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util-data.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 2017-2019 by Thomas Bock <[email protected]>
## Copyright 2020-2021, 2023-2024 by Thomas Bock <[email protected]>
## Copyright 2017 by Raphael Nömmer <[email protected]>
## Copyright 2017-2018 by Christian Hechtl <[email protected]>
## Copyright 2020, 2024 by Christian Hechtl <[email protected]>
## Copyright 2017 by Felix Prasse <[email protected]>
## Copyright 2017 by Ferdinand Frank <[email protected]>
## Copyright 2018-2019 by Jakob Kronawitter <[email protected]>
## Copyright 2019-2020 by Anselm Fehnker <[email protected]>
## Copyright 2020-2021, 2023 by Niklas Schneider <[email protected]>
## Copyright 2021 by Johannes Hostert <[email protected]>
## Copyright 2021 by Mirabdulla Yusifli <[email protected]>
## Copyright 2022 by Jonathan Baumann <[email protected]>
## Copyright 2022-2024 by Maximilian Löffler <[email protected]>
## Copyright 2024 by Leo Sendelbach <[email protected]>
## All Rights Reserved.
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Libraries ---------------------------------------------------------------
requireNamespace("R6") # for R6 classes
requireNamespace("logging") # for logging
requireNamespace("parallel") # for parallel computation
requireNamespace("lubridate") # for date conversion
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## Constants ---------------------------------------------------------------
## untracked file
UNTRACKED.FILE = "<untracked.file>"
## the empty string which resides in the artifact column when artifact == feature or artifact == function
## in the 'ProjectConf'
UNTRACKED.FILE.EMPTY.ARTIFACT = ""
UNTRACKED.FILE.EMPTY.ARTIFACT.TYPE = ""
## base artifacts (which one actually applies, depends on the artifact parameter in the 'ProjectConf')
BASE.ARTIFACTS = c(
"Base_Feature", ## when artifact == feature
"File_Level", ## when artifact == function
UNTRACKED.FILE ## when artifact == file
)
## mapping of data source to artifact column (for commits: filter artifacts based on the configuration options
## 'commits.filter.base.artifact' and 'commits.filter.untracked.files' of the corresponding 'ProjectConf' object)
DATASOURCE.TO.ARTIFACT.FUNCTION = list(
"commits" = "get.commits",
"mails" = "get.mails",
"issues" = "get.issues"
)
## mapping of data source to the appropiate getter for unfiltered date
## compared to \code{DATASOURCE.TO.ARTIFACT.FUNCTION}, which yields the getter for filtered data.
DATASOURCE.TO.UNFILTERED.ARTIFACT.FUNCTION = list(
"commits" = "get.commits.unfiltered",
"mails" = "get.mails.unfiltered",
"issues" = "get.issues.unfiltered"
)
## Yields the getters associated with additional data sources, e.g. author data.
DATASOURCE.TO.ADDITIONAL.ARTIFACT.FUNCTION = list(
"authors" = "get.authors",
"commit.messages" = "get.commit.messages",
"synchronicity" = "get.synchronicity",
"pasta" = "get.pasta",
"gender" = "get.gender",
"commit.interactions" = "get.commit.interactions",
"custom.event.timestamps" = "get.custom.event.timestamps"
)
#' Applies a function to list keys
#' Given a list, this function returns a modified list where the list keys have been
#' changed by \code{map.function}, while the values are left unchanged.
#'
#' @param lst the list to rename
#' @param map.function the function applied to \code{lst}'s keys
#'
#' @return \code{lst}, with the keys changed
rename.list.keys = function(lst, map.function) {
names(lst) = lapply(names(lst), map.function)
return(lst)
