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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 <hunsen@fim.uni-passau.de>
## Copyright 2017 by Raphael Nömmer <noemmer@fim.uni-passau.de>
## Copyright 2017-2018 by Christian Hechtl <hechtl@fim.uni-passau.de>
## Copyright 2024 by Christian Hechtl <hechtl@cs.uni-saarland.de>
## Copyright 2017-2019 by Thomas Bock <bockthom@fim.uni-passau.de>
## Copyright 2021, 2023-2024 by Thomas Bock <bockthom@cs.uni-saarland.de>
## Copyright 2018 by Barbara Eckl <ecklbarb@fim.uni-passau.de>
## Copyright 2018-2019 by Jakob Kronawitter <kronawij@fim.uni-passau.de>
## Copyright 2020 by Anselm Fehnker <anselm@muenster.de>
## Copyright 2021 by Niklas Schneider <s8nlschn@stud.uni-saarland.de>
## Copyright 2022 by Jonathan Baumann <joba00002@stud.uni-saarland.de>
## Copyright 2023-2025 by Maximilian Löffler <s8maloef@stud.uni-saarland.de>
## Copyright 2024 by Leo Sendelbach <s8lesend@stud.uni-saarland.de>
## 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
requireNamespace("lubridate") # for date conversion
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Vertex and edge types ---------------------------------------------------
## vertex types
TYPE.AUTHOR = "Author"
TYPE.ARTIFACT = "Artifact"
TYPE.COMMIT = "Commit"
## 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 = function(relation) sort(unique(relation)),
## 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
commits.network.commit.interaction = NULL, #igraph
commits.network.cochange = NULL, #igraph
## * * relation-to-vertex-kind mapping -----------------------------
#' Determine which vertex kind should be chosen 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",
commit.interaction = private$proj.data$get.project.conf.entry("artifact.codeface")
)
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$get.authors.by.data.source(data.sources = "commits")
## 2) only select author names
authors = authors["author.name"]
## 3) rename single column to "name" to correct mapping to vertex attribute "name"
colnames(authors) = "name"
## 4) set author list as vertices
author.net.data[["vertices"]] = authors
## construct network from obtained data
author.net = construct.network.from.edge.list(
author.net.data[["vertices"]],
author.net.data[["edges"]],
network.conf = private$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$authors.network.cochange = author.net
logging::logdebug("get.author.network.cochange: finished.")
return(author.net)
},
#' Build and get the author network with commit-interactions as the relation.
#'
#' @return the commit-interaction author network
get.author.network.commit.interaction = function() {
## get the authors that appear in the commit-interaction data as the vertices of the network
vertices = unique(c(private$proj.data$get.commit.interactions()[["base.author"]],
private$proj.data$get.commit.interactions()[["interacting.author"]]))
vertices = data.frame(name = vertices)
## get the commit-interaction data as the edge data of the network
edges = private$proj.data$get.commit.interactions()
## set the authors as the 'to' and 'from' of the network and order the dataframe
edges = edges[, c("base.author", "interacting.author", "func", "commit.hash",
"file", "base.hash", "base.func", "base.file")]
colnames(edges)[1] = "to"
colnames(edges)[2] = "from"
colnames(edges)[4] = "hash"
if (nrow(edges) > 0) {
edges[["artifact.type"]] = ARTIFACT.COMMIT.INTERACTION
}
author.net.data = list(vertices = vertices, edges = edges)
## construct the network
author.net = construct.network.from.edge.list(
author.net.data[["vertices"]],
author.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("author.directed"),
available.edge.attributes = private$proj.data$
get.data.columns.for.data.source("commit.interactions")
)
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$network.conf,
directed = FALSE,
respect.temporal.order = TRUE,
network.type = "artifact"
)
## construct network from obtained data
artifacts.net = construct.network.from.edge.list(
artifacts.net.data[["vertices"]],
artifacts.net.data[["edges"]],
network.conf = private$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::vertex_attr_names(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$artifacts.network.cochange = artifacts.net
logging::logdebug("get.artifact.network.cochange: finished.")
return(artifacts.net)
},
#' Build and get the commit-interaction based artifact network.
