From 7a58210ebb5e2326f92dd9817264e392000b48fe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Mon, 13 Feb 2023 14:24:17 +0100
Subject: [PATCH] tests: Adapt to changes.
---
R/shiny-ui-base.R | 5 -----
inst/testdata/example_db.csv | 5 +++++
tests/testthat/test-api.R | 22 +++----------------
tests/testthat/test-shiny-state.R | 36 -------------------------------
tests/testthat/test-state.R | 8 ++++---
5 files changed, 13 insertions(+), 63 deletions(-)
create mode 100644 inst/testdata/example_db.csv
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 78ca6f2..007489e 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1612,11 +1612,6 @@ mk_shinyscreen_server <- function(projects,init) {
"available" else "unavailable"
})
- output$metfrag_panel = renderUI({
- ctrls = make_metfrag_panel(envopts=init$envopts)
- do.call(tagList,ctrls)
- })
-
output$entry_mf_summ_fname = renderText({
kv = req(rf_get_cindex_kval())
metfrag_gen_entry_fname(kv)
diff --git a/inst/testdata/example_db.csv b/inst/testdata/example_db.csv
new file mode 100644
index 0000000..89126cf
--- /dev/null
+++ b/inst/testdata/example_db.csv
@@ -0,0 +1,5 @@
+"Identifier","FirstBlock","PubMed_Count","Patent_Count","Related_CIDs","Synonym","MolecularFormula","SMILES","InChI","InChIKey","MonoisotopicMass","CompoundName","AnnoTypeCount","AgroChemInfo","BioPathway","DrugMedicInfo","FoodRelated","PharmacoInfo","SafetyInfo","ToxicityInfo","KnownUse","DisorderDisease","Identification"
+"3","INCSWYKICIYAHB","11","280","9964159 23615184 45266758","(2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoic acid","C7H8O4","C1=CC(C(C(=C1)C(=O)O)O)O","InChI=1S/C7H8O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,5-6,8-9H,(H,10,11)","INCSWYKICIYAHB-UHFFFAOYSA-N","156.042259","5,6-dihydroxycyclohexa-1,3-diene-1-carboxylic acid","2","0","2","0","0","2","0","0","0","0","0"
+"4","HXKKHQJGJAFBHI","71","103352","4 111033 439938 446260 4631415 7311736 44150279","1-Aminopropan-2-ol","C3H9NO","CC(CN)O","InChI=1S/C3H9NO/c1-3(5)2-4/h3,5H,2,4H2,1H3","HXKKHQJGJAFBHI-UHFFFAOYSA-N","75.068414","1-aminopropan-2-ol","7","0","3","0","8","2","10","3","5","0","3"
+"5","HIQNVODXENYOFK","3","13","5 25244426","3-Amino-2-oxopropyl phosphate","C3H8NO5P","C(C(=O)COP(=O)(O)O)N","InChI=1S/C3H8NO5P/c4-1-3(5)2-9-10(6,7)8/h1-2,4H2,(H2,6,7,8)","HIQNVODXENYOFK-UHFFFAOYSA-N","169.014009","(3-amino-2-oxopropyl) dihydrogen phosphate","2","0","2","0","0","2","0","0","0","0","0"
+"6","VYZAHLCBVHPDDF","3142","20129","6","1-chloro-2,4-dinitrobenzene","C6H3ClN2O4","C1=CC(=C(C=C1[N+](=O)[O-])[N+](=O)[O-])Cl","InChI=1S/C6H3ClN2O4/c7-5-2-1-4(8(10)11)3-6(5)9(12)13/h1-3H","VYZAHLCBVHPDDF-UHFFFAOYSA-N","201.978134","1-chloro-2,4-dinitrobenzene","9","0","5","3","2","7","11","3","7","1","2"
diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R
index 860e1b8..7f9b16e 100644
