Fixed problem apparently due to using http protocol instead of https.

R/pmcOAI.R

@@ -1,6 +1,6 @@
 # Get XML from PMC-OAI service  (Pubmed Central Open Archives Initiative)
 
-# http://www.ncbi.nlm.nih.gov/pmc/tools/oai/
+# https://www.ncbi.nlm.nih.gov/pmc/tools/oai/
 
 pmcOAI <- function(id,  ...){
 
@@ -11,11 +11,11 @@ pmcOAI <- function(id,  ...){
    id2 <- gsub("PMC", "", id)
 
    # file name for attributes
-   file  <- paste("http://www.ncbi.nlm.nih.gov/pmc/articles/", id, sep="")
+   file  <- paste("https://www.ncbi.nlm.nih.gov/pmc/articles/", id, sep="")
 
    # use getURL in RCurl package (readlines returns incomplete line warning and does not get errors (just 404 NOT found)
-  #  url <- "http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:"   
-     url <- "http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:"
+  #  url <- "https://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:"   
+     url <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc&identifier=oai:pubmedcentral.nih.gov:"
 
    x <- getURL( paste0(url, id2), .encoding="UTF-8", ...)
 
@@ -25,12 +25,18 @@ pmcOAI <- function(id,  ...){
       if(error=="idDoesNotExist") stop("No results found using ", id)
 
       message("No full text in Open Access Subset, downloading metadata only" )        
-    #  url <- "http://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc_fm&identifier=oai:pubmedcentral.nih.gov:"
-       url <- "http://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc_fm&identifier=oai:pubmedcentral.nih.gov:"
+    #  url <- "https://www.pubmedcentral.nih.gov/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc_fm&identifier=oai:pubmedcentral.nih.gov:"
+       url <- "https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi?verb=GetRecord&metadataPrefix=pmc_fm&identifier=oai:pubmedcentral.nih.gov:"
 
       x <- getURL( paste0(url, id2), .encoding="UTF-8", ...)
 
    }
+
+   doc <- processXML(x)
+   doc
+}
+
+processXML <- function(x, id=NULL, file=NULL) {
    # Remove namespace for easier XPath queries
 #   x[1] <- gsub(" xmlns=[^ ]*" , "", x[1])
 # see PMC4515827 with tab before xmlns,  \txmlns=
@@ -43,10 +49,15 @@ pmcOAI <- function(id,  ...){
    x[n] <- gsub(">([^<])</xref>", ">^\\1</xref>", x[n])
 
    doc <- xmlParse(x)  
- 
+
    ## ADD attributes  
-   attr(doc, "id") <- id
-   attr(doc, "file") <- file
+   if (!is.null(id)) {
+    attr(doc, "id") <- id
+   }
+
+   if (!is.null(file)) {
+    attr(doc, "file") <- file
+   }
+
    doc
 }
-

README.md

@@ -16,3 +16,5 @@ to read zip, word tables and pdf supplementary files.
 Additional details about the package are on the [wiki pages](https://github.com/cstubben/pmcXML/wiki/Overview) and in [BMC Bioinformatics](http://www.biomedcentral.com/1471-2105/15/43/abstract).
 
 Stubben, CJ and JC Challacombe, 2014. Mining locus tags in PubMed Central to improve microbial gene annotation. BMC Bioinformatics 15:43.
+
+