Datashare: initial S3 support

[pdiakumis]

Setting up S3 support for umccrise and WTS results.
For now the following will work.
I'll add CLI support next.

d <- tibble::tribble(
  ~subject_id, ~library_id, ~wgts,
  "SBJ05374", "L2401596", "WGS",
  "SBJ05374", "L2401585", "WTS",
)
# log into AWS umccr prod
token <- rportal::orca_jwt() |> rportal::jwt_validate()
urls <- d2 |>
  dplyr::rowwise() |>
  dplyr::mutate(
    share = ifelse(
      type == "WGS",
      list(rportal::datashare_um_s3(.data$library_id, token)),
      list(rportal::datashare_wts_s3(.data$library_id, token))
    )
  )
# then just unnest the share list-col
urls |> tidyr::unnest(share)

[pdiakumis]

This should work now @ohofmann (subject id is optional, the URLs CSV will only contain the library id). Also note I haven't used --append in the first run.
Also-also note that I'm not grabbing FASTQs any more.
Also-also-also note I'm including BAM md5sum from Dragen.

./datashare.R --s3 --subject_id SBJ05374 --library_id_tumor L2401596 --csv_output urls.csv
./datashare.R --s3 --subject_id SBJ05857 --library_id_tumor L2401595 --csv_output urls.csv --append
./datashare.R --s3 --subject_id SBJ05854 --library_id_tumor L2401593 --csv_output urls.csv --append
./datashare.R --s3 --subject_id SBJ05853 --library_id_tumor L2401591 --csv_output urls.csv --append
./datashare.R --s3 --subject_id SBJ04893 --library_id_tumor L2401589 --csv_output urls.csv --append
./datashare.R --s3  --wts --subject_id SBJ05374 --library_id_tumor L2401585 --csv_output urls.csv --append
./datashare.R --s3  --wts --subject_id SBJ05857 --library_id_tumor L2401582 --csv_output urls.csv --append
./datashare.R --s3  --wts --subject_id SBJ05853 --library_id_tumor L2401579 --csv_output urls.csv --append
./datashare.R --s3  --wts --subject_id SBJ05854 --library_id_tumor L2401578 --csv_output urls.csv --append
./datashare.R --s3  --wts --subject_id SBJ04893 --library_id_tumor L2401577 --csv_output urls.csv --append

cut -d, -f1-6 urls.csv | head

libid,type,bname,size,lastmodified,filesystem
L2401596,BAM_normal,L2401015_normal.bam,70.61G,2024-11-11 14:11:27,s3
L2401596,BAM_tumor,L2401596_tumor.bam,163.29G,2024-11-11 14:11:29,s3
L2401596,BAMi_normal,L2401015_normal.bam.bai,8.94M,2024-11-11 14:11:27,s3
L2401596,BAMi_tumor,L2401596_tumor.bam.bai,9.56M,2024-11-11 14:11:29,s3
L2401596,BAMmd5sum_tumor,L2401015_normal.bam.md5sum,32,2024-11-11 14:11:27,s3
L2401596,BAMmd5sum_tumor,L2401596_tumor.bam.md5sum,32,2024-11-11 14:11:29,s3
L2401596,HTML_CPSR,SBJ05374__L2401596-normal.cpsr.html,4.06M,2024-11-11 18:02:35,s3
L2401596,HTML_CanRep,SBJ05374__L2401596_cancer_report.html,9.24M,2024-11-11 18:02:35,s3
L2401596,HTML_MultiQC,SBJ05374__L2401596-multiqc_report.html,3M,2024-11-11 18:02:35,s3

cut -d, -f1 urls.csv | uniq -c
   1 libid
  43 L2401596
  42 L2401595 # no DBS sigs for this one
  43 L2401593
  43 L2401591
  43 L2401589
   8 L2401585
   8 L2401582
   8 L2401579
   8 L2401578
   8 L2401577