R/usedListEntry.R

In Sage-Bionetworks/rSynapseClient: Synapse R Client from Sage Bionetworks

#
# Methods for creating a UsedEntity from an Entity, a URL or a list having an Entity with a boolean 'wasExecuted'
# The Entity may either be a SynapseEntity object, an entity ID, 
# or a "reference" (of the form list(targetId="syn123", targetVersionNumber=1) )
#
setMethod(
		f="usedListEntry",
		signature = signature("Entity"),
		definition = function(listEntry, ...) {
			otherParams<-list(...)
			if (is.null(otherParams$wasExecuted)) {
				wasExecuted<-FALSE
			} else {
				wasExecuted<-otherParams$wasExecuted
			}
			list(reference=getReference(listEntry), wasExecuted=wasExecuted, concreteType="org.sagebionetworks.repo.model.provenance.UsedEntity")
		}
)

setMethod(
		f="usedListEntry",
		signature = signature("character"),
		definition = function(listEntry, ...) {
			otherParams<-list(...)
			if (is.null(otherParams$wasExecuted)) {
				wasExecuted<-FALSE
			} else {
				wasExecuted<-otherParams$wasExecuted
			}
			if (isSynapseId(listEntry)) {
				list(reference=getReference(listEntry), wasExecuted=wasExecuted, concreteType="org.sagebionetworks.repo.model.provenance.UsedEntity")
			} else {
				# must be a URL
				list(url=listEntry, name=listEntry, wasExecuted=wasExecuted, concreteType="org.sagebionetworks.repo.model.provenance.UsedURL")
			}
		}
)

setMethod(
		f="usedListEntry",
		signature = signature("list"),
		definition = function(listEntry, ...) {
			if (!is.null(listEntry$reference)) {
				# the list is itself a UsedEntity
				if (is.null(listEntry$wasExecuted)) {
					otherParams<-list(...)
					if (is.null(otherParams$wasExecuted)) {
						listEntry$wasExecuted<-FALSE
					} else {
						listEntry$wasExecuted<-otherParams$wasExecuted
					}
				}
				if (is.null(listEntry$concreteType)) listEntry$concreteType<-"org.sagebionetworks.repo.model.provenance.UsedEntity"
				listEntry
			} else if (!is.null(listEntry$url)) {
				# the list is itself a UsedURL
				if (is.null(listEntry$wasExecuted)) listEntry$wasExecuted<-FALSE
				if (is.null(listEntry$concreteType)) listEntry$concreteType<-"org.sagebionetworks.repo.model.provenance.UsedURL"
				if (is.null(listEntry$name)) listEntry$name<-listEntry$url
				listEntry
			} else if (!is.null(listEntry$targetId)) {
				# then the arg is itself a reference
				otherParams<-list(...)
				if (is.null(otherParams$wasExecuted)) {
					wasExecuted<-FALSE
				} else {
					wasExecuted<-otherParams$wasExecuted
				}
				list(reference=listEntry, wasExecuted=wasExecuted, concreteType="org.sagebionetworks.repo.model.provenance.UsedEntity")
			} else if (!is.null(listEntry$entity)) {
				# get the reference and the 'executed' 
				usedEntity<-listEntry$entity
				executed<-listEntry$wasExecuted
				if (is.null(executed)) executed<-FALSE
				list(reference=getReference(usedEntity), wasExecuted=executed, concreteType="org.sagebionetworks.repo.model.provenance.UsedEntity")
			} else {
				stop ("Entity, ID or URL required.")
			}
		}
)