}
## Combine \code{DATASOURCE.TO.ARTIFACT.FUNCTION}, \code{DATASOURCE.TO.UNFILTERED.ARTIFACT.FUNCTION}
## and \code{DATASOURCE.TO.ADDITIONAL.ARTIFACT.FUNCTION} to build a list giving the getter associated with every
## possible data source stored in ProjectData.
DATASOURCE.FIELDS.TO.ARTIFACT.GLOBAL.FUNCTION = c(
DATASOURCE.TO.ADDITIONAL.ARTIFACT.FUNCTION,
DATASOURCE.TO.ARTIFACT.FUNCTION,
rename.list.keys(DATASOURCE.TO.UNFILTERED.ARTIFACT.FUNCTION, function(x) paste0(x, ".unfiltered"))
)
## mapping of data source to artifact column
DATASOURCE.TO.ARTIFACT.COLUMN = list(
"commits" = "artifact",
"mails" = "thread",
"issues" = "issue.id"
)
## the maximum time difference between subsequent mails of a patchstack
PATCHSTACK.MAIL.DECAY.THRESHOLD = lubridate::as.duration("30 seconds")
## configuration parameters that do not reset the environment when changed
CONF.PARAMETERS.NO.RESET.ENVIRONMENT = c("commit.messages",
"pasta",
"gender",
"synchronicity",
"synchronicity.time.window",
"commits.locked",
"issues.locked",
"mails.locked",
"custom.event.timestamps",
"custom.event.timestamps.locked",
"commit.interactions")
## / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
## ProjectData -------------------------------------------------------------
#' The class \code{ProjectData} provides convenient data handling for a project's data
#' in a lazy fashion.
#'
#' To configure an object of this data-handling class, a configuration object of class
#' \code{ProjectConf} must be passed to the initialization function. Data paths and
#' other configuration options are read from it.
#'
#' The following main data sources are handled:
#' - commits,
#' - mails, and
#' - issues.
#'
#' Furthermore, the following additional and orthogonal data sources are handled:
#' - synchronicity data and
#' - PaStA data.
#'
#' @seealso ProjectConf
ProjectData = R6::R6Class("ProjectData",
## * private -----------------------------------------------------------
private = list(
## * * configuration -----------------------------------------------
project.conf = NULL, # list
## * * raw data ----------------------------------------------------
## commits and commit data
commits = create.empty.commits.list(), # data.frame
commits.unfiltered = create.empty.commits.list(), # data.frame
commit.messages = create.empty.commit.message.list(), # data.frame
commit.interactions = create.empty.commit.interaction.list(), # data.frame
## mails
mails.unfiltered = create.empty.mails.list(), # data.frame
mails = create.empty.mails.list(), # data.frame
mails.patchstacks = list(), # list
## issues
issues.unfiltered = create.empty.issues.list(), #data.frame
issues = create.empty.issues.list(), #data.frame
## authors
authors = create.empty.authors.list(), # data.frame
## additional data sources
gender = create.empty.gender.list(), # data.frame
synchronicity = create.empty.synchronicity.list(), # data.frame
pasta = create.empty.pasta.list(), # data.frame
pasta.mails = create.empty.pasta.list(), # data.frame
pasta.commits = create.empty.pasta.list(), # data.frame
## timestamps of mail, issue and commit data
data.timestamps = data.frame(start = numeric(0), end = numeric(0)), # data.frame
## custom timestamps for splitting
custom.event.timestamps = list(), # list
## * * commit filtering --------------------------------------------
#' Filter commits by potentially removing commits to untracked files or to the base artifact (see parameters).
#'
#' @param commits the data.frame of commits on which filtering will be applied
#' @param remove.untracked.files flag whether untracked files are kept or removed
#' @param remove.base.artifact flag whether the base artifact is kept or removed
#' @param filter.bots flag whether commits by bots should be removed
#'
#' @return the commits after all filters have been applied
filter.commits = function(commits, remove.untracked.files, remove.base.artifact, filter.bots) {
logging::logdebug("filter.commits: starting.")
## filter out the untracked files
if (remove.untracked.files) {
commits = subset(commits, file != UNTRACKED.FILE)
}
## filter out the base artifacts (i.e., Base_Feature, File_Level)
if (remove.base.artifact) {
commits = subset(commits, !(artifact %in% BASE.ARTIFACTS))
}
## filter out all commits made by bots
if (filter.bots) {
commits = self$filter.bots(commits)
}
logging::logdebug("filter.commits: finished.")
return(commits)
},
## * * issue filtering --------------------------------------------
#' Filter issue by potentially removing all issue events that are not comments.
