Merge branch 'master' into release_1_0_0

ropensci · Sep 16, 2015 · 7d00904 · 7d00904
2 parents f48a104 + 3e28144
commit 7d00904
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Showing 5 changed files with 28 additions and 8 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,8 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
 S3method(as.data.frame,eInfoList)
+S3method(extract_from_esummary,esummary)
+S3method(extract_from_esummary,esummary_list)
 S3method(print,eInfoEntry)
 S3method(print,eInfoLink)
 S3method(print,eInfoSearch)

diff --git a/R/entrez_summary.r b/R/entrez_summary.r
@@ -66,7 +66,18 @@ entrez_summary <- function(db, id=NULL, web_history=NULL,
 #'@param simplify logical, if possible return a vector
 #'@return List or vector containing requested elements 
 extract_from_esummary <- function(esummaries, elements, simplify=TRUE){
-    fxn <- if (simplify & length(elements) == 1) "[[" else "["
+    UseMethod("extract_from_esummary", esummaries)
+}
+
+#'@export
+extract_from_esummary.esummary <- function(esummaries, elements, simplify=TRUE){
+    fxn <- if(simplify & length(elements)==1) `[[` else `[`
+    fxn(esummaries, elements)
+}
+
+#'@export
+extract_from_esummary.esummary_list <- function(esummaries, elements, simplify=TRUE){
+    fxn <- if (simplify & length(elements) == 1) `[[` else `[`
     sapply(esummaries, fxn, elements, simplify=simplify)
 }
 

diff --git a/README.Rmd b/README.Rmd
@@ -9,7 +9,7 @@ output:
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#"
 )
 knitr::opts_knit$set(upload.fun = knitr::imgur_upload, base.url = NULL)  
 
@@ -80,7 +80,7 @@ Now, what sorts of data are available from other NCBI database for this paper?
 
 ```{r links}
 hox_data <- entrez_link(db="all", id=hox_pmid, dbfrom="pubmed")
-hox_data
+hox_data$links
 ```
 
 Each of the character vectors in this object contain unique IDS for records in
@@ -92,7 +92,7 @@ In this case we'll get the protein sequences as genbank files, using '
 `entrez_fetch`:
 
 ```{r proteins}
-hox_proteins <- entrez_fetch(db="protein", id=hox_data$pubmed_protein, rettype="gb")
+hox_proteins <- entrez_fetch(db="protein", id=hox_data$links$pubmed_protein, rettype="gb")
 ```
 
 ###Retrieving datasets associated a particular organism.

diff --git a/man/linkout_urls.Rd b/man/linkout_urls.Rd
@@ -7,10 +7,11 @@
 linkout_urls(elink)
 }
 \arguments{
-\item{elink:}{elink object (returned by entrez_link) containing Urls}
-
-\item{list}{of character vectors, one per ID each containing of urls for that
-ID.}
+\item{elink}{elink object (returned by entrez_link) containing Urls}
+}
+\value{
+list of character vectors, one per ID each containing of urls for that
+ID.
 }
 \description{
 Extract urls from an elink object

diff --git a/tests/testthat/test_summary.r b/tests/testthat/test_summary.r
@@ -67,6 +67,12 @@ test_that("We can extract elements from esummary object", {
 
 })
 
+test_that("We can extract elements from a single esummary", {
+    expect_that(extract_from_esummary(pop_summ_xml[[1]], c("Title", "TaxId")), is_a("list"))
+    expect_that(extract_from_esummary(pop_summ_xml[[1]], "Gi"), is_a("integer"))
+    expect_that(extract_from_esummary(pop_summ_xml[[1]], "Gi", FALSE), is_a("list"))
+})
+
 test_that("We can get a list of one element if we ask for it", {
     expect_that(entrez_summary(db="popset", id=307075396, always_return_list=TRUE), is_a("list"))
     expect_that(entrez_summary(db="popset", id=307075396), is_a("esummary"))