#'
#' @return the commit-interaction based artifact network
get.artifact.network.commit.interaction = function() {
## initialize the vertices. They will be set correctly depending on the used config.
vertices = c()
## get the commit-interaction data as the edge data of the network
edges = private$proj.data$get.commit.interactions()
## set 'to' and 'from' of the network according to the config
## and order the dataframe accordingly
proj.conf.artifact = private$proj.data$get.project.conf.entry("artifact")
if (proj.conf.artifact == "file") {
## change the vertices to the files from the commit-interaction data
vertices = unique(c(private$proj.data$get.commit.interactions()[["base.file"]],
private$proj.data$get.commit.interactions()[["file"]]))
vertices = data.frame(name = vertices)
edges = edges[, c("file", "base.file", "func", "commit.hash",
"base.hash", "base.func", "base.author", "interacting.author")]
if (nrow(edges) > 0) {
edges[["artifact.type"]] = ARTIFACT.CODEFACE[[proj.conf.artifact]]
}
colnames(edges)[colnames(edges) == "commit.hash"] = "hash"
} else if (proj.conf.artifact == "function") {
## change the vertices to the functions from the commit-interaction data
vertices = unique(c(private$proj.data$get.commit.interactions()[["base.func"]],
private$proj.data$get.commit.interactions()[["func"]]))
vertices = data.frame(name = vertices)
edges = edges[, c("func", "base.func", "commit.hash", "file", "base.hash",
"base.file", "base.author", "interacting.author")]
if (nrow(edges) > 0) {
edges[["artifact.type"]] = ARTIFACT.CODEFACE[[proj.conf.artifact]]
}
colnames(edges)[colnames(edges) == "commit.hash"] = "hash"
} else {
## If neither 'function' nor 'file' was configured, send a warning
## and return an empty network
logging::logwarn("when creating a commit-interaction artifact network,
the artifact should be either 'file' or 'function'!")
return(create.empty.network(directed = private$network.conf$get.value("artifact.directed")))
}
colnames(edges)[1] = "to"
colnames(edges)[2] = "from"
artifact.net.data = list(vertices = vertices, edges = edges)
## construct the network
artifact.net = construct.network.from.edge.list(
artifact.net.data[["vertices"]],
artifact.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("artifact.directed"),
available.edge.attributes = private$proj.data$
get.data.columns.for.data.source("commit.interactions")
)
return(artifact.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$get.revision.callgraph())
file = file.path(file.dir, file.name)
## read network from disk
artifacts.net = igraph::read_graph(file, format = "pajek")
# set vertex labels properly (copy "id" attribute to "name" attribute)
artifacts.net = igraph::set_vertex_attr(
artifacts.net,
"name",
igraph::V(artifacts.net),
igraph::vertex_attr(artifacts.net, "id")
)
## process vertex names in artifact networks for consistent names:
## Since feature and file networks may have unique naming structures, the names
## need to be processed in order to match the ones coming from other analyses
## (e.g. Codeface):
## (1) retrieve parameters for processing
names = igraph::vertex_attr(artifacts.net, "name")
artifact = private$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_attr(artifacts.net, "name", value = names)
## set edge attribute 'artifact.type' as the raw data do not contain this!
artifacts.net = igraph::set_edge_attr(
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)
}
if (private$proj.data$get.project.conf()$get.entry("issues.only.comments")) {
logging::logwarn(paste(
"Create an edge-less artifact network as 'issues.only.comments' is set.",
"Comments in issues cannot create issue edges."
