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util-networks.R
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## This file is part of coronet, which is free software: you
## can redistribute it and/or modify it under the terms of the GNU General
## Public License as published by the Free Software Foundation, version 2.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License along
## with this program; if not, write to the Free Software Foundation, Inc.,
## 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
##
## Copyright 2016-2019 by Claus Hunsen <[email protected]>
## Copyright 2017 by Raphael Nömmer <[email protected]>
## Copyright 2017-2018 by Christian Hechtl <[email protected]>
## Copyright 2017-2019 by Thomas Bock <[email protected]>
## Copyright 2018 by Barbara Eckl <[email protected]>
## Copyright 2018-2019 by Jakob Kronawitter <[email protected]>
## All Rights Reserved.
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Libraries ---------------------------------------------------------------
requireNamespace("R6") # for R6 classes
requireNamespace("logging") # for logging
requireNamespace("parallel") # for parallel computation
requireNamespace("plyr") # for dlply function
requireNamespace("igraph") # networks
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Vertex and edge types ---------------------------------------------------
## vertex types
TYPE.AUTHOR = "Author"
TYPE.ARTIFACT = "Artifact"
## edge types
TYPE.EDGES.INTRA = "Unipartite"
TYPE.EDGES.INTER = "Bipartite"
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Edge-attribute handling during simplification ---------------------------
## Edge-attribute contraction: configure handling of attributes by name
EDGE.ATTR.HANDLING = list(
## network-analytic data
weight = "sum",
type = "first",
relation = "first",
## commit data
changed.files = "sum",
added.lines = "sum",
deleted.lines = "sum",
diff.size = "sum",
artifact.diff.size = "sum",
## everything else
"concat"
)
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Constants ---------------------------------------------------------------
## mapping of relation to data source
RELATION.TO.DATASOURCE = list(
"cochange" = "commits",
"callgraph" = "commits",
"mail" = "mails",
"issue" = "issues"
)
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## NetworkBuilder ----------------------------------------------------------
#' The class \code{NetworkBuilder} provides convenient network construction in a
#' lazy fashion.
#'
#' To configure an object of this network-construction class, a configuration
#' object of class \code{NetworkConf} and a data-carrying object of class
#' \code{ProjectData} must be passed to the initialization function.
#'
#' The following types of networks can be constructed:
#' - author networks,
#' - artifact networks,
#' - bipartite networks, and
#' - multi networks (a combination of all other types of networks).
#'
#' @seealso NetworkConf
#' @seealso ProjectData
NetworkBuilder = R6::R6Class("NetworkBuilder",
## * private -----------------------------------------------------------
private = list(
## * * data and configuration --------------------------------------
proj.data = NULL,
proj.data.original = NULL,
network.conf = NULL,
## * * network caching ---------------------------------------------
authors.network.mail = NULL, # igraph
authors.network.cochange = NULL, # igraph
authors.network.issue = NULL, #igraph
artifacts.network.cochange = NULL, # igraph
artifacts.network.callgraph = NULL, # igraph
artifacts.network.mail = NULL, # igraph
artifacts.network.issue = NULL, # igraph
## * * relation-to-vertex-kind mapping -----------------------------
#' Determine which vertex kind should be chose for the vertex depending on the relation
#' between the vertices.
#'
#' @param relation the given relation
#'
#' @return the vertex kind to be used
get.vertex.kind.for.relation = function(relation) {
vertex.kind = switch(relation,
cochange = private$proj.data$get.project.conf.entry("artifact.codeface"),
callgraph = private$proj.data$get.project.conf.entry("artifact.codeface"),
mail = "MailThread",
issue = "Issue"
)
return(vertex.kind)
},
## * * data cutting ------------------------------------------------
#' Cut the data sources of the data object to the same date ranges.
cut.data.to.same.timestamps = function() {
cut.data = private$proj.data$get.data.cut.to.same.date(data.sources = private$get.data.sources())
private$proj.data = cut.data
},
#' Determine which data sources should be cut depending on the artifact and author relation.
