updated ontology (#38)

- stato now deprecated in favour of ontology
- ontology slots added for all struct objects
- ontology term and list objects  added
- can use the rols package and ols api
- updated autocomplete for all objects

Author: grlloyd

.Rbuildignore

@@ -10,3 +10,4 @@ LICENSE
 ^\README.md
 .travis.yml
 README.rst
+^\.github$

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.5.0
+Version: 1.5.1
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
@@ -26,9 +26,9 @@ Description: Defines and includes a set of class-based templates for developing
     using the class-based templates.
 License: GPL-3
 Encoding: UTF-8
-LazyData: true
 Collate:
     'generics.R'
+    'ontology_term_class.R'
     'struct_class.R'
     'parameter_class.R'
     'chart_class.R'
@@ -61,7 +61,7 @@ Suggests:
  ggplot2,
  magick
 VignetteBuilder: knitr
-Imports: methods, ontologyIndex,
+Imports: methods,ontologyIndex,
     datasets, graphics, stats, utils, knitr, 
-    SummarizedExperiment, S4Vectors
+    SummarizedExperiment, S4Vectors, rols
 biocViews: WorkflowStep

NAMESPACE

@@ -1,5 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,chart)
+S3method(.DollarNames,model)
+S3method(.DollarNames,optimiser)
+S3method(.DollarNames,preprocess)
+S3method(.DollarNames,resampler)
+S3method(.DollarNames,struct_class)
 export("output_list<-")
 export("output_value<-")
 export("param_list<-")
@@ -37,6 +43,9 @@ export(model_seq)
 export(model_train)
 export(models)
 export(new_struct)
+export(ontology)
+export(ontology_list)
+export(ontology_term)
 export(optimiser)
 export(output_ids)
 export(output_list)
@@ -87,6 +96,7 @@ exportMethods("predicted_name<-")
 exportMethods("result_name<-")
 exportMethods("seq_in<-")
 exportMethods("value<-")
+exportMethods(.DollarNames)
 exportMethods(as.DatasetExperiment)
 exportMethods(as.SummarizedExperiment)
 exportMethods(as.code)
@@ -106,6 +116,7 @@ exportMethods(model_predict)
 exportMethods(model_reverse)
 exportMethods(model_train)
 exportMethods(models)
+exportMethods(ontology)
 exportMethods(output_ids)
 exportMethods(output_list)
 exportMethods(output_name)

R/DatasetExperiment_class.R

@@ -226,3 +226,4 @@ setMethod(f = "export_xlsx",
     openxlsx::write.xlsx(OUT,file = outfile,rowNames = TRUE,colNames = TRUE)
   }
 )
+

R/chart_class.R

@@ -40,7 +40,7 @@ chart = function(...) {
 setMethod(f = "chart_plot",
     signature = "chart",
     definition = function(obj,dobj) {
-        warning(paste0('no chart defined for "',class(dobj),'"'))
+        warning('no chart defined for "',class(dobj),'"')
         return(obj)
     }
 )
@@ -52,3 +52,15 @@ setMethod(f = "show",
         callNextMethod()
     }
 )
+
+# autocompletion, return sample_meta column names
+#' @export
+#' @rdname autocompletion
+#' @method .DollarNames chart
+.DollarNames.chart <- function(x, pattern = "") {
+    .DollarNames.struct_class(x,pattern)
+}
+
+#' @export 
+#' @rdname autocompletion
+setMethod('.DollarNames','chart',.DollarNames.chart)

R/entity_class.R

@@ -14,6 +14,7 @@
 #' @param obj An entity object
 #' @param max_length Maximum length of value vector (default 1)
 #' @param value The value of the parameter/outputs
+#' @param ... additional inputs to the struct_class object
 #' @include generics.R struct_class.R
 #' @return An entity object
 #' @examples
@@ -29,8 +30,13 @@
 #' value(E)
 #' value(E) = 10
 #' @rdname entity
-entity = function(name, description=character(0), type='character', 
-    value=NULL,max_length=Inf) {
+entity = function(
+    name, 
+    description=character(0), 
+    type='character',
+    value=NULL,
+    max_length=Inf,
+    ...) {
 
     value=check_init_val(value,type)
 
