fix broken tests due to changes in rols

grlloyd · grlloyd · commit 396e9f8ab9aa · 2024-02-15T09:41:35.000Z
- ols apir was updated to use ols4, which led to breaking changes in the rols package
diff --git a/R/ontology_term_class.R b/R/ontology_term_class.R
@@ -12,7 +12,7 @@
 #' @param description (character) The description of the term
 #' @param iri (character) The Internationalized Resource Identifier for the term
 #' @param rols (logical) TRUE or FALSE to query the Ontology Lookup Service for
-#' missing label, description or iri if not provided as input. 
+#' missing label, description or iri if not provided as input.
 #' Default rols = TRUE
 #' @include generics.R
 #' @examples
@@ -28,28 +28,28 @@ ontology_term = function(
     iri=character(),
     rols=TRUE
 ) {
-    
+
     # ensure we have a colon separator
     id=gsub('[ :_-]',id,replacement = ':',perl=TRUE)
-    
+
     if (length(ontology)==0){
         # split the id and use that as basis for ontology
         ontology=regmatches(id,regexpr('^[^: _-]+[^: _-]',id))
         ontology=tolower(ontology)
     }
-    
+
     if (length(label)==0 | length(description)==0 | length(iri)==0 | length(ontology)==0) {
-        
+
             # do rols query
             db=rols::Ontology(ontology)
-            tm=rols::term(db,id)
-            
+            tm=rols::Term(db,id)
+
             label=rols::termLabel(tm)
             description=rols::termDesc(tm)
             iri=tm@iri
-        
+
     }
-    
+
     # new object
     out = .ontology_term(
         id=id,
@@ -72,24 +72,24 @@ ontology_term = function(
 )
 
 .ontology_slot = function(x,name) {
-    
+
     if (!(name %in% slotNames(x))) {
         stop('"',name,'" is not a valid slot name for ',
-            class(x)[1],'  objects.')    
+            class(x)[1],'  objects.')
     }
-    
+
     return(slot(x,name))
-    
+
 }
 
 #' Get/set ontology term slots
-#' 
-#' Dollar syntax can be used to as a shortcut for getting 
+#'
+#' Dollar syntax can be used to as a shortcut for getting
 #' values for ontology_term objects.
 #' @return Slot value
 #' @param x An ontology_term object
 #' @param name The name of the slot to access
-#' @examples 
+#' @examples
 #' \dontrun{
 #' OT = ontology_term(ontology='stato',id='STATO:0000555')
 #' }
@@ -104,7 +104,7 @@ setMethod(f = "$",
 setMethod(f = 'show',
     signature = c('ontology_term'),
     definition = function(object) {
-        
+
         # padding for long descriptions and names
         pad = '\n               '
         desc=paste0(strwrap(object$description,width=95,exdent = 2),collapse=pad)
@@ -114,16 +114,16 @@ setMethod(f = 'show',
         cat('label:         ',label,'\n',sep='')
         cat('description:   ',desc,'\n',sep='')
         cat('iri:           ',object$iri,'\n',sep='')
-        
+
     }
 )
 
 
 setAs("ontology_term", "data.frame",
     function(from)
         data.frame(
-            id=from@id, 
-            label=from@label, 
+            id=from@id,
+            label=from@label,
             description=from@description,
             ontology=from@ontology,
             iri=from@iri
@@ -151,32 +151,32 @@ setAs("ontology_term", "data.frame",
 #' }
 #' @rdname ontology
 ontology_list = function(terms=list()) {
-    
+
     if (is.null(terms) | length(terms)==0) {
         # empty list
         terms=list()
     }
-    
+
     if (is(terms,'character')){
         # try and convert to terms
         terms=lapply(terms,function(x){
             ontology_term(id=x)
         })
     }
-    
+
     # if ontology_item is provided convert to a list
     if (is(terms,'ontology_term')){
         terms=list(terms)
     }
-    
+
     # check all terms are ontology_item
     if (length(terms)>0) {
         ok=lapply(terms,is,class='ontology_term')
         if (!(all(unlist(ok)))){
             stop('all ontologies must be in "ontology_term" format')
         }
     }
-    
+
     # new object
     out = .ontology_list(
         terms = terms)
@@ -191,13 +191,13 @@ ontology_list = function(terms=list()) {
 )
 
 #' Get/set ontology_list slots
-#' 
-#' Dollar syntax can be used to as a shortcut for getting 
+#'
+#' Dollar syntax can be used to as a shortcut for getting
 #' values for ontology_list objects.
 #' @return Slot value
 #' @param x An ontology_term object
 #' @param name The name of the slot to access
-#' @examples 
+#' @examples
 #' \dontrun{
 #' OL = ontology_list('STATO:0000555')
 #' OL$terms
@@ -271,7 +271,7 @@ setAs("ontology_list", "data.frame",
 )
 