#'
#' @return the data sources to be cut
get.data.sources = function() {
author.relation = private$network.conf$get.value("author.relation")
artifact.relation = private$network.conf$get.value("artifact.relation")
data.sources = unique(c(RELATION.TO.DATASOURCE[[author.relation]],
RELATION.TO.DATASOURCE[[artifact.relation]]))
return(data.sources)
},
## * * author networks ---------------------------------------------
#' Get the co-change-based author relation as network.
#' If it does not already exist build it first.
#'
#' @return the author network with cochange relation
get.author.network.cochange = function() {
logging::logdebug("get.author.network.cochange: starting.")
## do not compute anything more than once
if (!is.null(private$authors.network.cochange)) {
logging::logdebug("get.author.network.cochange: finished. (already existing)")
return(private$authors.network.cochange)
}
## Get a list of all artifacts extracted from the commit data. Each artifact in this group is again a list
## of all authors that were involved in making changes to this artifact. In the following two steps, some of
## the artifacts are filtered from this list, which removes all information (including author information)
## about these artifacts. Since we only want to lose the edge information and not the information about
## authors, they will explicitly be added in a later step.
author.groups = private$proj.data$group.authors.by.data.column("commits", "artifact")
## 1) if configured in the 'NetworkConf, remove the base artifact
if (!private$network.conf$get.value("edges.for.base.artifacts")) {
author.groups = author.groups[!(names(author.groups) %in% BASE.ARTIFACTS)]
}
## 2) in any case, remove the untracked files
author.groups = author.groups[names(author.groups) != UNTRACKED.FILE.EMPTY.ARTIFACT]
## construct edge list based on artifact2author data
author.net.data = construct.edge.list.from.key.value.list(
author.groups,
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
respect.temporal.order = private$network.conf$get.value("author.respect.temporal.order")
)
## Add author vertices back into the graph. Previously, commit information on untracked files
## ('UNTRACKED.FILE') and, if configured, the base artifact ('BASE.ARTIFACTS') has been removed and, hence,
## also corresponding author information. Re-add author vertices back to the network now by accessing the
## complete author list:
## 1) get all authors on commits
authors = private$proj.data$get.authors.by.data.source(data.source = "commits")
## 2) only select author names
authors = authors["author.name"]
## 3) rename single column to "name" to correct mapping to vertex attribute "name"
colnames(authors) = "name"
## 4) set author list as vertices
author.net.data[["vertices"]] = authors
## construct network from obtained data
author.net = construct.network.from.edge.list(
author.net.data[["vertices"]],
author.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("commits")
)
## store network
private$authors.network.cochange = author.net
logging::logdebug("get.author.network.cochange: finished.")
return(author.net)
},
#' Get the thread-based author relation as network.
#' If it does not already exist build it first.
#'
#' @return the author network with mail relation
get.author.network.mail = function() {
logging::logdebug("get.author.network.mail: starting.")
## do not compute anything more than once
if (!is.null(private$authors.network.mail)) {
logging::logdebug("get.author.network.mail: finished. (already existing)")
return(private$authors.network.mail)
}
## construct edge list based on thread2author data
author.net.data = construct.edge.list.from.key.value.list(
private$proj.data$group.authors.by.data.column("mails", "thread"),
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
respect.temporal.order = private$network.conf$get.value("author.respect.temporal.order")
)
## construct network from obtained data
author.net = construct.network.from.edge.list(
author.net.data[["vertices"]],
author.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("mails")
)
## store network
private$authors.network.mail = author.net
logging::logdebug("get.author.network.mail: finished.")
return(author.net)
},
##get the issue based author relation as network
get.author.network.issue = function() {
logging::logdebug("get.author.network.issue: starting.")
if (!is.null(private$authors.network.issue)) {
logging::logdebug("get.author.network.issue: finished. (already existing)")
return(private$authors.network.issue)
}
## construct edge list based on issue2author data
author.net.data = construct.edge.list.from.key.value.list(
private$proj.data$group.authors.by.data.column("issues", "issue.id"),
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
respect.temporal.order = private$network.conf$get.value("author.respect.temporal.order")
)
## construct network from obtained data
author.net = construct.network.from.edge.list(
author.net.data[["vertices"]],
author.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("issues")
)
private$authors.network.issue = author.net
logging::logdebug("get.author.network.issue: finished.")
return(author.net)
},
## * * artifact networks -------------------------------------------
#' Get the co-change-based artifact network,
#' If it does not already exist build it first.
