--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abstracts_by_pmids.R	Thu Sep 24 02:01:50 2020 +0000
@@ -0,0 +1,142 @@
+#!/usr/bin/env Rscript
+#TOOL2 abstracts_by_pmids
+#
+#This tool retrieves for all PMIDs in each row of a table the according abstracts and saves them in additional columns.
+#
+#Input: Tab-delimited table with columns containing PMIDs. The names of the PMID columns should start with “PMID”, e.g. “PMID_1”, “PMID_2” etc.
+#
+#Output: Input table with additional columns containing abstracts corresponding to the PMIDs from PubMed. 
+#The abstract columns are called "ABSTRACT_1", "ABSTARCT_2" etc. 
+#
+# Usage: $ T2_abstracts_by_pmid.R [-h] [-i INPUT] [-o OUTPUT]
+# 
+# optional arguments:
+# -h, --help                 show help message
+# -i INPUT, --input INPUT    input file name. add path if file is not in working directory
+# -o OUTPUT, --output OUTPUT output file name. [default "T2_output"]
+
+
+if ( '--install_packages' %in% commandArgs()) {
+  print('Installing packages')
+  if (!require('argparse')) install.packages('argparse', repo="http://cran.rstudio.com/");
+  if (!require("reutils")) install.packages("reutils", repo="http://cran.rstudio.com/");
+  if (!require('easyPubMed')) install.packages('easyPubMed', repo="http://cran.rstudio.com/" );
+  if (!require('textclean')) install.packages('textclean', repo="http://cran.rstudio.com/");
+}
+
+suppressPackageStartupMessages(library("argparse"))
+library("reutils")
+suppressPackageStartupMessages(library("easyPubMed"))
+suppressPackageStartupMessages(library("textclean"))
+
+parser <- ArgumentParser()
+parser$add_argument("-i", "--input", 
+                    help = "input fie name. add path if file is not in workind directory")
+parser$add_argument("-o", "--output", default="abstracts_by_pmids_output",
+                    help = "output file name. [default \"%(default)s\"]")
+parser$add_argument("--install_packages", action="store_true", default=FALSE,
+                    help="If you want to auto install missing required packages.")
+
+args <- parser$parse_args()
+
+data = read.delim(args$input, stringsAsFactors=FALSE, header= TRUE, sep='\t')
+pmids_cols_index <- grep("PMID", names(data))
+
+fetch_abstracts = function(PMIDs, row){
+  
+  efetch_result <- NULL
+  try_num <- 1
+  t_0 <- Sys.time()
+  
+  while(is.null(efetch_result)) {
+    
+    # Timing check: kill at 3 min
+    if (try_num > 1){
+      Sys.sleep(time = 1*try_num)
+      cat("Problem to receive PubMed data or error is received. Please wait. Try number: ",try_num,"\n") 
+    }
+    
+    t_1 <- Sys.time()
+    
+    if(as.numeric(difftime(t_1, t_0, units = "mins")) > 3){
+      message("Killing the request! Something is not working. Please, try again later","\n")
+      return(data)
+    }
+
+    efetch_result <- tryCatch({    
+      suppressWarnings(efetch(uid=PMIDs, db="pubmed", retmode = "xml"))
+    }, error = function(e) {
+      NULL
+    })
+    
+    if(!is.null(as.list(efetch_result$errors)$error)){
+      if (as.list(efetch_result$errors)$error == "HTTP error: Status 400; Bad Request") {
+        efetch_result <- NULL
+      }
+    }
+      
+    try_num <- try_num + 1
+    
+  } #while loop end
+
+  # articles to list
+  xml_data <- strsplit(efetch_result$content, "<PubmedArticle(>|[[:space:]]+?.*>)")[[1]][-1]
+  xml_data <- sapply(xml_data, function(x) {
+    #trim extra stuff at the end of the record
+    if (!grepl("</PubmedArticle>$", x))
+      x <- sub("(^.*</PubmedArticle>).*$", "\\1", x) 
+    # Rebuid XML structure and proceed
+    x <- paste("<PubmedArticle>", x)
+    gsub("[[:space:]]{2,}", " ", x)}, 
+    USE.NAMES = FALSE, simplify = TRUE)
+  
+  abstract.text = sapply(xml_data, function(x){
+    custom_grep(x, tag="AbstractText", format="char")}, 
+    USE.NAMES = FALSE, simplify = TRUE)
+  
+  abstracts <- sapply(abstract.text, function(x){
+    if (length(x) > 1){
+      x <- paste(x, collapse = " ", sep = " ")
+      x <- gsub("</{0,1}i>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}b>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
+    } else if (length(x) < 1) {
+      x <- NA
+    } else {
+      x <- gsub("</{0,1}i>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}b>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}sub>", "", x, ignore.case = T)
+      x <- gsub("</{0,1}exp>", "", x, ignore.case = T)
+    }
+    x
+  }, 
+  USE.NAMES = FALSE, simplify = TRUE)
+  
+  abstracts = as.character(abstracts)
+  
+  if(length(abstracts)>0){
+    data[row,sapply(1:length(abstracts),function(i){paste0("ABSTRACT_",i)})] <- abstracts
+    cat(length(abstracts)," abstracts for PMIDs of row ", row, " are added in the table.","\n")
+  }
+  
+  return(data)
+}
+    
+
+for(row in 1:nrow(data)){
+  PMIDs= as.character(unique(data[row, pmids_cols_index]))
+  PMIDs = PMIDs[!PMIDs=="NA"]
+  
+  if(length(PMIDs) > 0){
+    data = tryCatch(fetch_abstracts(PMIDs, row),
+                    error=function(e){ 
+                      Sys.sleep(3)
+                      })
+  } else {
+    print(paste("No PMIDs in row", row))
+  }
+}
+
+write.table(data, args$output, sep = '\t', row.names = FALSE, col.names = TRUE)
+