 #' catenate ontology_lists
-#' 
+#'
 #' ontology_lists can be catenated with other ontology lists or with ontology_items.
 #' @param x an ontology_list()
 #' @param ... any number of ontology_list() or ontology_item() objects to catenate
@@ -282,15 +282,15 @@ setMethod(f = "c",
         y=list(...)
         check=all(unlist(lapply(y,is,class2='ontology_list')))
         if (!check) {stop('can only combine ontology_list objects')}
-        
+
         x=x@terms
         y=lapply(y,function(x){
             return(x@terms)
         })
-        
+
         terms=c(x,unlist(y))
         out=ontology_list(terms)
-        
+
         return(out)
     }
-)
+)
diff --git a/tests/testthat/test-base.R b/tests/testthat/test-base.R
@@ -2,7 +2,7 @@
 test_that('struct objects can be created and modified',{
     # a test object
     test_object=struct_class(
-        name = 'test_name', 
+        name = 'test_name',
         description=c(
             'A'='test_desc_A',
             'B'='test_desc_B'),
@@ -15,14 +15,14 @@ test_that('struct objects can be created and modified',{
             pages = '122-128',
             author = as.person("Nestor F. Perez and Joan Ferre and Ricard Boque"),
             title = paste0('Calculation of the reliability of ',
-                'classification in discriminant partial least-squares ',
-                'binary classification'),
+                           'classification in discriminant partial least-squares ',
+                           'binary classification'),
             journal = "Chemometrics and Intelligent Laboratory Systems"
         ),
         ontology='STATO:0000572'
-        
-        )
-    
+
+    )
+
     # name
     expect_equal({test_object$name},'test_name') # get
     expect_equal({test_object$name='cabbage';test_object$name},'cabbage') # set
@@ -37,26 +37,30 @@ test_that('struct objects can be created and modified',{
     expect_equal({test_object$description='cabbage';test_object$description},'cabbage') #set
     # show
     expect_output(show(test_object),'A "struct_class" object')
-    
+
     expect_error({
-        test_object=struct_class(name = 'test_name', description='test_desc','type' = 'test_type',
-            citations= list(bibentry(
-                bibtype ='Article',
-                year = 2009,
-                volume = 95,
-                number = 2,
-                pages = '122-128',
-                author = as.person("Nestor F. Perez and Joan Ferre and Ricard Boque"),
-                title = paste0('Calculation of the reliability of ',
-                    'classification in discriminant partial least-squares ',
-                    'binary classification'),
-                journal = "Chemometrics and Intelligent Laboratory Systems"
-            ),
+        test_object=struct_class(
+            name = 'test_name',
+            description='test_desc',
+            type = 'test_type',
+            citations= list(
+                bibentry(
+                    bibtype ='Article',
+                    year = 2009,
+                    volume = 95,
+                    number = 2,
+                    pages = '122-128',
+                    author = as.person("Nestor F. Perez and Joan Ferre and Ricard Boque"),
+                    title = paste0('Calculation of the reliability of ',
+                                   'classification in discriminant partial least-squares ',
+                                   'binary classification'),
+                    journal = "Chemometrics and Intelligent Laboratory Systems"
+                ),
                 'cake'
-                
+
             ))
     })
-    
+
     cit=citations(test_object)
     expect_true(length(cit)==2)
     lib=libraries(test_object)
@@ -69,12 +73,12 @@ test_that('struct objects can be created and modified',{
             description = 'test_ontology',
             iri = 'test_ontology',
             rols=FALSE
-            )
         )
     )
+    )
     expect_true(length(ont)==1)
-    
-    
+
+
 })
 
 # test metric object
diff --git a/tests/testthat/test-ontology.R b/tests/testthat/test-ontology.R
@@ -8,7 +8,7 @@ test_that('ontology works as expected',{
     O=ontology_list('STATO:0000555')
     expect_true(is(O,'ontology_list'))
     expect_true(O[1]$id=='STATO:0000555')
-    
+
     # term to list
     O=ontology_list(ontology_term('STATO:0000555',rols=FALSE))
     expect_true(is(O,'ontology_list'))
@@ -22,36 +22,36 @@ test_that('ontology works as expected',{
     )
     expect_true(O[1]$id=='STATO:0000555')
     expect_true(O[2]$id=='STATO:0000555')
-    
+
     # assignment
     O[2]=ontology_term('STATO:0000555',rols=FALSE)
     expect_true(O[2]$id=='STATO:0000555')
-    
+
     # length
     expect_equal(length(O),2)
-    
+
     # ontology list to data.frame
     df=as(O,'data.frame')
     expect_equal(nrow(df),2)
     expect_equal(ncol(df),5)
     expect_equal(df[1,1],'STATO:0000555')
-    
+
     # catenate several ontology_lists
     O=c(O,O)
     expect_equal(length(O),4)
     expect_true(is(O,'ontology_list'))
-    
+
     # ontology method
     M=example_model(ontology='STATO:0000555')
     expect_equal(M$ontology,'STATO:0000555')
-    
+
     expect_error(O$cake)
-    
+
     expect_output(show(O[1]),"STATO:0000555",regexp = 'STATO:0000555')
 
     O=ontology_list()
     expect_equal(length(O),0)
-    
+
     expect_error(c(O,struct_class()))
     expect_error({O[1] = struct_class()})
     expect_error(ontology_list(terms=list(O,struct_class())))