#'
#' @return the artifact network with cochange realtion
get.artifact.network.cochange = function() {
logging::logdebug("get.artifact.network.cochange: starting.")
## do not compute anything more than once
if (!is.null(private$artifacts.network.cochange)) {
logging::logdebug("get.artifact.network.cochange: finished. (already existing)")
return(private$artifacts.network.cochange)
}
## construct edge list based on commit--artifact data
artifacts.net.data.raw = private$proj.data$group.artifacts.by.data.column("commits", "hash")
artifacts.net.data = construct.edge.list.from.key.value.list(
artifacts.net.data.raw,
network.conf = private$network.conf,
directed = FALSE
)
## construct network from obtained data
artifacts.net = construct.network.from.edge.list(
artifacts.net.data[["vertices"]],
artifacts.net.data[["edges"]],
network.conf = private$network.conf,
directed = FALSE,
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("commits")
)
## remove the artifact vertices stemming from untracked files if existing
if ("name" %in% igraph::list.vertex.attributes(artifacts.net) &&
length(igraph::V(artifacts.net)[name == UNTRACKED.FILE.EMPTY.ARTIFACT]) > 0) {
artifacts.net = igraph::delete.vertices(artifacts.net, UNTRACKED.FILE.EMPTY.ARTIFACT)
}
## store network
private$artifacts.network.cochange = artifacts.net
logging::logdebug("get.artifact.network.cochange: finished.")
return(artifacts.net)
},
#' Get the call-graph-based artifact network.
#' If it does not already exist build it first.
#' IMPORTANT: This only works for range-level analyses!
#'
#' @return the artifact network with callgraph relation
get.artifact.network.callgraph = function() {
logging::logdebug("get.artifact.network.callgraph: starting.")
## do not compute anything more than once
if (!is.null(private$artifacts.network.callgraph)) {
logging::logdebug("get.artifact.network.callgraph: finished. (already existing)")
return(private$artifacts.network.callgraph)
}
## check if revision for call-graphs is set
if (!("RangeData" %in% class(private$proj.data)) ||
is.na(private$proj.data$get.revision.callgraph())) {
logging::logerror("The call-graph revision is not set. Aborting...")
logging::logerror("This may be due to project-level analysis.
The call-graph data is only available in range-level analysis.")
stop("Trying to get call-graph data before setting a revision.")
}
## construct path and file
file.dir = private$proj.data$get.data.path.callgraph()
file.name = sprintf("cg_nw_%s_%s.net",
private$proj.data$get.project.conf.entry("artifact.short"),
private$proj.data$get.revision.callgraph())
file = file.path(file.dir, file.name)
## read network from disk
artifacts.net = igraph::read.graph(file, format = "pajek")
# set vertex labels properly (copy "id" attribute to "name" attribute)
artifacts.net = igraph::set.vertex.attribute(
artifacts.net,
"name",
igraph::V(artifacts.net),
igraph::get.vertex.attribute(artifacts.net, "id")
)
## process vertex names in artifact networks for consistent names:
## Since feature and file networks may have unique naming structures, the names
## need to be processed in order to match the ones coming from other analyses
## (e.g. Codeface):
## (1) retrieve parameters for processing
names = igraph::get.vertex.attribute(artifacts.net, "name")
artifact = private$proj.data$get.project.conf.entry("artifact")
## (2) different replacings for different artifacts
## feature
if (artifact == "feature") {
names = gsub("^CONFIG_", "ENABLE_", names) # BusyBox
names = gsub("^1$", "Base_Feature", names) # Base feature
}
## file
else if (artifact == "file" || artifact == "function") {
## transform to relative paths
names = gsub("^/local/bockthom/TypeChef-BusyboxAnalysis/gitbusybox/", "", names) # BusyBox
names = gsub("^/local/bockthom/openssl/", "", names) # OpenSSL
names = gsub("^/local/bockthom/sqlite/\\./", "", names) # SQLite
names = gsub("^/local/bockthom/sqlite/", "", names) # SQLite
## remove call-graph extension
names = gsub(".cg", "", names, fixed = TRUE)
}
## (3) set processed names inside graph object
artifacts.net = igraph::set.vertex.attribute(artifacts.net, "name", value = names)
