Merge branch ols4

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rols
 Type: Package
 Title: An R interface to the Ontology Lookup Service
-Version: 2.31.0
+Version: 2.99.0
 Authors@R: c(person(given = "Laurent", family = "Gatto",
                     email = "[email protected]",
                     role = c("aut","cre")),
@@ -13,17 +13,18 @@ Description: The rols package is an interface to the Ontology Lookup
              Service (OLS) to access and query hundred of ontolgies
              directly from R.
 Depends: methods
-Imports: httr, progress, jsonlite, utils, Biobase,
-         BiocGenerics (>= 0.23.1)
+Imports: httr2, jsonlite,
+         utils, Biobase, BiocGenerics (>= 0.23.1)
 Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19),
           testthat, lubridate, DT, rmarkdown,
 biocViews: ImmunoOncology, Software, Annotation, MassSpectrometry, GO
 VignetteBuilder: knitr
 License: GPL-2
 Encoding: UTF-8
-URL: http://lgatto.github.com/rols/
+URL: http://lgatto.github.io/rols/
 BugReports: https://github.com/lgatto/rols/issues
-Collate: AllClasses.R AllGenerics.R utils.R cvparam.R
-         methods-OlsSearch.R methods-Ontologies.R methods-Terms.R
-         methods-Properties.R zzz.R
-RoxygenNote: 6.1.0
+Collate: AllClasses.R AllGenerics.R utils.R
+         Ontologies.R Terms.R
+         cvparam.R OlsSearch.R
+         Properties.R zzz.R
+RoxygenNote: 7.3.0

NAMESPACE

@@ -1,61 +1,61 @@
-import(methods)
-import(utils)
-import(httr)
-import(jsonlite)
-import(progress)
-importFrom(Biobase, validMsg)
-importFrom(BiocGenerics, Ontology)
-importClassesFrom(Biobase, Versioned)
-
-exportClasses(CVParam,
-              Term, Terms,
-              Ontology, Ontologies,
-              OlsSearch,
-              Property, Properties)
-
-S3method(as.data.frame, OlsSearch)
+# Generated by roxygen2: do not edit by hand
 
-exportMethods(show,
-              "[", "[[", lapply,
-              coerce,
-              length,
-              unique,
-              ## Ontology/ies
-              Ontology, Ontologies,
-              olsRoot,
-              olsPrefix,
-              olsDesc,
-              olsTitle,
-              olsStatus,
-              olsNamespace,
-              ## Term/s
-              all.equal,
-              termLabel,
-              termPrefix,
-              termNamespace,
-              termOntology,
-              termDesc,
-              term, terms,
-              termId,
-              ## Property/ies
-              properties)
-
-
-export(charIsCVParam, CVParam,
-       ## Ontology/ies
-       olsVersion,
-       olsLoaded,
-       olsUpdated,
-       ## Term/s
-       isObsolete,
-       isRoot,
-       termSynonym,
-       children, parents,
-       ancestors, descendants,
-       derivesFrom, partOf,
-       as.Term.data.frame,
-       as.Terms.data.frame,
-       ## Search/select
-       OlsSearch,
-       olsSearch,
-       olsRows, "olsRows<-", allRows)
+S3method(as.character,CVParam)
+S3method(as.data.frame,OlsSearch)
+S3method(as.data.frame,Ontologies)
+export("olsRows<-")
+export(CVParam)
+export(OlsSearch)
+export(allRows)
+export(ancestors)
+export(as.Term.data.frame)
+export(as.Terms.data.frame)
+export(charIsCVParam)
+export(children)
+export(cvCharToCVPar)
+export(descendants)
+export(olsRows)
+export(olsSearch)
+export(parents)
+exportMethods("[")
+exportMethods("[[")
+exportMethods(Ontologies)
+exportMethods(Ontology)
+exportMethods(Properties)
+exportMethods(Term)
+exportMethods(Terms)
+exportMethods(isObsolete)
+exportMethods(isRoot)
+exportMethods(lapply)
+exportMethods(length)
+exportMethods(olsConfig)
+exportMethods(olsDesc)
+exportMethods(olsLinks)
+exportMethods(olsLoaded)
+exportMethods(olsNamespace)
+exportMethods(olsPrefix)
+exportMethods(olsStatus)
+exportMethods(olsTitle)
+exportMethods(olsUpdated)
+exportMethods(olsVersion)
+exportMethods(ontologyUrl)
+exportMethods(rep)
+exportMethods(show)
+exportMethods(termDesc)
+exportMethods(termId)
+exportMethods(termLabel)
+exportMethods(termLinks)
+exportMethods(termNamespace)
+exportMethods(termOntology)
+exportMethods(termPrefix)
+exportMethods(termSynonym)
+exportMethods(unique)
+import(httr2)
+import(methods)
+importFrom(Biobase,validMsg)
+importFrom(jsonlite,fromJSON)
+importFrom(utils,URLencode)
+importFrom(utils,head)
+importFrom(utils,packageVersion)
+importFrom(utils,tail)
+importMethodsFrom(BiocGenerics,Ontology)

NEWS.md

@@ -1,3 +1,9 @@
+# rols 2.99
+
+## CHANGES IN VERSION 2.99.0
+
+- Refactoring to use REST API for OLS4.
+
 # rols 2.29
 
