updated parsing of empty investigator fields.

hugheylab · May 23, 2023 · 4a0ff68 · 4a0ff68
1 parent b0cda50
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Showing 6 changed files with 14 additions and 10 deletions.
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 1.0.15
-Date: 2022-12-13 21:38:16 UTC
-SHA: 4b014e60c1e04e8711dd6613ac5e63a90888fdd6
+Version: 1.0.16
+Date: 2023-02-12 15:41:49 UTC
+SHA: b0cda50ec63986ee6160581dc70e904cf88a3dec
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pmparser
 Title: Create and Maintain a Relational Database of Data from PubMed/MEDLINE
-Version: 1.0.16
+Version: 1.0.17
 Authors@R: c(person('Jake', 'Hughey', , 'jakejhughey@gmail.com', c('aut', 'cre')),
   person('Josh', 'Schoenbachler', , 'josh.schoenbachler@gmail.com', 'aut'),
   person('Elliot', 'Outland', , 'ehoutland@gmail.com', 'aut'))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,6 @@
+# pmparser 1.0.17
+* Updated parsing of empty investigator fields.
+
 # pmparser 1.0.16
 * Updated readme table in test standards.
 

diff --git a/R/parse_element.R b/R/parse_element.R
@@ -325,7 +325,8 @@ parseMesh = function(pmXml, dPmid, con = NULL, tableSuffix = NULL) {
   x5 = xml_find_all(x4, './/QualifierName', flatten = FALSE)
   nQualPerDesc = lengths(x5)
 
-  descPos = unlist(lapply(nDescPerPmid[nDescPerPmid > 0], function(n) 1:n))
+  descPos = unlist(lapply(
+    nDescPerPmid[nDescPerPmid > 0], function(n) seq_len(n)))
 
   if (length(nQualPerDesc) > 0 && sum(nQualPerDesc) > 0) {
     x6 = data.table(

diff --git a/R/parse_person.R b/R/parse_person.R
@@ -108,8 +108,8 @@ parsePerson = function(pmXml, dPmid, con = NULL, tableSuffix = NULL,
     x10[is.na(n_affil_ids), n_affil_ids := 0]
     x10[, n_person_ids := n_total_ids - n_affil_ids]
 
-    if (nrow(x10) > 0) {
-      x11 = x10[n_person_ids > 0, .(id_pos = 1:n_person_ids), by = cols]
+    if (nrow(x10) > 0 && any(x10$n_person_ids > 0)) {
+      x11 = x10[n_person_ids > 0, .(id_pos = seq_len(n_person_ids)), by = cols]
 
       dAllId[, id_pos := seq_len(.N), by = cols]
       dPersonId = merge(dAllId, x11, by = c(cols, 'id_pos'))

diff --git a/cran-comments.md b/cran-comments.md
@@ -16,14 +16,14 @@
   Found the following files/directories:
     'lastMiKTeXException'
 
-See results for [Windows](https://builder.r-hub.io/status/pmparser_1.0.16.tar.gz-7c295fe76dd64afdac4541030567c42f), [Ubuntu](https://builder.r-hub.io/status/pmparser_1.0.16.tar.gz-aa5fdb1f25ae49aabe4188b7cffba9ab), and [Fedora](https://builder.r-hub.io/status/pmparser_1.0.16.tar.gz-bf42f4c7ae324c94bcd7a0fb8ca9b8cc).
+See results for [Windows](https://builder.r-hub.io/status/pmparser_1.0.17.tar.gz-aac25aa5452a4d71849cc4b1efc67ced), [Ubuntu](https://builder.r-hub.io/status/pmparser_1.0.17.tar.gz-a892eda3b5a542dc9a28e7a330f41b06), and [Fedora](https://builder.r-hub.io/status/pmparser_1.0.17.tar.gz-b9631972a174459a833eebd5f0744c95).
 
 ### GitHub Actions
 
   0 errors ✓ | 0 warnings ✓ | 0 notes ✓
 
-See results for Mac, Windows, and Ubuntu [here](https://github.com/hugheylab/pmparser/actions/runs/4156795437).
+See results for Mac, Windows, and Ubuntu [here]().
 
 ## Changes from current CRAN release
 
-The test standards have been updated to include the latest version of the readme file on PubMed, which was the source of the test failures.
+* Updated parsing of empty investigator fields.