## set edge attribute 'artifact.type' as the raw data do not contain this!
artifacts.net = igraph::set.edge.attribute(
artifacts.net, "artifact.type",
value = private$proj.data$get.project.conf.entry("artifact.codeface")
)
## store network
private$artifacts.network.callgraph = artifacts.net
logging::logdebug("get.artifact.network.callgraph: finished.")
return(artifacts.net)
},
#' Get the mail-based artifact network.
#' If it does not already exist build it first.
#'
#' @return the artifact network with mail relation
get.artifact.network.mail = function() {
logging::logdebug("get.artifact.network.mail: starting.")
## do not compute anything more than once
if (!is.null(private$artifacts.network.mail)) {
logging::logdebug("get.artifact.network.mail: finished. (already existing)")
return(private$artifacts.network.mail)
}
## log warning as we do not have relations among threads right now
logging::logwarn(paste(
"There exist no actual artifact network with the relation 'mail'.",
"Return an edge-less network now."
))
## construct edgeless network with mandatory edge and vertex attributes
directed = private$network.conf$get.value("artifact.directed")
artifacts = private$proj.data$get.artifacts("mails") # thread IDs
artifacts.net = create.empty.network(directed = directed, add.attributes = TRUE) +
igraph::vertices(artifacts)
## store network
private$artifacts.network.mail = artifacts.net
logging::logdebug("get.artifact.network.mail: finished.")
return(artifacts.net)
},
#' Get the issue-based artifact network.
#' If it does not already exist build it first.
#'
#' @return the artifact network with issue relation
get.artifact.network.issue = function() {
logging::logdebug("get.artifact.network.issue: starting.")
## do not compute anything more than once
if (!is.null(private$artifacts.network.issue)) {
logging::logdebug("get.artifact.network.issue: finished. (already existing)")
return(private$artifacts.network.issue)
}
## log warning as we do not have relations among issues right now
logging::logwarn(paste(
"There exist no actual artifact network with the relation 'issue'.",
"Return an edge-less network now."
))
## construct edgeless network with mandatory edge and vertex attributes
directed = private$network.conf$get.value("artifact.directed")
artifacts = private$proj.data$get.artifacts("issues") # issue IDs
artifacts.net = create.empty.network(directed = directed, add.attributes = TRUE) +
igraph::vertices(artifacts)
## store network
private$artifacts.network.issue = artifacts.net
logging::logdebug("get.artifact.network.issue: finished.")
return(artifacts.net)
},
## * * bipartite relations ------------------------------------------
#' Get the key-value data for the bipartite relations,
#' which are implied by the "artifact.relation" from the network configuration.
#'
#' @return a named list of data for the bipartite relations, each with the attributes
#' 'vertex.kind' denoting the artifact type for the relations
#' and 'relation' denoting the respective network-configuration entry; the names
#' are the relations configured by the attribute 'artifact.relation' of the
#' network configuration
get.bipartite.relations = function() {
logging::logdebug("get.bipartite.relations: starting.")
