Error Retrieving Cell Line Datasets from PharmacoGx - Build Blocked

[jjacobson95]

In build/broad_sanger/03-createDrugFile.R, I am receiving the following error. I will look into this. It might just be a version / dependency issue.

Error in parse_con(txt, bigint_as_char) : 
  lexical error: invalid char in json text.
                                       Please use the correct dataset 
                     (right here) ------^
Calls: <Anonymous> ... fromJSON -> parse_and_simplify -> parseJSON -> parse_con
Execution halted
Error on or near line 10 while executing: Rscript 03-createDrugFile.R CTRPv2,GDSC,gCSI,PRISM,CCLE,FIMM

[jjacobson95]

PharmacoGx data is no longer accessible. Looks like it has been down for at least 3 weeks.

Someone already created an issue on their github but there is no response yet.

Data: https://www.pmgenomics.ca/bhklab/sites/default/files/downloads/

Error:

> PharmacoGx::availablePSets()
Error in parse_con(txt, bigint_as_char) : 
  lexical error: invalid char in json text.
                                       Please use the correct dataset 
                     (right here) ------^
> 

[sgosline]

Have you not run the build in the past few weeks?

[jjacobson95]

Last time I ran the full build was on the 15th/16th. I've done some partial ones since, but mostly been working on the sample/drug mapping update. Looks like their whole site is down now too. https://pharmacodb.pmgenomics.ca/

[sgosline]

OK, Can you try to salvage the files to assemble a build? I'll check in with the PI. We might need to rewrite everything if we can't figure it out.

[jjacobson95]

Yes, will do

[jjjermiah]

Developer from BHKLab here, apologies for this.

Is this an R package that depends on PharmacoGx?

The fix should be pushed to Bioconductor's release branch but may take some time to reflect when installing.

temporarily we have a tool for just downloading datasets
https://github.com/bhklab/orcestra-downloader

i will post updates as i have them.

Once again, apologies!

[sgosline]

Not an R package - a larger workflow. I created an issue (#287) to move to orcestra-downloader when we have the chance. Will close this one once the new build is up on Bioconductor! Thanks.

[jjacobson95]

Thanks @jjjermiah! Looks like this is still unavailable. Do you have any estimate on when this will be released?

[jjjermiah]

https://www.bioconductor.org/packages/release/bioc/html/PharmacoGx.html
Version 3.10.1 is now available on Bioconductor's Release Branch. Please let me know if this is still causing issues.

[jjacobson95]

Great, this immediate issue appears to be resolved. I'll let you know if any other issues arise