R/Init_methods.R

In eugeniaeueu/Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

#' @importFrom utils download.file
#' @importFrom rJava .jinit
initJavaLibs <- function(libLoc, mem = "12G") {
    # Check if library directory is missing
    
    # Starting the java engine
    .jinit(force.init = TRUE)
    if (missing(libLoc)) {
        libLoc = system.file("extdata", "java", package = "OnassisJavaLibs")
    }
    
    path = Sys.glob(paste0(libLoc, "/*.jar"))
    available_local_files <- list.files(libLoc, full.names = FALSE, pattern = "\\.jar$")
    
    # Check if all the files are there
    if (!"conceptmapper-0.0.1-SNAPSHOT-jar-with-dependencies.jar" %in% available_local_files) 
        stop("Conceptmapper jar not available")
    
    if (!"similarity-0.0.1-SNAPSHOT-jar-with-dependencies.jar" %in% available_local_files) 
        stop("Similarity jar not available")
    
    
    if (length(path) > 0) {
        sapply(path, function(path_entry) rJava::.jaddClassPath(path_entry))
    }
    
    rJava::.jaddClassPath(dirname(path))
}




# Init method that is called when a new CMdictionary is created
setMethod("initialize", "CMdictionary", function(.Object) {
    .Object@dictInfo = list("Empty dictionary", "NA", "NA", "0")
    names(.Object@dictInfo) <- c("Dictionary_type", "Dictionary_source", "Synonym_type", 
        "taxid")
    .Object@dict_location = tempdir()
    .Object@dictRef = .jnull("java/io/File")
    .Object
})






# This method initializes an empty CMoptions object
setMethod("initialize", "CMoptions", function(.Object) {
    .Object
})




setMethod("initialize", "EntityFinder", function(.Object) {
    
    # Creating a conceptmapper type system
    type_system_array_list <- .jnew("java/util/ArrayList")
    
    ccp_nlp_type_system <- .jfield("edu/ucdenver/ccp/nlp/uima/util/TypeSystemUtil", 
        name = "CCP_TYPE_SYSTEM")
    
    sentence_detector_type_system_str <- "org.cleartk.token.type.Sentence"
    
    conceptmapper_type_system <- "edu.ucdenver.ccp.nlp.wrapper.conceptmapper.TypeSystem"
    
    dictTerm <- "analysis_engine.primitive.DictTerm"
    
    tokenizer <- "org.apache.uima.conceptMapper.support.tokenizer.TokenAnnotation"
    
    vector_of_ts <- c(ccp_nlp_type_system, sentence_detector_type_system_str, conceptmapper_type_system, 
        dictTerm, tokenizer)
    
    
    type_system_description <- J("org/uimafit/factory/TypeSystemDescriptionFactory")$createTypeSystemDescription(vector_of_ts)
    
    .Object@typeSystemRef <- type_system_description
    return(.Object)
})






setMethod("initialize", "Similarity", function(.Object) {
    .Object@similarityInstance <- .jnew("iit/comp/epigen/nlp/similarity/Similarity")
    .Object@pairwiseConfig = NA_character_
    .Object@icConfig = NA_character_
    .Object@groupConfig = NA_character_
    .Object
})