relations = private$network.conf$get.variable("artifact.relation")
logging::logdebug("Using bipartite relations '%s'.", relations)
bip.relations = lapply(relations, function(relation) {
## get data for current bipartite relation
data.source = RELATION.TO.DATASOURCE[[relation]]
bip.relation = private$proj.data$group.artifacts.by.data.column(data.source, "author.name")
## set vertex.kind and relation attributes
attr(bip.relation, "vertex.kind") = private$get.vertex.kind.for.relation(relation)
attr(bip.relation, "relation") = relation
return (bip.relation)
})
names(bip.relations) = relations
logging::logdebug("get.bipartite.relations: finished.")
return(bip.relations)
}
),
## * * public ----------------------------------------------------------
public = list(
#' Constructor of the class. Constructs a new instance based on the
#' given data object and the network configuration
#'
#' @param project.data the given data object
#' @param network.conf the network configuration
initialize = function(project.data, network.conf) {
## check arguments
private$proj.data.original = verify.argument.for.parameter(project.data, "ProjectData", "NetworkBuilder$new")
private$proj.data = project.data$clone()
private$network.conf = verify.argument.for.parameter(network.conf, "NetworkConf", "NetworkBuilder$new")
## cut data if needed
if (private$network.conf$get.value("unify.date.ranges")) {
private$cut.data.to.same.timestamps()
}
if (class(self)[1] == "NetworkBuilder") {
logging::loginfo("Initialized network builder for data %s.",
private$proj.data$get.class.name())
}
},
## * * resetting environment ---------------------------------------
#' Reset the current environment in order to rebuild it.
#' Has to be called whenever the data or configuration get changed.
reset.environment = function() {
private$authors.network.mail = NULL
private$authors.network.cochange = NULL
private$authors.network.issue = NULL
private$artifacts.network.cochange = NULL
private$artifacts.network.callgraph = NULL
private$proj.data = private$proj.data.original
if (private$network.conf$get.value("unify.date.ranges")) {
private$cut.data.to.same.timestamps()
}
},
## * * configuration -----------------------------------------------
#' Get the current network configuration.
#'
#' @return the 'network.conf' of the current instance of the class
get.network.conf = function() {
return(private$network.conf)
},
#' Set the current network configuration to the given one.
#'
#' @param network.conf the new network configuration.
#' @param reset.environment parameter to determine whether the environment
#' has to be reset or not [default: FALSE]
set.network.conf = function(network.conf, reset.environment = FALSE) {
private$network.conf = network.conf
if (reset.environment) {
self$reset.environment()
}
},
#' Get a value of the network configuration
#'
#' @return the value of the given entry name
get.network.conf.entry = function(entry) {
return(private$network.conf$get.value(entry))
},
#' Set a value of the network configuration and reset the environment
set.network.conf.entry = function(entry, value) {
private$network.conf$update.value(entry, value)
},
#' Get the project data Object of the NetworkBuilder.
#' This Method is mainly used for testing purposes at the moment.
#'
#' @return the project data object of the NetworkBuilder
get.project.data = function() {
return(private$proj.data)
},
#' Update the network configuration based on the given list
#' of values and reset the environment afterwards
#'
#' @param updated.values the new values for the network configuration
update.network.conf = function(updated.values = list()) {
private$network.conf$update.values(updated.values = updated.values)
self$reset.environment()
},
## * * networks ----------------------------------------------------
#' Get the generic author network.
#'
#' @return the generic author network
get.author.network = function() {
logging::loginfo("Constructing author network.")