#'
#' @param issues the data.frame of issues on which filtering will be applied
#' @param issues.only.comments flag whether non-comment issue events are removed
#' @param filter.bots flag whether bot issues are to be removed
#'
#' @return the issues after all filters have been applied
filter.issues = function(issues, issues.only.comments, filter.bots) {
logging::logdebug("filter.issues: starting.")
if (issues.only.comments) {
issues = issues[issues[["event.name"]] == "commented", ]
}
## filter out all issues made by bots
if (filter.bots) {
issues = self$filter.bots(issues)
}
logging::logdebug("filter.issues: finished.")
return(issues)
},
## * * mail filtering ----------------------------------------------
#' Filter patchstack mails from the mails that are currently cached in the field \code{mails} and return them.
#' Store detected patchstacks in the field \code{patchstack.mails}. They are used later in the
#' function \code{filter.pasta.data} to also accommodate for the deleted mails in the PaStA data.
#'
#' In a thread, a patchstack spans the first sequence of mails where each mail has been authored by the thread
#' creator and has been sent within a short time window (see \code{PATCHSTACK.MAIL.DECAY.THRESHOLD}) after the
#' preceding mail.
#' The mails spanned by a patchstack are called 'patchstack mails'.
#'
#' For each patchstack, all patchstack mails but the first one are filtered.
#'
#' @return the mail data after filtering patchstack mails
filter.patchstack.mails = function() {
logging::logdebug("filter.patchstack.mails: starting.")
## return immediately if no mails are available
if (!self$is.data.source.cached("mails.unfiltered")) {
private$mails.patchstacks = NULL
return(private$mails)
}
## retrieve mails grouped by thread IDs
thread.data = self$group.authors.by.data.column("mails", "thread")
## extract the patchstack mails and the filtered mails for each thread
result = parallel::mclapply(thread.data, function(thread) {
## ensure that all mails within the thread are ordered correctly
thread = thread[order(thread[["date"]]), ]
running = TRUE
i = 1
## find the largest index 'i' for which holds that each mail up to index 'i' has been authored by the
## thread creator and that all mails up to index 'i' have been received within a succesive time window
## of 'PATCHSTACK.MAIL.DECAY.THRESHOLD'
while (i < nrow(thread) && running) {
if (thread[1, "author.name"] == thread[i + 1, "author.name"] &&
thread[i + 1, "date"] - thread[i, "date"] <= PATCHSTACK.MAIL.DECAY.THRESHOLD) {
i = i + 1
} else {
running = FALSE
}
}
## return the mails of the thread with all patchstack mails but the first one being removed
return(list(keep = thread[setdiff(seq_len(nrow(thread)), seq_len(i)[-1]), ],
patchstack = thread[seq_len(i), ]))
})
## override thread data with filtered thread data
thread.data = lapply(result, function(x) x[["keep"]])
## flatten the list of mail-dataframes (i.e. thread.data) to a single mail-dataframe
mails = plyr::rbind.fill(thread.data)
## Retrieve patchstacks from the result above which are used to manipulate the PaStA data. This needs to be
## done because the PaStA data relates to some of the filtered mails and must be adjusted accordingly.
patchstacks = lapply(result, function(x) x[["patchstack"]])
## only patchstacks that contain at least two mails are considered patchstacks
patchstacks = patchstacks[lapply(patchstacks, nrow) > 1]
## store patchstack information
private$mails.patchstacks = patchstacks
logging::logdebug("filter.patchstack.mails: finished.")
return(mails)
},
#' Filter mail data by for example removing all mails that have been sent by bots.
#'
#' @param mails the data.frame of mails on which filtering will be applied
#' @param filter.bots flag whether bot mails are to be removed
#'
#' @return the mails after all filters have been applied
filter.mails = function(mails, filter.bots) {
logging::logdebug("filter.mails: starting.")