@@ -40,7 +46,8 @@ entity = function(name, description=character(0), type='character',
         description=description,
         type=type,
         value=value,
-        max_length=max_length
+        max_length=max_length,
+        ...
     )
     return(out)
 }
@@ -54,7 +61,8 @@ entity = function(name, description=character(0), type='character',
         description = 'no description provided',
         value = character(0),
         type = 'character',
-        max_length = Inf
+        max_length = Inf,
+        ontology=character()
     ),
     validity = function(object) {
         check_length = length(value(object)) <= max_length(object)

R/enum_class.R

@@ -28,7 +28,7 @@
 #' @inheritParams entity
 #' @rdname enum
 enum = function(name, description=character(0), type='character', 
-    value=character(0),max_length=1,allowed) {
+    value=character(0),max_length=1,allowed,...) {
 
     # new object
     out = .enum(
@@ -37,7 +37,8 @@ enum = function(name, description=character(0), type='character',
         type=type,
         value=value,
         max_length=max_length,
-        allowed=allowed
+        allowed=allowed,
+        ...
     )
     return(out)
 }
@@ -72,7 +73,7 @@ setMethod(f = "value<-",
         if (value %in% obj@allowed) {
             obj@value = value
         } else {
-            stop(paste0(value,' is not a valid choice for this enum.'))
+            stop(value,' is not a valid choice for this enum.')
         }
         return(obj)
     }

R/generics.R

@@ -1,3 +1,4 @@
+
 #####################################
 ###### parameter class generics #####
 #####################################
@@ -632,8 +633,8 @@ setGeneric("as_data_frame",function(M,...)standardGeneric("as_data_frame"))
 
 #' Citations for an object
 #' 
-#' All \code{struct} objects have a "citations" slot, which is a character array of
-#' references relevant to the object. The \code{citations} method gathers
+#' All \code{struct} objects have a "citations" slot, which is a list of
+#' references in bibtex format. The \code{citations} method gathers
 #' citations from an object and all \code{struct} objects that it inherits to generate
 #' a complete list.
 #' @param obj a struct object
@@ -661,3 +662,18 @@ setGeneric("citations",function(obj)standardGeneric("citations"))
 #' @export
 setGeneric("libraries",function(obj)standardGeneric("libraries"))
 
+#' Ontology for an object
+#' 
+#' All \code{struct} objects have an "ontology" slot, which is a list of
+#' ontology items for the object. The \code{ontology} method gathers
+#' ontology items from an object and all \code{struct} objects that it inherits to generate
+#' a complete list.
+#' @param obj a struct object
+#' @param cache a named list of ontology_terms for offline use. Terms from the cache are search 
+#' based on the name of the list items matching the ontology id. If cache=NULL then the OLS API is used to lookup terms.
+#' @examples 
+#' M = example_model()
+#' ontology(M,cache=NULL)
+#' @rdname ontology
+#' @export
+setGeneric("ontology",function(obj,cache=NULL)standardGeneric("ontology"))

R/iterator_class.R

@@ -276,5 +276,15 @@ setMethod(f = 'as.code',
 
 
 
+# autocompletion, return sample_meta column names
+#' @export
+#' @method .DollarNames chart
+#' @rdname autocompletion
+.DollarNames.iterator<- function(x, pattern = "") {
+  .DollarNames.struct_class(x,pattern)
+}
 
+#' @export 
+#' @rdname autocompletion
+setMethod('.DollarNames','iterator',.DollarNames.iterator)
 

R/metric_class.R

@@ -110,3 +110,15 @@ setMethod(f = "show",
         cat('\n')
     }
 )
+
+# autocompletion, return sample_meta column names
+#' @export
+#' @rdname autocompletion
+#' @method .DollarNames chart
+.DollarNames.metric<- function(x, pattern = "") {
+    .DollarNames.struct_class(x,pattern)
+}
+
+#' @export 
+#' @rdname autocompletion
+setMethod('.DollarNames','metric',.DollarNames.metric)