diff --git a/R/shiny-state.R b/R/shiny-state.R index 5e47651e720a007e3b2390045b2183f8ceae4f61..78dd2ed9137f701b78f20ad9b46a371d73948565 100644 --- a/R/shiny-state.R +++ b/R/shiny-state.R @@ -358,11 +358,11 @@ app_state2state <- function(input,gui,envopts,m=NULL) { m$conf = input2conf_metfrag(input,conf=m$conf) m$conf$paths$data <- gui$paths$data - saveRDS(m$conf,"~/scratch/m.conf.prerun.rds") + m$run <- new_runtime_state(project=gui$paths$project, envopts = envopts, conf=m$conf) - saveRDS(m$run,"~/scratch/m.run.rds") + m$input$tab$mzml <- gui2datatab(gui) diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R index 95003936f2db90d02ec148ac95bf9c9421b10c91..d547df90fdc4efcf5be7944202a46587e6f2765d 100644 --- a/R/shiny-ui-base.R +++ b/R/shiny-ui-base.R @@ -1139,6 +1139,7 @@ mk_shinyscreen_server <- function(projects,init) { rvs$status$rt_stat = m$conf$tolerance[["rt"]] rvs$status$is_extracted_stat = "In progress." rv_extr_flag(T) + rv_presc_flag(F) }) @@ -1150,21 +1151,15 @@ mk_shinyscreen_server <- function(projects,init) { isolate({ if (rv_extr_flag()) { rv_extr_flag(F) - m =rvs$m - - promises::future_promise(run(m=m,phases=c("setup","comptab","extract"))) %...>% { - rvs$m = . - rvs$status$is_extracted_stat = "Yes." - fn_c_state = file.path(rvs$m$run$paths$project, - paste0("extract.",shinyscreen:::FN_CONF)) - yaml::write_yaml(x=rvs$m$conf,file=fn_c_state) - message("(extract) Done extracting.") - message("(extract) Config written to ", fn_c_state) - shinymsg("Extraction has been completed.") - - } - - + rvs$m = run(m=rvs$m,phases=c("setup","comptab","extract")) + rvs$status$is_extracted_stat = "Yes." + rvs$status$is_qa_stat = "No." + fn_c_state = file.path(rvs$m$run$paths$project, + paste0("extract.",shinyscreen:::FN_CONF)) + yaml::write_yaml(x=rvs$m$conf,file=fn_c_state) + message("(extract) Done extracting.") + message("(extract) Config written to ", fn_c_state) + shinymsg("Extraction has been completed.") } }) }) @@ -1196,14 +1191,9 @@ mk_shinyscreen_server <- function(projects,init) { if (rv_presc_flag()) { shinymsg("Prescreening started. Please wait.") rv_presc_flag(F) - m =rvs$m - promises::future_promise(run(m=m,phases="prescreen")) %...>% { - rvs$m = . - rvs$status$is_qa_stat = "Yes." - shinymsg("Prescreening has been completed.") - - - } + m = run(m=rvs$m,phases="prescreen") + rvs$status$is_qa_stat = "Yes." + shinymsg("Prescreening has been completed.") } }) })