## construct network
relations = private$network.conf$get.value("author.relation")
networks = lapply(relations, function(relation) {
network = switch(
relation,
cochange = private$get.author.network.cochange(),
mail = private$get.author.network.mail(),
issue = private$get.author.network.issue(),
stop(sprintf("The author relation '%s' does not exist.", rel))
## TODO construct edge lists here and merge those (inline the private methods)
)
## set edge attributes on all edges
igraph::E(network)$type = TYPE.EDGES.INTRA
igraph::E(network)$relation = relation
return(network)
})
net = merge.networks(networks)
## add all missing authors to the network if wanted
if (private$network.conf$get.value("author.all.authors")) {
authors.all = private$proj.data$get.authors()[[ "author.name" ]]
authors.net = igraph::get.vertex.attribute(net, "name")
net = net + igraph::vertices(setdiff(authors.all, authors.net))
}
## remove all authors from the corresponding network who do not have touched any artifact
if (private$network.conf$get.value("author.only.committers")) {
## authors-artifact relation
authors.from.net = igraph::get.vertex.attribute(net, "name")
authors.from.artifacts = lapply(private$get.bipartite.relations(), function(bipartite.relation) {
return(names(bipartite.relation))
})
authors.from.artifacts = unlist(authors.from.artifacts)
if (!is.null(authors.from.artifacts)) {
net = igraph::delete.vertices(net, setdiff(authors.from.net, authors.from.artifacts))
}
}
## set vertex attributes for identifaction
igraph::V(net)$kind = TYPE.AUTHOR
igraph::V(net)$type = TYPE.AUTHOR
## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(net, "range") = private$proj.data$get.range()
}
return(net)
},
#' Get the generic artifact network.
#'
#' @return the generic artifact network
get.artifact.network = function() {
logging::loginfo("Constructing artifact network.")
## construct network
relations = private$network.conf$get.value("artifact.relation")
networks = lapply(relations, function(relation) {
network = switch(
relation,
cochange = private$get.artifact.network.cochange(),
callgraph = private$get.artifact.network.callgraph(),
mail = private$get.artifact.network.mail(),
issue = private$get.artifact.network.issue(),
stop(sprintf("The artifact relation '%s' does not exist.", relation))
)
## set edge attributes on all edges
igraph::E(network)$type = TYPE.EDGES.INTRA
igraph::E(network)$relation = relation
## set vertex attribute 'kind' on all edges, corresponding to relation
vertex.kind = private$get.vertex.kind.for.relation(relation)
network = igraph::set.vertex.attribute(network, "kind", value = vertex.kind)
return(network)
})
net = merge.networks(networks)
## set vertex and edge attributes for identifaction
igraph::V(net)$type = TYPE.ARTIFACT
## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(net, "range") = private$proj.data$get.range()
}
return(net)
},
#' Get the (real) bipartite network.
#'
#' @return the bipartite network
get.bipartite.network = function() {
## get data by the chosen relation
bipartite.relation.data = private$get.bipartite.relations()
directed = private$network.conf$get.value("author.directed")
vertex.data = lapply(bipartite.relation.data, function(net.to.net) {
## extract vertices for author network
if (private$network.conf$get.value("author.all.authors")) {
author.vertices = private$proj.data$get.authors()[[ "author.name" ]]
} else {
author.vertices = names(net.to.net)
}
## select all artifact vertices
artifact.vertices = unique(unlist(lapply(net.to.net, function(df) {
return(df[["data.vertices"]])
})))
## get vertex.kind from bipartite relation
vertex.kind = attr(net.to.net, "vertex.kind")
## join author and artifact vertices to the list of all vertices in the network
vertices = data.frame(
name = c(author.vertices, artifact.vertices),
kind = c(
rep(TYPE.AUTHOR, length(author.vertices)),
rep(vertex.kind , length(artifact.vertices))
),
type = c(
rep(TYPE.AUTHOR, length(author.vertices)),
rep(TYPE.ARTIFACT, length(artifact.vertices))
)
)
return(vertices)
})
## Merge network data and construct a vertex-only network for now:
## 1) construct vertex data (without edges)
vertex.data = merge.network.data(vertex.data = vertex.data, edge.data = NULL)[["vertices"]]
## 2) remove empty artifact, if names are available
if ("name" %in% colnames(vertex.data)) {
vertex.data = subset(vertex.data, !(name == UNTRACKED.FILE.EMPTY.ARTIFACT & type == TYPE.ARTIFACT))
}
## 3) obtain all possible data columns, i.e., edge attributes
available.edge.attributes = lapply(
private$network.conf$get.variable("artifact.relation"),
function(relation) {
data.source = RELATION.TO.DATASOURCE[[relation]]
