Ensure pubmed records are assigned only one PMID

Prior to this commit, pubmed records hat contained a lit of cited papers
could generate a "pmid" field in teh pubmed record that included all
pmids. This commit fixes bug #131 and provides a test against
regression.

Thanks @agbarnett for the bug report

R/parse_pubmed_xml.r

@@ -58,8 +58,8 @@ parse_one_pubmed <- function(paper){
     res$issue <- get_value(".//JournalIssue/Issue")
     res$pages <- get_value(".//MedlinePgn")
     res$key_words <- get_value(".//DescriptorName")
-    res$doi <- get_value(".//ArticleId[@IdType='doi']")
-    res$pmid <- get_value(".//ArticleId[@IdType='pubmed']")
+    res$doi <- get_value(".//PubmedData/ArticleIdList/ArticleId[@IdType='doi']")
+    res$pmid <- get_value(".//PubmedData/ArticleIdList/ArticleId[@IdType='pubmed']")
     res$abstract <- get_value(".//AbstractText")
 
     structure(res, class="pubmed_record", empty=FALSE) 

tests/testthat/test_parse.r

@@ -10,6 +10,10 @@ parsed_raw <- parse_pubmed_xml(raw_rec)
 parsed_rec <- parse_pubmed_xml(xml_rec)
 parsed_multi <- parse_pubmed_xml(multi_rec)
 
+multi_pmid_eg <- parse_pubmed_xml(
+       entrez_fetch(db="pubmed", id='29743284', rettype="xml")
+)
+
 test_that("pubmed file parsers work",{
     expect_that(raw_rec, is_a("character"))
 
@@ -27,6 +31,12 @@ test_that("pubmed file parsers work",{
     # re-introduced there will be 25 authors in each record and this will fail
     expect_that(length(parsed_multi[[1]]$authors), equals(1))
 
+    # Bug #131 related to extracting all PMIDs from a pubmed xml that contained
+    # references, not just the one true pm od teh artcle. Testing we don't
+    # regress 
+
+    expect_that(length(multi_pmid_eg$pmid), equals(1))
+
 })
 
 test_that("we can print pubmed records", {