))
}
## construct edge list based on issue-artifact data
artifacts.net.data.raw = private$proj.data[[DATASOURCE.TO.ARTIFACT.FUNCTION[["issues"]]]]()
## obtain issue-connecting events
add.links = artifacts.net.data.raw[artifacts.net.data.raw$event.name == "add_link" &
artifacts.net.data.raw$event.info.2 == "issue", ]
referenced.bys = artifacts.net.data.raw[artifacts.net.data.raw$event.name == "referenced_by" &
artifacts.net.data.raw$event.info.2 == "issue", ]
## the codeface extraction for jira issues creates duplicate events, linking the referenced issue
## to the referencing issue, in addition to the correct events, linking the referencing issue to
## the referenced issue. We can only deduplicate them, if we build an undirected network, as otherwise,
## we would need to guess the correct direction.
if (!private$network.conf$get.entry("artifact.directed")) {
## obtain 'add_link' events from jira
jira.add.links = add.links[add.links$issue.source == "jira", ]
matched = list()
## iterate over all add_link events from jira
for (i in 1:nrow(jira.add.links)) {
add.link = jira.add.links[i, ]
## ensure not to remove both duplicate edges
if (any(sapply(matched, function(entry) identical(entry, add.link)))) {
next
}
## match any 'add_link' events, that are the reverse direction of 'add.link',
## but have the same timestamp and author information
match = jira.add.links[(
jira.add.links$issue.id == add.link$event.info.1 &
jira.add.links$event.info.1 == add.link$issue.id &
jira.add.links$date == add.link$date &
jira.add.links$author.name == add.link$author.name), ]
## if a match is found, remove 'add.link' and its corresponding 'referenced_by' event
if (nrow(match) > 0) {
add.links = add.links[!(
add.links$issue.id == match$issue.id &
add.links$event.info.1 == match$event.info.1 &
add.links$date == match$date &
add.links$author.name == match$author.name), ]
referenced.bys = referenced.bys[!(
referenced.bys$issue.id == add.link$issue.id &
referenced.bys$event.info.1 == add.link$event.info.1 &
referenced.bys$date == add.link$date &
referenced.bys$author.name == add.link$author.name), ]
matched = append(matched, list(match))
}
}
}
if (nrow(add.links) != nrow(referenced.bys)) {
logging::logwarn("Inconsistent issue data. Unequally many 'add_link' and 'referenced_by' issue-events.")
}
vertices = unique(artifacts.net.data.raw["issue.id"])
edge.list = data.frame()
# edges in artifact networks can not have the 'artifact' attribute but should instead have
# the 'author.name' attribute as events caused by authors connect issues
edge.attributes = private$network.conf$get.value("edge.attributes")
artifact.index = match("artifact", edge.attributes, nomatch = NA)
if (!is.na(artifact.index)) {
edge.attributes = edge.attributes[-artifact.index]
edge.attributes = c(edge.attributes, c("author.name"))
}
## connect corresponding add_link and referenced_by issue-events
edge.list = plyr::rbind.fill(parallel::mclapply(split(add.links, seq_len(nrow(add.links))), function(from) {
## get edge attributes
cols.which = edge.attributes %in% colnames(from)
edge.attrs = from[, edge.attributes[cols.which], drop = FALSE]
## construct edge
to = subset(referenced.bys,
event.info.1 == from[["issue.id"]] &
author.name == from[["author.name"]] &
date == from[["date"]])
if (!all(is.na(to))) {
combination = list("from" = from[["issue.id"]], "to" = to[["issue.id"]])
combination = cbind(combination, edge.attrs, row.names = NULL) # add edge attributes
return(combination) # return the combination for this row
}
}))
artifacts.net.data = list(
vertices = data.frame(
name = vertices
),
edges = edge.list
)
## construct network from obtained data
artifacts.net = construct.network.from.edge.list(
artifacts.net.data[["vertices"]],
artifacts.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("artifact.directed"),
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("issues")
)
## store network
private$artifacts.network.issue = artifacts.net
logging::logdebug("get.artifact.network.issue: finished.")
return(artifacts.net)
},
#' Build and get the commit network with commit-interactions as the relation.
#'
#' @return the commit-interaction commit network
get.commit.network.commit.interaction = function() {
logging::logdebug("get.commit.network.commit.interaction: starting.")
