I work from home.

Thank you!!!

[EliotRagueneau]

Dear Kiko,

I have now unblocked you, I would however like to understand better your needs because you shouldn't have to send so many queries to get content.
Could you explain to me your requirements, so that I can help you get the right data in a simpler way?

As a rule of thumb, I would suggest you to avoid scanning fully a website endpoint, or to add a reasonable delay between 2 queries, as yours were inflicting a lot of stress on our servers, hence why we blocked your ip

[EliotRagueneau]

Feel free to contact me directly at eragueneau@ebi.ac.uk, and in the future help@reactome.org

[KikoSchmiko]

Thank you for your help!!

I am very sorry! I am somewhat new to APIs and didn’t understand that, I will run one at a time and with a system sleep! Is there a duration for that you recommend?

Regarding what I’m doing in case there is a way I could be doing it better, I currently have eight distinct patients, who each have up to six distinct drug treatments, who each have up to ten distinct cell types. On my end I am running a DEA of two treatments versus DMSO to get logfold change, then I am making my own list of genes where the expression between the two treatments differs, and I am trying to submit that list to see what pathways may be enriched. I hope this makes sense, and I am sorry again!!

I really appreciate your help!!

Also I will email you instead if needed in the future!

Also I edited to add regarding what reactome content I need: I need the csv with the pathways, entities found etc, and I also need the submitted entities found, and then I also need the pdf files for users in my lab that prefer to view those since they come with helpful information about the top pathways.

I can email now if that works better but have responded here in case it helps anyone else!

Thank you!!!