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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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")), | ||
|
|
@@ -13,8 +13,8 @@ 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 | ||
|
|
@@ -23,7 +23,8 @@ License: GPL-2 | |
| Encoding: UTF-8 | ||
| 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 | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
|
|
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| 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) | ||
|
|
||
|
|
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| 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) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| }) | ||
|
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|
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| .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")) | ||
|
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| .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")) | ||
|
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| Terms <- setClass("Terms", slots = c(x = "list")) | ||
|
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| .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")) | ||
|
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| .Property <- setClass("Property", | ||
| contains = "Term") | ||
| Properties <- setClass("Properties", contains = "Terms") | ||
| setClassUnion("NullOrLogical", c("NULL", "logical")) |
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