data.cols = private$proj.data$get.data.columns.for.data.source(data.source)
return(data.cols)
}
)
available.edge.attributes = unlist(available.edge.attributes, recursive = FALSE)
available.edge.attributes = available.edge.attributes[
!duplicated(names(available.edge.attributes)) # remove duplicates based on names
]
## 4) construct network without edges
vertex.network = construct.network.from.edge.list(
vertices = vertex.data,
edge.list = create.empty.edge.list(),
network.conf = private$network.conf,
directed = directed,
available.edge.attributes = available.edge.attributes
)
## explicitly add vertex attributes if vertex data was empty
if (nrow(vertex.data) == 0) {
vertex.network = add.attributes.to.network(vertex.network, "vertex", attributes = list(
name = "character", kind = "character", type = "character"
))
}
## add edges to the vertex network
network = add.edges.for.bipartite.relation(
vertex.network,
bipartite.relations = bipartite.relation.data,
private$network.conf,
available.edge.attributes = available.edge.attributes
)
## remove vertices that are not committers if wanted
if (private$network.conf$get.value("author.only.committers")) {
committers = unique(private$proj.data$get.commits()[["author.name"]])
authors = igraph::get.vertex.attribute(network, "name", igraph::V(network)[ type == TYPE.AUTHOR ])
authors.to.remove = setdiff(authors, committers)
network = igraph::delete.vertices(network, authors.to.remove)
}
## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(network, "range") = private$proj.data$get.range()
}
return(network)
},
#' Get all networks as list.
#' Build unification to avoid null-pointers.
#'
#' @return all networks in a list
get.networks = function() {
logging::loginfo("Constructing all networks.")
## author-artifact relation
authors.to.artifacts = private$get.bipartite.relations()
## bipartite network
bipartite.net = self$get.bipartite.network()
## author relation
authors.net = self$get.author.network()
## artifact relation
artifacts.net = self$get.artifact.network()
return(list(
"authors.to.artifacts" = authors.to.artifacts,
"bipartite.net" = bipartite.net,
"authors.net" = authors.net,
"artifacts.net" = artifacts.net
))
},
#' Get the multi network.
#' The multi network is basically the result of 'get.networks' combined
#' in one network.
#'
#' @return the multi network
get.multi.network = function() {
logging::loginfo("Constructing multi network.")
## construct the network parts we need for the multi network
networks = self$get.networks()
authors.to.artifacts = networks[["authors.to.artifacts"]]
authors.net = networks[["authors.net"]]
igraph::V(authors.net)$kind = TYPE.AUTHOR
artifacts.net = networks[["artifacts.net"]]
## remove authors from author-artifact relation, if needed:
## we only add bipartite edges for authors already present in the author network (this can be
## configured by 'author.only.committers', for example), thus, we need to remove any authors
## from the author--artifact relation that are superfluous
authors.from.net = igraph::get.vertex.attribute(authors.net, "name")
## save relation and intersect the author vertices from the author network and the
## bipartite networks
authors.to.artifacts = mapply(function(a2a.rel, relation.type) {
authors.from.artifacts = names(a2a.rel)
a2a = a2a.rel[ intersect(authors.from.net, authors.from.artifacts) ]
attr(a2a, "relation") = relation.type
return(a2a)
}, authors.to.artifacts, names(authors.to.artifacts), SIMPLIFY = FALSE)
## unify vertices with artifacts from bipartite and artifact relation:
## when the source for artifacts is different for the bipartite relation and the artifact relation (e.g.,
## "cochange" and "callgraph"), then the vertex names need to be unified so that all vertices are
## represented properly and, more important here, all bipartite relations can be added
artifacts = lapply(authors.to.artifacts, function(a2a.rel) {
artifact.list = plyr::rbind.fill(a2a.rel)[ c("data.vertices", "artifact.type") ]
artifact.list = unique(artifact.list)
return(artifact.list)
})
artifacts.all = plyr::rbind.fill(artifacts)
artifacts.from.net = igraph::get.vertex.attribute(artifacts.net, "name")
artifacts.to.add = setdiff(artifacts.all[["data.vertices"]], artifacts.from.net)
artifacts.to.add.kind = artifacts.all[
artifacts.all[["data.vertices"]] %in% artifacts.to.add, "artifact.type"
]
artifacts.net = artifacts.net + igraph::vertices(artifacts.to.add, type = TYPE.ARTIFACT,
kind = artifacts.to.add.kind)
## check directedness and adapt artifact network if needed
if (igraph::is.directed(authors.net) && !igraph::is.directed(artifacts.net)) {
logging::logwarn("Author network is directed, but artifact network is not. Converting artifact network...")
