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epmc_search: populate the hit_count attribute even with zero results #58

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epmc_search: populate the hit_count attribute even with zero results #58

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2c6462d
epmc_search: populate the hit_count attribute even with zero results
arvi1000 Jun 12, 2024
8ec3dc2
Generated documentation changes
arvi1000 Jul 1, 2024
57f7c63
Update for smaller result set
arvi1000 Jul 1, 2024
dd395e1
update tests; blank results now return blank 0x0 tibbles, not NULL
arvi1000 Jul 1, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ Imports:
tibble,
tidyr,
rlang
RoxygenNote: 7.2.3
RoxygenNote: 7.3.1
Suggests:
testthat,
knitr,
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5 changes: 4 additions & 1 deletion R/epmc_search.r
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Expand Up @@ -104,7 +104,10 @@ epmc_search <- function(query = NULL,
hits <- epmc_hits(query, synonym = synonym)
if (hits == 0) {
message("There are no results matching your query")
md <- NULL
# return an empty tibble
md <- tibble::tibble()
# populate the hit_count attribute even with zero results
attr(md, "hit_count") <- hits
} else {
limit <- as.integer(limit)
limit <- ifelse(hits <= limit, hits, limit)
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4 changes: 2 additions & 2 deletions man/epmc_annotations_by_id.Rd
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4 changes: 2 additions & 2 deletions man/epmc_ftxt.Rd
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2 changes: 1 addition & 1 deletion man/europepmc.Rd
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7 changes: 5 additions & 2 deletions tests/testthat/test_epmc_db.r
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Expand Up @@ -2,7 +2,10 @@ context("testing epmc_db")

test_that("epmc_db returns", {
skip_on_cran()
a <- epmc_db("12368864", db = "uniprot", limit = 50)
# as of July 2024, this result only returns 10 results, so limit must
# be <= that
a_limit <- 7
a <- epmc_db("12368864", db = "uniprot", limit = a_limit)
b <- epmc_db("25249410", db = "embl")
c <- epmc_db("14756321", db = "uniprot")
d <- epmc_db("11805837", db = "pride")
Expand Down Expand Up @@ -31,7 +34,7 @@ test_that("epmc_db returns", {



expect_equal(nrow(a), 50)
expect_equal(nrow(a), a_limit)

# fails correctly
expect_error(epmc_db("14756321"), "Please restrict reponse to a database")
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4 changes: 2 additions & 2 deletions tests/testthat/test_epmc_search.r
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Expand Up @@ -31,19 +31,19 @@ test_that("epmc_search returns", {
expect_is(k, "list")
expect_is(l, "data.frame")

#are diminsions correct?
# are dimensions correct?
expect_equal(nrow(e), 250)
expect_equal(ncol(e), 4)
expect_equal(nrow(f), 25)
expect_equal(nrow(h), 100)
expect_equal(length(i), 125)
expect_equal(nrow(j), 0)
expect_equal(nrow(l), 100)


# fails correctly
expect_message(epmc_search("123haha"),
"There are no results matching your query")
expect_null(j)
expect_error(epmc_search(query = "malaria", limit = TRUE))
expect_error(epmc_search(query = "malaria", verbose = "kdk"))
expect_error(epmc_search(query = "malaria", synonym = "yes"))
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