diff BiodbEntry.R @ 1:253d531a0193 draft

planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b

--- a/BiodbEntry.R	Tue Jul 12 12:02:37 2016 -0400
+++ b/BiodbEntry.R	Sat Sep 03 17:02:01 2016 -0400
@@ -20,16 +20,20 @@
 		callSuper(...) # calls super-class initializer with remaining parameters
 	})
 	
-	#############
-	# SET FIELD #
-	#############
+	###################
+	# SET FIELD VALUE #
+	###################
 	
+	BiodbEntry$methods(	setFieldValue = function(field, value) {
+		.self$setField(field, value)
+	})
+
 	BiodbEntry$methods(	setField = function(field, value) {
 
 		class = .self$getFieldClass(field)
 
 		# Check cardinality
-		if (class != 'data.frame' && .self$getFieldCardinality(field) == RBIODB.CARD.ONE && length(value) > 1)
+		if (class != 'data.frame' && .self$getFieldCardinality(field) == BIODB.CARD.ONE && length(value) > 1)
 			stop(paste0('Cannot set more that one value to single value field "', field, '" in BiodEntry.'))
 
 		# Check value class
@@ -45,15 +49,23 @@
 	})
 
 	###################
+	# GET FIELD NAMES #
+	###################
+
+	BiodbEntry$methods(	getFieldNames = function(field) {
+		return(names(.self$.fields))
+	})
+
+	###################
 	# GET FIELD CLASS #
 	###################
-	
+
 	BiodbEntry$methods(	getFieldClass = function(field) {
 
-		if ( ! field %in% RBIODB.FIELDS[['name']])
+		if ( ! field %in% BIODB.FIELDS[['name']])
 			stop(paste0('Unknown field "', field, '" in BiodEntry.'))
 
-		field.class <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'class']
+		field.class <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'class']
 
 		return(field.class)
 	})
@@ -64,21 +76,25 @@
 	
 	BiodbEntry$methods(	getFieldCardinality = function(field) {
 
-		if ( ! field %in% RBIODB.FIELDS[['name']])
+		if ( ! field %in% BIODB.FIELDS[['name']])
 			stop(paste0('Unknown field "', field, '" in BiodEntry.'))
 
-		field.card <- RBIODB.FIELDS[which(field == RBIODB.FIELDS[['name']]), 'cardinality']
+		field.card <- BIODB.FIELDS[which(field == BIODB.FIELDS[['name']]), 'cardinality']
 
 		return(field.card)
 	})
 	
-	#############
-	# GET FIELD #
-	#############
+	###################
+	# GET FIELD VALUE #
+	###################
 	
+	BiodbEntry$methods(	getFieldValue = function(field) {
+		return(.self$getField(field))
+	})
+
 	BiodbEntry$methods(	getField = function(field) {
 
-		if ( ! field %in% RBIODB.FIELDS[['name']])
+		if ( ! field %in% BIODB.FIELDS[['name']])
 			stop(paste0('Unknown field "', field, '" in BiodEntry.'))
 
 		if (field %in% names(.self$.fields))
@@ -97,11 +113,11 @@
 	
 	BiodbEntry$methods(	.compute.field = function(field) {
 
-		if ( ! is.null(.self$.factory) && field %in% names(RBIODB.FIELD.COMPUTING)) {
-			for (db in RBIODB.FIELD.COMPUTING[[field]]) {
+		if ( ! is.null(.self$.factory) && field %in% names(BIODB.FIELD.COMPUTING)) {
+			for (db in BIODB.FIELD.COMPUTING[[field]]) {
 				db.id <- .self$getField(paste0(db, 'id'))
 				if ( ! is.na(db.id)) {
-					db.compound <- .self$.factory$createEntry(db, type = RBIODB.COMPOUND, id = db.id)
+					db.compound <- .self$.factory$createEntry(db, type = BIODB.COMPOUND, id = db.id)
 					if ( ! is.null(db.compound)) {
 						.self$setField(field, db.compound$getField(field))
 						return(TRUE)
@@ -112,6 +128,24 @@
 
 		return(FALSE)
 	})
+	
+	############################
+	# GET FIELDS AS DATA FRAME #
+	############################
+	
+	BiodbEntry$methods(	getFieldsAsDataFrame = function(field) {
+
+		df <- data.frame()
+
+		# Loop on all fields
+		for (f in names(.self$.fields))
+
+			# If field class is a basic type
+			if (.self$getFieldClass(f) %in% c('character', 'logical', 'integer', 'double'))
+				df[1, f] <- .self$getFieldValue(f)
+
+		return(df)
+	})
 
 	###########
 	# FACTORY #