artifacts.net = igraph::as.directed(artifacts.net, mode = "mutual")
} else if (!igraph::is.directed(authors.net) && igraph::is.directed(artifacts.net)) {
logging::logwarn("Author network is undirected, but artifact network is not. Converting artifact network...")
artifacts.net = igraph::as.undirected(artifacts.net, mode = "each", edge.attr.comb = EDGE.ATTR.HANDLING)
}
## reduce memory consumption by removing temporary data
rm(networks)
gc()
## combine the networks:
## 1) merge the existing networks
u = igraph::disjoint_union(authors.net, artifacts.net)
## 2) add the bipartite edges
u = add.edges.for.bipartite.relation(u, authors.to.artifacts, private$network.conf)
## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(u, "range") = private$proj.data$get.range()
}
return(u)
}
)
)
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Network and edge construction -------------------------------------------
#' Construct a edge list from the given list of lists.
#' For example for a list of authors per thread, where all authors are connected if they are
#' in the same thread (sublist).
#'
#' Important: The input needs to be compatible with the function \code{get.key.to.value.from.df}.
#'
#' If \code{directed}, as default, the order of things in the sublist is respected (if
#' \code{respect.temporal.order} is not set manually) and the 'edge.attr's hold the
#' vector of possible edge attributes in the given list.
#'
#' @param list the list of lists with data
#' @param network.conf the network configuration
#' @param directed whether or not the network should be directed [default: FALSE]
#' @param respect.temporal.order whether to respect the temporal order when constructing edges,
#' 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]
#'
#' @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) {
logging::loginfo("Create edges.")
logging::logdebug("construct.edge.list.from.key.value.list: starting.")
## if no value for respect.temporal.order is specified (indicated by an NA value
## coming from the network configuration), use the value of directed parameter instead
if (is.na(respect.temporal.order)) {
respect.temporal.order = directed
}
## initialize an edge list to fill and the set of vertices
vertices.processed = c()
edge.list = data.frame()
keys = names(list)
keys.number = length(list)
if (respect.temporal.order) {
## for all subsets (sets), connect all items in there with the previous ones
edge.list.data = parallel::mclapply(list, function(set) {
number.edges = sum(seq_len(nrow(set)) - 1)
logging::logdebug("[%s/%s] Constructing edges for %s '%s': starting (%s edges to construct).",
match(attr(set, "group.name"), keys), keys.number,
attr(set, "group.type"), attr(set, "group.name"), number.edges)
## Skip artifacts with many, many edges
if (number.edges > network.conf$get.value("skip.threshold")) {
logging::logwarn("Skipping edges for %s '%s' due to amount (> %s).",
attr(set, "group.type"), attr(set, "group.name"), network.conf$get.value("skip.threshold"))
return(NULL)
}
## queue of already processed artifacts
edge.list.set = data.frame()
vertices.processed.set = c()
## connect the current item to all previous ones
for (item.no in seq_len(nrow(set))) {
item = set[item.no, ]
## get vertex data
item.vertex = item[["data.vertices"]]
## 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]
## construct edges
combinations = expand.grid(item.vertex, vertices.processed.set, stringsAsFactors = default.stringsAsFactors())
if (nrow(combinations) > 0 & nrow(item.edge.attrs) == 1) {
combinations = cbind(combinations, item.edge.attrs, row.names = NULL) # add edge attributes
}
edge.list.set = rbind(edge.list.set, combinations) # add to edge list