Explain use-case of dataset testing

TIBHannover · Sep 3, 2018 · d3db77d · d3db77d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BacDiveR
 Title: A Programmatic Interface For BacDive, The DSMZ's Bacterial Diversity Metadatabase
-Version: 0.5.1
+Version: 0.6.0
 Authors@R: person("Katrin", "Leinweber", email = "katrin.leinweber@tib.eu",
                   role = c("aut", "cre"),
                   comment = c(ORCID = "0000-0001-5135-5758"))

diff --git a/NEWS.md b/NEWS.md
@@ -11,6 +11,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 ### Security
 
+# BacDiveR 0.6.0
+
+### Added
+
+- The vignette [Logic-Checking BacDive Datasets](https://tibhannover.github.io/BacDiveR/articles/logic-checking-bacdive-datasets.html)
+
+### Changed
+
+- `retrieve_search_results()` now returns `NULL` when no results are found, in 
+  order to ease integration of datasets into `testthat` tests.
+
 ## BacDiveR 0.5.1
 
 ### Fixed

diff --git a/R/retrieve_search_results.R b/R/retrieve_search_results.R
@@ -19,8 +19,10 @@ retrieve_search_results <- function(queryURL)
   if (!grepl(pattern = paste0("$", download_param), x = queryURL))
     queryURL <- paste0(queryURL, download_param)
 
-  result_IDs <-
-    strsplit(x = RCurl::getURL(queryURL), split = "\\n")[[1]]
+  payload <- RCurl::getURL(queryURL)
 
-  aggregate_datasets(result_IDs, from_IDs = TRUE)
+  if (grepl("^[[:digit:]]", payload))
+    aggregate_datasets(strsplit(x = payload, split = "\\n")[[1]], from_IDs = TRUE)
+  else if (grepl("^<!DOCTYPE", payload))
+    NULL # needed for logic-checking datasets, see vignette
 }
diff --git a/tests/testthat/test-retrieve_search_results.R b/tests/testthat/test-retrieve_search_results.R
@@ -12,3 +12,11 @@ test_that("downloading a dataset from an 'advanced search' URL works", {
   expect_equal(Millers_strains[[1]], "Borrelia mayonii")
   expect_equal(Millers_strains[[2]], "Bacillus wiedmannii")
 })
+
+
+test_that("Inconsistent datasets get corrected", {
+  inconsistent_data <- retrieve_search_results(
+    "https://bacdive.dsmz.de/advsearch?advsearch=search&site=advsearch&searchparams[20][contenttype]=text&searchparams[20][typecontent]=contains&searchparams[20][searchterm]=Sea+of+Japan&searchparams[17][searchterm]=Europe")
+
+  expect_false(is.null(inconsistent_data))
+})
diff --git a/vignettes/BacDive-geo-logic-fault.png b/vignettes/BacDive-geo-logic-fault.png
diff --git a/vignettes/BacDive.bib b/vignettes/BacDive.bib
@@ -22,3 +22,26 @@ @article{BD16
 doi = {10.1093/nar/gkv983},
 URL = {https://academic.oup.com/nar/article/44/D1/D581/2503137}
 }
+
+@Article{TT,
+    author = {Hadley Wickham},
+    title = {testthat: Get Started with Testing},
+    journal = {The R Journal},
+    year = {2011},
+    volume = {3},
+    pages = {5--10},
+    url = {https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf},
+  }
+
+@book{T,
+  author = {Hadley Wickham},
+  langid = {english},
+  location = {{Sebastopol, CA}},
+  title = {R {{Packages}}: {{Organize}}, {{Test}}, {{Document}}, and {{Share Your Code}}},
+  edition = {1st edition},
+  isbn = {978-1-4919-1059-7},
+  url = {http://r-pkgs.had.co.nz/},
+  publisher = {{O'Reilly Media}},
+  date = {2015-04-13}
+}
+
diff --git a/vignettes/logic-checking-bacdive-datasets.Rmd b/vignettes/logic-checking-bacdive-datasets.Rmd
@@ -0,0 +1,76 @@
+---
+title: "Logic-Checking BacDive Datasets"
+author: "Katrin Leinweber"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEncoding{UTF-8}
+  %\VignetteEngine{knitr::rmarkdown}
+editor_options: 
+  chunk_output_type: inline
+bibliography: BacDive.bib
+---
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+### Example of a data inconsistency
+
+Just as the correctness of data analysis code should be tested automatically, the
+consistency of data should be evaluated and monitored as well. Using [BacDive's advanced search](https://bacdive.dsmz.de/AdvSearch)
+and [BacDiveR's `retrieve_search_results()`](https://tibhannover.github.io/BacDiveR/reference/retrieve_search_results.html)
+several examples of geographic inconsistencies have been found. Presumably due to
+an overly strict location-to-country-to-continent mapping, several samples collected
+from seas neighbouring Russia (like the [Sea of Japan)](https://bacdive.dsmz.de/advsearch?site=advsearch&searchparams%5B20%5D%5Bcontenttype%5D=text&searchparams%5B20%5D%5Btypecontent%5D=contains&searchparams%5B20%5D%5Bsearchterm%5D=Sea+of+Japan&searchparams%5B100%5D%5Bcontenttype%5D=text&searchparams%5B100%5D%5Btypecontent%5D=contains&searchparams%5B100%5D%5Bsearchterm%5D=&searchparams%5B17%5D%5Bsearchterm%5D=Europe&advsearch=search),
+were assigned to Europe.
+
+![Two datasets with a geo-logic fault (pun intended)](BacDive-geo-logic-fault.png)
+
+While one may debate where exactly border between Asia and Europe runs through Russia,
+it is clear that its Eastern shoreline is located well within Asia. These and
+other datasets with East Russian locations have been reported to the BacDive team
+and a portion of those was corrected in [BacDive's 04.07.2018 release](https://bacdive.dsmz.de/news).
+
+```{r data}
+library(BacDiveR)
+  
+inconsistent_data <- retrieve_search_results(
+  "https://bacdive.dsmz.de/advsearch?advsearch=search&site=advsearch&searchparams[20][contenttype]=text&searchparams[20][typecontent]=contains&searchparams[20][searchterm]=Sea+of+Japan&searchparams[17][searchterm]=Europe"
+  )
+```
+
+As long as this specific inconsistency is not fixed, the above should display:
+`Data download in progress for BacDive-IDs: 131115 139987`.
+
+
+### How to test datasets
+
+If a BacDive user finds an inconsistency within the datasets they use, BacDiveR's
+`retrieve_search_results()` can be used to construct a test-case for such a problem.
+In the following example, the test fails as long as BacDive contains datasets with
+the above-described discrepancy between the `geo_loc_name` and `continent` fields.
+
+```{r test, error=TRUE}
+library(testthat)
+
+test_that("No inconsistent datasets exist", {
+  expect_null(inconsistent_data)
+})
+```
+
+Once the inconsistency is corrected in BacDive, the advanced search returns no
+results any more, and the above test passes. It can thus be used to monitor the
+resolution of such a problem after [reporting](https://bacdive.dsmz.de/?site=contact)
+it. Furthermore, the users is alerted (by the test failing again) in case new 
+datasets appear in BacDive with the same inconsistency.
+
+### References
+
+See [testthat.R-lib.org](https://testthat.r-lib.org/) and the
+[related "R Packages" chapter](http://r-pkgs.had.co.nz/tests.html) to learn
+more about testing in R [@TT; @T].