version 1.0.4

cran · Mar 6, 2024 · b015034 · b015034
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: pubmedtk
 Title: 'Pubmed' Toolkit
-Version: 1.0.3
+Version: 1.0.4
 Authors@R: 
     person("Benjamin Gregory", "Carlisle", , "murph@bgcarlisle.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8975-0649"))
@@ -13,13 +13,13 @@ BugReports: https://github.com/bgcarlisle/pubmedtk/issues
 Imports: magrittr, dplyr, xml2, jsonlite, httr, assertthat, stringr,
         rlang, utils
 Encoding: UTF-8
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Suggests: testthat (>= 3.0.0)
 Config/testthat/edition: 3
 NeedsCompilation: no
-Packaged: 2024-02-27 21:32:56 UTC; researchfairy
+Packaged: 2024-03-05 21:30:14 UTC; researchfairy
 Author: Benjamin Gregory Carlisle [aut, cre]
     (<https://orcid.org/0000-0001-8975-0649>)
 Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
 Repository: CRAN
-Date/Publication: 2024-02-27 22:10:02 UTC
+Date/Publication: 2024-03-05 21:50:02 UTC
diff --git a/MD5 b/MD5
@@ -1,16 +1,16 @@
-d74039c1b79d5a9ebc39043948578b39 *DESCRIPTION
+ea884b89843afc9f048a3d904aa16079 *DESCRIPTION
 8a026120dcc725392c4ee42947836dd7 *NAMESPACE
-bb1137b7e7fa08d2a4a5c3f2629dc6a5 *NEWS.md
+76ef1a53de3be22b96662f6a186e8bb4 *NEWS.md
 8955382c87b4259347a9795e96374e1b *R/get_metadata_from_one_pmid.R
 b336b3373ca3defbd504ef1f26c4374b *R/get_metadata_from_pmids.R
 5a94e597d6070fc87d68b74da0af20e8 *R/get_pmids_from_one_search.R
-c41f5b9a4dde11446b51ed075b602da8 *R/get_pmids_from_searches.R
-cb39efb5cfaab813d5cc28fdccb08820 *R/intersection_check.R
+d663220941beeed2b85d1552957e933c *R/get_pmids_from_searches.R
+2cd33a1c07e9fb86ed9febdc4bee1f2e *R/intersection_check.R
 13052b679e6fc07acd9354dd425f66c1 *R/pubmedtk-package.R
 3031a6da4184e2ef0d70326a322b6db7 *README.md
 ce08ae537b3af2b74c4232625e08bb0d *man/get_metadata_from_one_pmid.Rd
 942fa522c3d35d12cfa4a463c87aec18 *man/get_metadata_from_pmids.Rd
 63d138c944ce4e2967767118f5366533 *man/get_pmids_from_one_search.Rd
 18b91fb07d0d397a18b66514884b6078 *man/get_pmids_from_searches.Rd
-ae2567cfe18b0fcbd3dca90d0ca183d4 *man/intersection_check.Rd
+70a10406be28c11975a79c1d2547904f *man/intersection_check.Rd
 d710b8f21360c200f05eb3a276d2f4f8 *man/pubmedtk-package.Rd
diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,21 @@
+# pubmedtk 1.0.4
+
+* Fixed bug in `intersection_check()` where it would crash if the
+  column supplied was not named "pmid"
+* Fixed bug in `get_pmids_from_searches()` where an NA search can
+  cause unexpected results
+* Added `quiet` option to `intersection_check()` to disable progress
+  messages during download
+
+---
+
 # pubmedtk 1.0.3
 
 * Added `$abstract` download to `get_metadata_from_one_pmid()` and
   corresponding column to `get_metadata_from_pmids()`
 
+---
+
 # pubmedtk 1.0.2
 
 * Added optional progress feedback during download for

diff --git a/R/get_pmids_from_searches.R b/R/get_pmids_from_searches.R
@@ -131,18 +131,28 @@ get_pmids_from_searches <- function (
 
         for (query in queries) {
 
-            ## Perform search
-            pm_search_result <- get_pmids_from_one_search(
-                query,
-                api_key
-            )
+            ## Error checking
+            if (! is.na(query)) {
+                ## Perform search
+                pm_search_result <- get_pmids_from_one_search(
+                    query,
+                    api_key
+                )
+            } else {
+
+                pm_search_result <- list(
+                    pubmed_search_success = FALSE,
+                    n_results = 0,
+                    pmids = NA
+                )
+            }
 