## do not compute anything more than once
if (!is.null(private$commits.network.commit.interaction)) {
logging::logdebug("get.commit.network.commit.interaction: finished. (already existing)")
return(private$commits.network.commit.interaction)
}
## get the hashes that appear in the commit-interaction data as the vertices of the network
vertices = unique(c(private$proj.data$get.commit.interactions()[["base.hash"]],
private$proj.data$get.commit.interactions()[["commit.hash"]]))
vertices = data.frame(name = vertices)
## get the commit-interaction data as the edge data of the network
edges = private$proj.data$get.commit.interactions()
## set the commits as the 'to' and 'from' of the network and order the dataframe
edges = edges[, c("base.hash", "commit.hash", "func", "interacting.author",
"file", "base.author", "base.func", "base.file")]
if (nrow(edges) > 0) {
edges[["artifact.type"]] = ARTIFACT.COMMIT.INTERACTION
}
colnames(edges)[1] = "to"
colnames(edges)[2] = "from"
commit.net.data = list(vertices = vertices, edges = edges)
## construct the network
commit.net = construct.network.from.edge.list(
commit.net.data[["vertices"]],
commit.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("commit.directed"),
available.edge.attributes = private$proj.data$
get.data.columns.for.data.source("commit.interactions")
)
private$commits.network.commit.interaction = commit.net
logging::logdebug("get.commit.network.commit.interaction: finished.")
return(commit.net)
},
#' Get the cochange-based commit network,
#' If it does not already exist build it first.
#'
#' @return the commit network with cochange realtion
get.commit.network.cochange = function() {
logging::logdebug("get.commit.network.cochange: starting.")
## do not compute anything more than once
if (!is.null(private$commits.network.cochange)) {
logging::logdebug("get.commit.network.cochange: finished. (already existing)")
return(private$commits.network.cochange)
}
## construct edge list based on commit--artifact data
commit.net.data.raw = private$proj.data$group.commits.by.data.column("artifact")
commit.net.data = construct.edge.list.from.key.value.list(
commit.net.data.raw,
network.conf = private$network.conf,
directed = private$network.conf$get.value("commit.directed"),
respect.temporal.order = TRUE,
network.type = "commit"
)
## construct network from obtained data
commit.net = construct.network.from.edge.list(
commit.net.data[["vertices"]],
commit.net.data[["edges"]],
network.conf = private$network.conf,
directed = private$network.conf$get.value("commit.directed"),
available.edge.attributes = private$proj.data$get.data.columns.for.data.source("commits")
)
## store network
private$commits.network.cochange = commit.net
logging::logdebug("get.commit.network.cochange: finished.")
return(commit.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$authors.network.cochange = NULL
private$authors.network.issue = NULL
private$authors.network.mail = NULL
private$artifacts.network.callgraph = NULL
private$artifacts.network.cochange = NULL
private$artifacts.network.issue = NULL
private$artifacts.network.mail = NULL
private$commits.network.commit.interaction = NULL
private$commits.network.cochange = NULL
private$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$get.value(entry))
},
#' Set a value of the network configuration and reset the environment.
#'
#' @param entry the configuration option to set
#' @param value the new value that is assigned to the configuration parameter
set.network.conf.entry = function(entry, value) {
private$network.conf$update.value(entry, value)
self$reset.environment()
},
#' 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 [default: list()]
update.network.conf = function(updated.values = list()) {
private$network.conf$update.values(updated.values = updated.values)
self$reset.environment()
},
#' Get the ProjectData object of the NetworkBuilder.
#' This method is mainly used for testing purposes at the moment.
#'
#' @return the project data object of the NetworkBuilder
get.project.data = function() {
return(private$proj.data)
},
## * * 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$get.author.network.cochange(),
commit.interaction = private$get.author.network.commit.interaction(),
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::vertex_attr(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::vertex_attr(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)$type = TYPE.AUTHOR
## simplify network if wanted
if (private$network.conf$get.value("simplify")) {
net = simplify.network(net, simplify.multiple.relations =
private$network.conf$get.value("simplify.multiple.relations"))
}
## add range attribute for later analysis (if available)
if ("RangeData" %in% class(private$proj.data)) {
attr(net, "range") = private$proj.data$get.range()
}
net = convert.edge.attributes.to.list(net)
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(),
commit.interaction = private$get.artifact.network.commit.interaction(),