Remove 'artifact' attribute from edges of artifact networks

In artifact networks, artifacts should not be able to create edges,
but authors should. Remove 'artifact' attribute from edges of artifact
networks and append 'author.name' instead. This solves the issue of
duplicate edges between two artifacts that are only differentiable by the
'artifact' attribute.

This fixes #232.

Signed-off-by: Maximilian Löffler <s8maloef@stud.uni-saarland.de>

util-networks.R

@@ -316,7 +316,9 @@ NetworkBuilder = R6::R6Class("NetworkBuilder",
             artifacts.net.data = construct.edge.list.from.key.value.list(
                 artifacts.net.data.raw,
                 network.conf = private$network.conf,
-                directed = FALSE
+                directed = FALSE,
+                respect.temporal.order = TRUE,
+                artifact.edges = TRUE
             )
 
             ## construct network from obtained data
@@ -970,11 +972,14 @@ NetworkBuilder = R6::R6Class("NetworkBuilder",
 #'                               i.e., whether to only add edges from the later event to the previous one.
 #'                               If \code{NA} is passed, the default value is taken.
 #'                               [default: directed]
+#' @param artifact.edges whether the key value data represents edges in an artifact network based
+#'                       on the cochange relation
+#'                       [default: \code{FALSE}]
 #'
 #' @return a list of two data.frames named 'vertices' and 'edges' (compatible with return value
 #'         of \code{igraph::as.data.frame})
 construct.edge.list.from.key.value.list = function(list, network.conf, directed = FALSE,
-                                                   respect.temporal.order = directed) {
+                                        respect.temporal.order = directed, artifact.edges = FALSE) {
     logging::loginfo("Create edges.")
     logging::logdebug("construct.edge.list.from.key.value.list: starting.")
 
@@ -991,7 +996,7 @@ construct.edge.list.from.key.value.list = function(list, network.conf, directed
     keys = names(list)
     keys.number = length(list)
 
-    if (respect.temporal.order) {
+    if (respect.temporal.order || artifact.edges) {
 
         ## for all subsets (sets), connect all items in there with the previous ones
         edge.list.data = parallel::mclapply(list, function(set) {
@@ -1018,9 +1023,21 @@ construct.edge.list.from.key.value.list = function(list, network.conf, directed
                 ## get vertex data
                 item.vertex = item[["data.vertices"]]
 
+                ## if edges in an artifact network contain the \code{artifact} attribute 
+                ## replace it with the \code{author.name} attribute as artifacts cannot cause 
+                ## edges in artifact networks, authors can
+                edge.attributes = network.conf$get.value("edge.attributes")
+                if (artifact.edges) {
+                    artifact.index = match("artifact", edge.attributes, nomatch = NA)
+                    if (!is.na(artifact.index)) {
+                        edge.attributes = edge.attributes[-artifact.index]
+                        edge.attributes = c(edge.attributes, c("author.name"))
+                    }
+                }
+
                 ## get edge attributes
-                cols.which = network.conf$get.value("edge.attributes") %in% colnames(item)
-                item.edge.attrs = item[ , network.conf$get.value("edge.attributes")[cols.which], drop = FALSE]
+                cols.which = edge.attributes %in% colnames(item)
+                item.edge.attrs = item[ , edge.attributes[cols.which], drop = FALSE]
 
                 ## construct edges
                 combinations = expand.grid(item.vertex, vertices.processed.set, stringsAsFactors = FALSE)
@@ -1367,9 +1384,7 @@ create.empty.network = function(directed = TRUE, add.attributes = FALSE) {
             date = c("POSIXct", "POSIXt"), artifact.type = "character", weight = "numeric",
             type = "character", relation = "character"
         )
-        mandatory.edge.attributes = names(mandatory.edge.attributes.classes)
         mandatory.vertex.attributes.classes = list(name = "character", kind = "character", type = "character")
-        mandatory.vertex.attributes = names(mandatory.vertex.attributes.classes)
 
         net = add.attributes.to.network(net, "vertex", mandatory.vertex.attributes.classes)
         net = add.attributes.to.network(net, "edge", mandatory.edge.attributes.classes)