Issue #54: UniProt unit test for P01133

cycle20 · Mar 26, 2023 · 80f77c8 · 80f77c8
1 parent c1ca510
commit 80f77c8
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Showing 2 changed files with 33 additions and 105 deletions.
diff --git a/R/dataPatch.R b/R/dataPatch.R
@@ -78,8 +78,6 @@ main <- function() {
     ## NOTE: this filter drops some not well-curated compounds
     filter(!is.na(source))
 
-  checkDataCoverage(clueTable)
-
   clueTable <- targetList %>%
     left_join(clueTable) %>%
     rowwise() %>%
@@ -92,8 +90,6 @@ main <- function() {
   print(result)
   saveRDS(result, file = CLUE.PATCHED.OUTPUT)
 
-  # TODO: should be another logic: checkDataCoverage(result)
-
   warnings()
   return(result)
 }
@@ -130,107 +126,6 @@ patch <- function(clueTable) {
 }
 
 
-#' Check gaps in our data set
-#'
-#' @param clueTable
-#'
-#' @return Invisible NULL
-checkDataCoverage <- function(clueTable) {
-  separator <- paste(rep("#", 75), collapse = "")
-  print(glue::glue("\n\n{separator}"))
-  print(glue::glue("{separator}", "  !!! START OF DATA INTEGRITY TEST !!!"))
-  print(glue::glue("{separator}\n\n"))
-
-  ## internal helper function
-  checkTable <- function(table, msg, stop = FALSE) {
-   n <- nrow(table)
-   prefix <- glue::glue("\n\n>>>>>>>> {msg}: {n} ...")
-   if (nrow(table) > 0) {
-     print(glue::glue("{prefix} IS NOT OK!"))
-     print(table)
-     if (stop) stop("Unexpected data state")
-   } else
-     print(glue::glue("{prefix} IS OK!"))
-  }
-
-  ## FDA Orange issue
-  distinctTable <- clueTable %>%
-    select(
-      pert_iname,
-      # moa,
-      final_status,
-      status_source,
-      orange_book
-    ) %>%
-    distinct() %>%
-    rowwise() %>%
-    filter(grepl("FDA Orange", status_source))
-  checkTable(distinctTable, "FDA Orange")
-
-  ## FDA Orange issue V2
-  distinctTable <- clueTable %>%
-    select(
-      pert_iname,
-      final_status,
-      status_source,
-      orange_book
-    ) %>%
-    distinct() %>%
-    rowwise() %>%
-    filter(!is.na(orange_book) && is.na(status_source))
-  checkTable(distinctTable, "FDA.V2 orange_book has value")
-
-  ## FDA Launched check
-  distinctTable <- clueTable %>%
-    select(
-      pert_iname,
-      final_status,
-      status_source,
-      orange_book
-    ) %>%
-    distinct() %>%
-    rowwise() %>%
-    filter(final_status == "Launched" &&
-      is.na(orange_book) && is.na(status_source))
-  checkTable(distinctTable, "FDA Launched check")
-
-  ## PubChem/ChEMBL check
-  distinctTable <- clueTable %>%
-    select(
-      pert_iname,
-      final_status,
-      pubchem_cid,
-      chembl_id,
-      inchi_key,
-      pert_id,
-      ttd_id,
-      drugbank_id,
-      source,
-      status_source
-    ) %>%
-    distinct() %>%
-    rowwise() %>%
-    filter(is.na(pubchem_cid) && is.na(chembl_id))
-  checkTable(distinctTable, "PubChem/ChEMBL check")
-
-  distinctTable <- clueTable %>%
-    select(final_status, status_source) %>%
-    distinct() %>%
-    filter(final_status == "Preclinical" && !is.na(status_source))
-  checkTable(distinctTable, "Preclinical status_source", stop = TRUE)
-
-##  print("Foreced quit")
-##  quit(save = "no")
-
-
-  print(glue::glue("{separator}"))
-  print(glue::glue("{separator}", "  !!! END OF DATA INTEGRITY TEST !!!"))
-  print(glue::glue("{separator}"))
-
-  return(invisible(NULL))
-}
-
-
 #' Cross-checking columns
 #'
 #' @param clueTable Input dataframe.

diff --git a/inst/tinytest/test_uniprot.R b/inst/tinytest/test_uniprot.R
@@ -0,0 +1,33 @@
+##
+## test_uniprot.R
+##
+
+setwd('../..')
+source("R/dataPatch.R")
+
+## arrange
+clueTable <- tibble::as_tibble(list(
+  UNIPROT_KB_ID = c(
+    'P01133'
+  )
+))
+
+## act
+clueTable <- xmlUniProt(clueTable)
+
+## assert
+
+# P01133
+expect_equal(
+  target = "calcium ion binding",
+  current = clueTable$UniProtData[["P01133"]][["molecularFunction"]][["GO:0005509"]]
+)
+expect_equal(
+  target = "extracellular exosome",
+  current = clueTable$UniProtData[["P01133"]][["subCellularLocation"]][["GO:0070062"]]
+)
+expect_equal(
+  target = "positive regulation of MAPK cascade",
+  current = clueTable$UniProtData[["P01133"]][["biologicalProcess"]][["GO:0043410"]]
+)
+# GO:0070062