diff --git a/inst/reports/seqrunsum/funcs.R b/inst/reports/seqrunsum/funcs.R index 5938fbc..f3f7886 100644 --- a/inst/reports/seqrunsum/funcs.R +++ b/inst/reports/seqrunsum/funcs.R @@ -40,7 +40,7 @@ funcs <- list( clrs <- RColorBrewer::brewer.pal.info |> tibble::rownames_to_column(var = "name") |> tibble::as_tibble() |> - filter(name %in% c("Set3", "Set2", "Pastel2", "Pastel1")) |> + filter(name %in% c("Set3", "Set2", "Pastel2", "Pastel1", "Set1")) |> select(name, maxcolors) |> arrange(desc(name)) |> rowwise() |> diff --git a/inst/reports/seqrunsum/report.qmd b/inst/reports/seqrunsum/report.qmd index 6d3d25d..7e2bb16 100644 --- a/inst/reports/seqrunsum/report.qmd +++ b/inst/reports/seqrunsum/report.qmd @@ -27,8 +27,8 @@ format: body-width: 1300px params: title: "UMCCR PortalDB Workflow Summary" - date_start: "2024-05-20" - date_end: "2024-05-22" + date_start: "2024-05-30" + date_end: "2024-06-03" --- ```{r} @@ -61,8 +61,8 @@ source(here("inst/reports/seqrunsum/funcs.R")) ```{r eval=interactive()} params <- list( - date_start = "2024-05-20", - date_end = "2024-05-22" + date_start = "2024-05-31", + date_end = "2024-06-03" ) ``` @@ -98,6 +98,7 @@ wfs <- tibble::tribble( invisible(capture.output(rportal::awsvault_profile("upro"))) query_wf <- glue('WHERE "start" >= date(\'{dstart}\') AND "start" <= date(\'{dend}\') ORDER BY "start" DESC;') pmeta_rds <- here(glue("nogit/data_portal/workflows/{as.Date(date_end)}.rds")) +# fs::dir_create(here(glue("nogit/data_portal/workflows"))) # pmeta_raw <- rportal::portaldb_query_workflow(query_wf) # saveRDS(pmeta_raw, file = pmeta_rds) pmeta_raw <- readr::read_rds(pmeta_rds) @@ -127,6 +128,7 @@ sbjids <- funcs$get_ids(pmeta_tidy, "SubjectID") # not used anywhere (yet?) ```{r} #| label: query_limsrow_table +# fs::dir_create(here(glue("nogit/data_portal/lims"))) lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds")) libidsq <- paste(libids, collapse = "|") query_lims <- glue("WHERE REGEXP_LIKE(\"library_id\", '{libidsq}');")