--- a/tests/testthat/test-api.R
+++ b/tests/testthat/test-api.R
@@ -9,29 +9,13 @@ test_that("Preparation for app start",{withr::with_tempdir({
dir.create(ddbdir)
mrt = "mrt.fake.jar"
saveRDS("",file=mrt)
- expect_error(prepare_app(dir_before=dbef,
- projects=dproj,
- top_data_dir=ddata,
- metfrag_db_dir=ddbdir,
- metfrag_runtime="absent.jar"),
- class="mf-jar-absent")
-
expect_error(prepare_app(dir_before=dbef,
projects="absent",
- top_data_dir=ddata,
- metfrag_db_dir=ddbdir,
- metfrag_runtime=mrt),
+ top_data_dir=ddata),
class="projects-absent")
expect_error(prepare_app(dir_before=dbef,
projects=dproj,
- top_data_dir="absent",
- metfrag_db_dir=ddbdir,
- metfrag_runtime=mrt),
+ top_data_dir="absent"),
class="top-data-dir-absent")
- expect_error(prepare_app(dir_before=dbef,
- projects=dproj,
- top_data_dir=ddata,
- metfrag_db_dir="absent",
- metfrag_runtime=mrt),
- class="mf-db-dir-absent")
+
})})
diff --git a/tests/testthat/test-shiny-state.R b/tests/testthat/test-shiny-state.R
index 0b57b7c..8b13789 100644
--- a/tests/testthat/test-shiny-state.R
+++ b/tests/testthat/test-shiny-state.R
@@ -1,37 +1 @@
-test_that("Test make_metfrag_panel (local and remote)",{
- withr::with_tempdir({
- mfdb = "demodb.csv"
- mfdbdir = "demodir"
- dir.create(mfdbdir)
- mfjar = "demomf.jar"
- saveRDS("",file.path(mfdbdir,mfdb))
- saveRDS("",mfjar)
- eo = envopts(metfrag_db_dir = mfdbdir,
- metfrag_jar = mfjar)
-
- xx = make_metfrag_panel(eo)
- res = sapply(METFRAG_DATABASE_TYPE,function (p) {grepl(p,xx[[6L]])})
- expect_true(all(res))
- })
-})
-
-test_that("Test make_metfrag_panel (remote)",{
- withr::with_tempdir({
- mfjar = "demomf.jar"
- saveRDS("",mfjar)
- eo = envopts(metfrag_jar = mfjar)
- xx = make_metfrag_panel(eo)
- res = sapply(METFRAG_REMOTE_DATABASE_TYPE,function (p) {grepl(p,xx[[6L]])})
- expect_true(all(res))
-
- res2 = sapply(METFRAG_LOCAL_DATABASE_TYPE,function (p) {grepl(p,xx[[6L]])})
- expect_false(any(res2))
- })
-})
-
-test_that("Test make_metfrage_panel (disabled)",{
- eo = envopts()
- xx = make_metfrag_panel(eo)
- expect_true(length(xx)==1L)
-})
diff --git a/tests/testthat/test-state.R b/tests/testthat/test-state.R
index 51696a2..dc26280 100644
--- a/tests/testthat/test-state.R
+++ b/tests/testthat/test-state.R
@@ -33,9 +33,11 @@ test_that("Test full project creation.",{
dir.create(db_dir)
mf_jar = "bingo.jar"
saveRDS(" ",mf_jar)
- mf_db = file.path(db_dir,"bingo.csv")
- saveRDS(" ",mf_db)
- conf$metfrag$db_file = basename(mf_db)
+ db = data.frame(a=1,b=2)
+ mf_or_db = system.file("testdata","example_db.csv",package="shinyscreen")
+ file.copy(from = mf_or_db,
+ to = db_dir)
+ conf$metfrag$db_file = basename(mf_or_db)
yaml::write_yaml(conf,file.path(ppath,FN_CONF))
eo = envopts(metfrag_db_dir=db_dir,
metfrag_jar=mf_jar)
--
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