run-GetPMID-writeLines-publish.R

In sbalci/AutoJournalWatch: Auto Journal Watch.

# /Users/serdarbalciold/AutoJournalWatch/run-GetPMID-writeLines-publish.R

options(repos = c("https://cran.microsoft.com/snapshot/2020-05-01"))


# Daily cron Journal Watch ----
# load library ----
print(paste0("Load Library Started at: ", Sys.time()))
source("~/AutoJournalWatch/R/loadLibrary.R")
print(paste0("Load Library Ended at: ", Sys.time()))
# check time and then run ----
previousrun <- 
    if (file.exists("~/AutoJournalWatch/lastrun.log")) {
        readLines("~/AutoJournalWatch/lastrun.log")    
    } else{
        Sys.time() - as.difftime(13, units = "hours")
    }

if (as.POSIXlt(previousrun) + as.difftime(12, units = "hours") < Sys.time()) {
    
    # read previous data ----
    

    load("~/JournalWatchPBPath/.RData")
    
    
    
    # read feeds
    # print(paste0("Read Feeds Started at: ", Sys.time()))
    # source(file = "~/AutoJournalWatch/R/readFeeds.R")
    # print(paste0("Read Feeds Ended at: ", Sys.time()))
    # append csv files
    # print(paste0("append csv files Started at: ", Sys.time()))
    # source(file = "~/AutoJournalWatch/R/appendcsv.R")
    # print(paste0("append csv files Ended at: ", Sys.time()))
    Sys.sleep(6)
    # Get PMID list from e-utilities ----
    # search topic ----
    print(paste0("define topics Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/topic.R")
    print(paste0("define topics Ended at: ", Sys.time()))
    # journal list ----
    print(paste0("Read Journal List Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/journals.R")
    print(paste0("Read Journal List Ended at: ", Sys.time()))
    # searchQuery ----
    print(paste0("Read searchQuery Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/searchQuery.R")
    print(paste0("Read searchQuery Started at: ", Sys.time()))
    # date range ----
    # source("~/AutoJournalWatch/R/dateRange.R")
    # generate search formula ----
    print(paste0("Read searchFormula Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/searchFormula.R")
    print(paste0("Read searchFormula Ended at: ", Sys.time()))
    Sys.sleep(6)
    # generate search formula ----
    # print(paste0("Read searchFormulaDocker Started at: ", Sys.time()))
    # source("~/AutoJournalWatch/R/searchFormulaDocker.R")
    # print(paste0("Read searchFormulaDocker Ended at: ", Sys.time()))
    # write sh file ----
    print(paste0("Read searchFormula Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/generateSH.R")
    print(paste0("Read searchFormula Started at: ", Sys.time()))
    Sys.sleep(6)
    # run sh file: eutilities get PMID save temporary list ----
    print(paste0("run SH File Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/runSH.R")
    print(paste0("run SH File Ended at: ", Sys.time()))
    Sys.sleep(6)
    # combine temporary list with existing list ----
    print(paste0("read and Combine Files Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/readCombineFiles.R")
    print(paste0("read and Combine Files Ended at: ", Sys.time()))
    # write files ----
    print(paste0("write files Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/writeFiles.R")
    print(paste0("write files Ended at: ", Sys.time()))
    # remove temporary files ----
    print(paste0("remove temporary files Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/removeTemporaryFiles.R")
    print(paste0("remove temporary files Ended at: ", Sys.time()))
    Sys.sleep(6)
    # read combined PMID list ----
    print(paste0("read combined PMID list Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/readCombinedFiles.R")
    print(paste0("read combined PMID list Ended at: ", Sys.time()))
    Sys.sleep(6)
    # write code to Rmd ----
    print(paste0("write code to Rmd Started at: ", Sys.time()))
    
    suppressPackageStartupMessages( {
        if (!require("magicfor")) {install.packages("magicfor")}
    })
    suppressPackageStartupMessages(library("magicfor"))
    
    
    source("~/AutoJournalWatch/R/rmdGenerationFunction_pancreas.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_gallbladder.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_bileducts.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_ampulla.R")
    print(paste0("write code to Rmd Ended at: ", Sys.time()))
    Sys.sleep(6)
    # write code to Rmd
    print(paste0("write code to new Rmd Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/rmdGenerationFunction_new_pancreas.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_new_gallbladder.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_new_bileducts.R")
    source("~/AutoJournalWatch/R/rmdGenerationFunction_new_ampulla.R")
    print(paste0("write code to new Rmd Ended at: ", Sys.time()))
    # copy and rename files ----
    print(paste0("copy and rename files Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/copyRenameFiles.R")
    print(paste0("copy and rename files Ended at: ", Sys.time()))
    Sys.sleep(1)
    # Generate email ----
    # print(paste0("Generate email Started at: ", Sys.time()))
    # source("~/AutoJournalWatch/R/generateEmail.R")
    # print(paste0("Generate email Ended at: ", Sys.time()))
    
    
    # Generate wordpress post ----
    print(paste0("Generate wordpress Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/generateWP.R")
    print(paste0("Generate wordpress Ended at: ", Sys.time()))
    
    
    # Update Git and Email ----
    
    # Git Update AutoJournalWatch ----
    print(paste0("Git Update AutoJournalWatch Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/gitUpdateAutoJW.R")
    print(paste0("Git Update AutoJournalWatch Ended at: ", Sys.time()))
    Sys.sleep(10)

    # Send email
    # print(paste0("Send email Started at: ", Sys.time()))
    # source("~/AutoJournalWatch/R/email_new_articles.R")
    # print(paste0("Send email Ended at: ", Sys.time()))

    # Send wordpress ----
    print(paste0("Send wordpress Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/WP_new_articles.R")
    print(paste0("Send wordpress Ended at: ", Sys.time()))
    
    
    
    
    # render RecentPBPathJW Rmd Files ----
    print(paste0("Render RecentPBPathJW.Rmd Files Started at: ", Sys.time()))
    
    suppressPackageStartupMessages( {
        if (!require("here")) {install.packages("here")}
    })
    suppressPackageStartupMessages(library("here"))
    
    
    source("~/AutoJournalWatch/R/renderRmdFiles.R")
    print(paste0("Render Rmd Files Ended at: ", Sys.time()))
    Sys.sleep(60)
    # Git Update PBPath JournalWatch ----
    print(paste0("Git Update PBPath JournalWatch Started at: ", Sys.time()))
    source("~/AutoJournalWatch/R/gitUpdatePBPathJW.R")
    print(paste0("Git Update PBPath JournalWatch Ended at: ", Sys.time()))
    Sys.sleep(1)
    
    # Save Execution Time ----
    write(x = as.character(Sys.time()), file = "~/AutoJournalWatch/lastrun.log")
    
    # save data image ----
    
    save.image(file = "~/JournalWatchPBPath/.RData")

    
} else {
    print(paste0("Already searched within previous day. If want to run the code delete AutoJournalWatch/lastrun.log file.", Sys.time()))
}