tests: Adapt to changes.

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)

inst/testdata/example_db.csv

+"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"

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")
+
 })})

tests/testthat/test-shiny-state.R

-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)
-})

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)