             ## Apply it to the data frame
 
             df <- df %>%
                 dplyr::mutate(
                            pubmed_search_success = ifelse(
-                               !!dplyr::sym(column) == query,
+                               ! is.na (query) & !!dplyr::sym(column) == query,
                                pm_search_result$pubmed_search_success,
                                .data$pubmed_search_success
                            )
@@ -151,7 +161,7 @@ get_pmids_from_searches <- function (
             df <- df %>%
                 dplyr::mutate(
                            n_results = ifelse(
-                               !!dplyr::sym(column) == query,
+                               ! is.na(query) & !!dplyr::sym(column) == query,
                                pm_search_result$n_results,
                                .data$n_results
                            )
@@ -160,7 +170,7 @@ get_pmids_from_searches <- function (
             df <- df %>%
                 dplyr::mutate(
                            pmids = ifelse(
-                               !!dplyr::sym(column) == query,
+                               ! is.na(query) & !!dplyr::sym(column) == query,
                                    ifelse(
                                        ! is.na(pm_search_result$pmids),
                                        jsonlite::toJSON(pm_search_result$pmids),

diff --git a/R/intersection_check.R b/R/intersection_check.R
@@ -10,6 +10,9 @@
 #' 
 #' @param api_key A valid Pubmed API key
 #'
+#' @param quiet A boolean TRUE or FALSE. If TRUE, no progress messages
+#'     will be printed during download. FALSE by default.
+#'
 #' @param batch_size An integer greater than 0 and less than 10000
 #'
 #' @return A data frame containing the original columns, as well as
@@ -60,7 +63,8 @@ intersection_check <- function (
                                 column,
                                 query,
                                 api_key,
-                                batch_size = 1000
+                                batch_size = 1000,
+                                quiet = FALSE
                                 ) {
 
     out <- tryCatch({
@@ -135,7 +139,9 @@ intersection_check <- function (
             dplyr::slice_head() %>%
             dplyr::select(!!dplyr::sym(column))
 
-        message(paste(nrow(pmids), "unique PMID's to check"))
+        if (! quiet) {
+            message(paste(nrow(pmids), "unique PMID's to check"))
+        }
 
         ## Add new columns
         pmids$pm_checked <- FALSE
@@ -147,7 +153,8 @@ intersection_check <- function (
                 dplyr::filter(! .data$pm_checked) %>%
                 utils::head(n=batch_size)
 
-            pmid_search_term <- pmid_batch$pmid %>%
+            pmid_search_term <- pmid_batch %>%
+                dplyr::pull(!!dplyr::sym(column)) %>%
                 paste(collapse="[PMID] OR ") %>%
                 paste0("[PMID]")
 
@@ -185,22 +192,22 @@ intersection_check <- function (
             pmids <- pmids %>%
                 dplyr::mutate(
                     pm_checked = ifelse(
-                        .data$pmid %in% pmid_batch$pmid,
+                        !!dplyr::sym(column) %in% dplyr::pull(pmid_batch, !!dplyr::sym(column)),
                         TRUE,
                         .data$pm_checked
                     )
                 ) %>%
                 dplyr::mutate(
                     found_in_pm_query = ifelse(
-                        .data$pmid %in% found_pmids,
+                        !!dplyr::sym(column) %in% found_pmids,
                         TRUE,
                         .data$found_in_pm_query
                     )
                 ) %>%
                 dplyr::mutate(
                     found_in_pm_query = ifelse(
-                        .data$pmid %in% pmid_batch$pmid &
-                        ! .data$pmid %in% found_pmids,
+                        !!dplyr::sym(column) %in% dplyr::pull(pmid_batch, !!dplyr::sym(column)) &
+                        ! (!!dplyr::sym(column) %in% found_pmids),
                         FALSE,
                         .data$found_in_pm_query
                     )
@@ -211,13 +218,15 @@ intersection_check <- function (
                 nrow()
 
             prop_done <- round(100 * n_done / nrow(pmids), digits=3)
-
-            message(
-                paste0(
-                    prop_done,
-                    "% done"
+
+            if (! quiet) {
+                message(
+                    paste0(
+                        prop_done,
+                        "% done"
+                    )
                 )
-            )
+            }
         }
 
         out <- df %>%

diff --git a/man/intersection_check.Rd b/man/intersection_check.Rd