improve worker log

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BioInstaller
 Title: Integrator of Bioinformatics Resources
-Version: 0.3.5.5000
+Version: 0.3.5.6000
 Authors@R: person("Jianfeng", "Li", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2349-208X"))
 Maintainer: Jianfeng Li <[email protected]>
 Description:

inst/extdata/config/shiny/shiny.bioinstaller.parameters.toml

@@ -1,16 +1,14 @@
 [bioinstaller.ui.sections]
 order = ["bioinstaller_input_box", "bioinstaller_output_table", "bioinstaller_output_text"]
 [bioinstaller.ui.sections.ui_basic]
-bioinstaller_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
-bioinstaller_output_text = "title = 'Output of bioinstaller', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+bioinstaller_input_box = "title = 'BioInstaller query', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+bioinstaller_output_text = "title = 'Output of bioinstaller (Text)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 bioinstaller_output_table = "title = 'Output of bioinstaller (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 
 [bioinstaller.paramters.bioinstaller_input_box]
 # For reading annovarR shiny APP bioinstaller tool input files  
 section_type = "input"
-rcmd_last = """
-
-"""
+rcmd_last = ""
 progressbar_message = "Running BioInstaller functions."
 render_id = "bioinstaller_input_box"
 

inst/extdata/config/shiny/shiny.conda.parameters.toml

@@ -8,9 +8,7 @@ conda_output_box_table = "title = 'Output of conda (Table)', status = 'primary',
 [conda.paramters.conda_input_box]
 # For reading annovarR shiny APP conda tool input files  
 section_type = "input"
-rcmd_last = """
-
-"""
+rcmd_last = ""
 progressbar_message = "Running conda functions."
 render_id = "conda_input_box"
 

inst/extdata/config/shiny/shiny.pubmed.parameters.toml

@@ -1,7 +1,7 @@
 [pubmed.ui.sections]
 order = ["pubmed_input_box", "pubmed_output_table"]
 [pubmed.ui.sections.ui_basic]
-pubmed_input_box = "title = 'Input', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
+pubmed_input_box = "title = 'Input (Pubmed)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 pubmed_output_table = "title = 'Output of pubmed (Table)', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE"
 
 [pubmed.paramters.pubmed_input_box]
@@ -80,7 +80,9 @@ if (!is.null(objs) && (max_n_items >= 500)){
     title.tmp <- unlist(title.tmp)
     pmid.tmp <- unlist(pmid.tmp)
     res <- suppressWarnings(rentrez::parse_pubmed_xml(fetch.pubmed.tmp))
-    doi.tmp <- unlist(lapply(res, function(x) {if (length(x$doi) == 0) return(NA); x$doi}))
+    if (length(res[[1]]) == 1 && length(res$doi) == 0) {doi.tmp <- NA} 
+    else if (length(res[[1]]) == 1 && length(res$doi) != 0) {doi.tmp <- res$doi}
+    else { doi.tmp <- unlist(lapply(res, function(x) {if (length(x$doi) == 0) return(NA); x$doi})) }
     result <- cbind(pmid.tmp, doi.tmp, title.tmp, abstracts.tmp, publish.year.tmp, journal.name.tmp, book.name.tmp)
 }
 colnames(result) <- c("PMID", "DOI", "Title", "Abstract", "PublishDate", "JournalName", "BookName")

inst/extdata/shiny/global_var.R

@@ -436,6 +436,8 @@ get_tabItem_ui <- function(tabitem = "instant") {
 
 get_bioinstaller_installed <- function() {
   items_db <- Sys.getenv('BIO_SOFTWARES_DB_ACTIVE')
+  if (!file.exists(items_db) || file.size (items_db) == 0 || 
+      configr::get.config.type (items_db) == FALSE) return(data.frame())
   x <- configr::read.config(items_db)
   if (is.list(x)) {item_name <- names(x);x <- data.table::rbindlist(x)} else {return(data.frame())}
   return(cbind(item_name, x))

inst/extdata/shiny/worker.R

@@ -97,6 +97,14 @@ while (TRUE) {
       params[[item]] <- NULL
     }
     log_file <- sprintf("%s/%s.log", log_dir, qqkey)
+    log_con <- file(log_file)
+    sink(log_con, append = TRUE)
+    sink(log_con, append = TRUE, type = "message")
+    cat(sprintf("@@Task start at:@@ %s\n", format(Sys.time(), "%Y-%m-%d %H:%M:%S")))
+    cat(sprintf("@@Worker nodename:@@ %s\n", Sys.info()[["nodename"]]))
+    cat(sprintf("@@Worker user:@@ %s\n", Sys.getenv("USER")))
+    cat(sprintf("@@Worker locale:@@ %s\n", Sys.getlocale()))
+    cat(sprintf("@@Worker PID:@@ %s\n", Sys.getpid()))
     con <- DBI::dbConnect(RSQLite::SQLite(), db_path)
     need.initial <- nrow(DBI::dbGetQuery(con, sprintf("SELECT * FROM %s WHERE key = \"%s\"",
                                                       task_table, qqkey))) == 0
@@ -121,24 +129,25 @@ while (TRUE) {
     if (tolower(qqcommand_type) == "r") {
       cat(sprintf("%s Running R command for key %s
 ", format(Sys.time(), "%Y %m-%d %X"), qqkey))
-      log_con <- file(log_file)
-      sink(log_con, append = TRUE)
-      sink(log_con, append = TRUE, type = "message")
       worker_do_env <- new.env()
       if (is.null(req_pkgs) | req_pkgs == "") {cmd <- ""} else {
         cmd <- 'sapply(req_pkgs, function(x){require(x, character.only = TRUE)})'
       }
 
       if (qqcommand != "") {
         status <- tryCatch({
+          cat(sprintf("@@CMD:@@ %s\n", cmd))
           eval(parse(text = cmd), envir = worker_do_env)
+          cat(sprintf("@@CMD:@@ %s\n", qqcommand))
+          cat("@@Params:@@\n")
+          print(params)
           do.call(eval(parse(text = qqcommand), envir = worker_do_env), params,
                   envir = worker_do_env)},
                            error = function(e) {
                              message(e$message)
                              FALSE
                            })
-        cat(status)
+        if (is.character(status) || is.numeric(status)) {cat(status)} else {print(status)}
       } else {
         status <- tryCatch({
          eval(parse(text = cmd), envir = worker_do_env)
@@ -152,7 +161,7 @@ while (TRUE) {
            eval(parse(text = last_cmd[[x]]), envir = worker_do_env)
          })
         }, error = function(e) {message(e$message)})
-        cat(status)
+        if (is.character(status) || is.numeric(status)) {cat(status)} else {print(status)}
       }
       sink()
       sink(type = "message")