 ## CHANGES IN VERSION 2.29.1

R/AllClasses.R

@@ -1,91 +1,3 @@
 setClassUnion("NullOrChar", c("NULL", "character"))
 setClassUnion("NullOrList", c("NULL", "list"))
-
-## a param is [CV label, accession, name|synonym, value]
-.CVParam <- setClass("CVParam",
-                     representation = representation(
-                         label = "character",
-                         accession = "character",
-                         name = "character",
-                         value = "character",
-                         user = "logical"),
-                     contains = "Versioned",
-                     prototype = prototype(
-                         user = FALSE,
-                         new("Versioned", versions=c(CVParam="0.2.0"))),
-                     validity = function(object) {
-                         msg <- validMsg(NULL, NULL)
-                         if (object@user) {
-                             if (!all(c(object@label, object@accession) == ""))
-                                 msg <- "Label and accession must be empty in UserParams."
-                         } else {
-                             x <- c(object@label, object@accession,
-                                    object@name, object@value) == ""
-                             if (!all(x)) {
-                                 ._term <- term(object@label, object@accession)
-                                 ._label <- termLabel(._term)
-                                 ._synonyms <- termSynonym(._term)
-                                 if (!(object@name %in% c(._label, ._synonyms)))
-                                     msg <- paste0("CVParam accession and name/synomyms do not match. Got [",
-                                                   paste(c(._label, ._synonyms), collapse = ", "),
-                                                   "], expected '", object@name, "'.")
-                             }
-                         }
-                         if (is.null(msg)) TRUE else msg
-                     })
-
-
-.Ontology <- setClass("Ontology",
-                      slots = c(loaded = "NullOrChar",
-                                updated = "NullOrChar",
-                                status = "NullOrChar",
-                                message = "NullOrChar",
-                                version = "NullOrChar",
-                                numberOfTerms = "integer",
-                                numberOfProperties = "integer",
-                                numberOfIndividuals = "integer",
-                                config = "list"
-                                ))
-
-.Ontologies <- setClass("Ontologies", slots = c(x = "list"))
-
-.Term <- setClass("Term",
-                  slots = c(iri = "character",
-                            label = "character",
-                            description = "NullOrList",
-                            annotation = "list",
-                            synonym = "NullOrList",
-                            ontology_name = "character",
-                            ontology_prefix = "character",
-                            ontology_iri = "character",
-                            is_obsolete = "logical",
-                            is_defining_ontology = "logical",
-                            has_children = "logical",
-                            is_root = "logical",
-                            short_form = "character",
-                            obo_id = "NullOrChar",
-                            links = "list"))
-
-Terms <- setClass("Terms", slots = c(x = "list"))
-
-.OlsSearch <- setClass("OlsSearch",
-                       slots = c(q = "character",
-                                 ontology = "character",
-                                 type = "character",
-                                 slim = "character",
-                                 fieldList = "character",
-                                 queryFields = "character",
-                                 exact = "logical",
-                                 groupField = "logical",
-                                 obsoletes = "logical",
-                                 local = "character",
-                                 childrenOf = "character",
-                                 rows = "integer",
-                                 start = "integer",
-                                 url = "character",
-                                 numFound = "integer",
-                                 response = "data.frame"))
-
-.Property <- setClass("Property",
-                      contains = "Term")
-Properties <- setClass("Properties", contains = "Terms")
+setClassUnion("NullOrLogical", c("NULL", "logical"))

R/AllGenerics.R

@@ -1,5 +1,6 @@
 setGeneric("Ontologies", function(object) standardGeneric("Ontologies"))
-## setGeneric("Ontology", function(object) standardGeneric("Ontology")) 
+setGeneric("Terms", function(object, ...) standardGeneric("Terms"))
+setGeneric("Term", function(object, ...) standardGeneric("Term"))
 
 setGeneric("olsPrefix", function(object, ...) standardGeneric("olsPrefix"))
 setGeneric("olsDesc", function(object, ...) standardGeneric("olsDesc"))
@@ -10,11 +11,12 @@ setGeneric("olsLoaded", function(object, ...) standardGeneric("olsLoaded"))
 setGeneric("olsUpdated", function(object, ...) standardGeneric("olsUpdated"))
 setGeneric("olsStatus", function(object, ...) standardGeneric("olsStatus"))
 setGeneric("olsNamespace", function(object, ...) standardGeneric("olsNamespace"))
+setGeneric("olsLinks", function(object, ...) standardGeneric("olsLinks"))
+setGeneric("olsConfig", function(object, ...) standardGeneric("olsConfig"))
 
+setGeneric("termLinks", function(object, ...) standardGeneric("termLinks"))
 setGeneric("termLabel", function(object, ...) standardGeneric("termLabel"))
 setGeneric("termPrefix", function(object, ...) standardGeneric("termPrefix"))
-setGeneric("terms", function(x, ...) standardGeneric("terms"))
-setGeneric("term", function(object, id, ...) standardGeneric("term"))
 setGeneric("termId", function(object, ...) standardGeneric("termId"))
 setGeneric("isObsolete", function(object, ...) standardGeneric("isObsolete"))
 setGeneric("isRoot", function(object, ...) standardGeneric("isRoot"))
@@ -23,7 +25,7 @@ setGeneric("termDesc", function(object, ...) standardGeneric("termDesc"))
 setGeneric("termNamespace", function(object, ...) standardGeneric("termNamespace"))
 setGeneric("termOntology", function(object, ...) standardGeneric("termOntology"))
 
-setGeneric("properties", function(object, ...) standardGeneric("properties"))
+setGeneric("Properties", function(object, ...) standardGeneric("Properties"))
 
 ## private
 setGeneric("ontologyUrl", function(object, ...) standardGeneric("ontologyUrl"))