## filter out all mails made by bots
if (filter.bots) {
mails = self$filter.bots(mails)
}
logging::logdebug("filter.mails: finished.")
return(mails)
},
## * * commit message data ------------------------------------------
#' Add the columns \code{title} and \code{message} to commits using the selected
#' configuration option of \code{commit.messages} and the results of the function \code{get.commit.messages}.
update.commit.message.data = function() {
logging::loginfo("Merging commit messages into commit data.")
if (self$is.data.source.cached("commits.unfiltered")) {
## remove the columns that are present in case that the parameter was changed to from "messages" to
## "none" or "title"
private$commits.unfiltered = private$commits.unfiltered[ , colnames(private$commits.unfiltered) != "message"]
private$commits.unfiltered = private$commits.unfiltered[ , colnames(private$commits.unfiltered) != "title"]
## when 'none' is selected, we are ready here, else merge the possibly new data to the cleaned commits
if (private$project.conf$get.value("commit.messages") != "none") {
## get commit messages
commit.messages = private$commit.messages
## now there are only three columns left: commit.id, title, message
## check whether to include only title or also the messages
if (private$project.conf$get.value("commit.messages") == "title") {
commit.messages = commit.messages[ , colnames(commit.messages) != "message"]
}
## get a vector with the column names in the right order
col.names = unique(c(colnames(private$commits.unfiltered), colnames(commit.messages)))
## merge them into the commit data
private$commits.unfiltered = merge(private$commits.unfiltered, commit.messages,
by = c("commit.id", "hash"), all.x = TRUE, sort = FALSE)
## adjust the column order
private$commits.unfiltered = private$commits.unfiltered[col.names]
}
}
if (self$is.data.source.cached("commits")) {
## remove the columns that are present in case that the parameter was changed to from "messages" to
## "none" or "title"
private$commits = private$commits[ , colnames(private$commits) != "message"]
private$commits = private$commits[ , colnames(private$commits) != "title"]
## when 'none' is selected, we are ready here, else merge the possibly new data to the cleaned commits
if (private$project.conf$get.value("commit.messages") != "none") {
## get commit messages
commit.messages = private$commit.messages
## now there are only three columns left: commit.id, title, message
## check whether to include only title or also the messages
if (private$project.conf$get.value("commit.messages") == "title") {
commit.messages = commit.messages[ , colnames(commit.messages) != "message"]
}
## get a vector with the column names in the right order
col.names = unique(c(colnames(private$commits), colnames(commit.messages)))
## merge them into the commit data
private$commits = merge(private$commits, commit.messages,
by = c("commit.id", "hash"), all.x = TRUE, sort = FALSE)
## adjust the column order
private$commits = private$commits[col.names]
}
}
## get the caller function as a string
stacktrace = get.stacktrace(sys.calls())
caller = get.second.last.element(stacktrace)
## only print warning if this function has not been called by 'cleanup.commit.message.data' including the
## case that it is called manually, i.e. the stack is too short.
if (is.na(caller) || paste(caller, collapse = " ") != "cleanup.commit.message.data()") {
logging::logwarn("There might be commit message data that does not appear in the commit data.
To clean this up you can call the function 'cleanup.commit.message.data()'.")
}
},
## * * Commit Interaction data --------------------------------------------------
#' Update the commit-interactions
#'
#' This method should be called whenever the field \code{commit.interactions} is changed.
update.commit.interactions = function() {
if (self$is.data.source.cached("commit.interactions")) {
## check if caller was 'set.commits'. If so, or if commits are already filtered,
## do not get the commits again.
stacktrace = get.stacktrace(sys.calls())
caller = get.second.last.element(stacktrace)
if (!self$is.data.source.cached("commits.unfiltered") &&
(is.na(caller) || paste(caller, collapse = " ") != "self$set.commits(commit.data)")) {
self$get.commits()
}
## remove existing columns named 'base.author' and 'interaction.author'
indices.to.remove = which("base.author" == colnames(private$commit.interactions))
if (length(indices.to.remove) > 0) {
private$commit.interactions = private$commit.interactions[, -indices.to.remove]
}
indices.to.remove = which("interacting.author" == colnames(private$commit.interactions))
if (length(indices.to.remove) > 0) {
private$commit.interactions = private$commit.interactions[, -indices.to.remove]
}
## get relevant data from commits
commit.data.subset = data.frame(hash = private$commits.unfiltered[["hash"]],
author.name = private$commits.unfiltered[["author.name"]])
commit.data.subset = commit.data.subset[!duplicated(commit.data.subset[["hash"]]),]
## merge commit interactions with commits and change colnames to avoid duplicates
commit.interaction.data = merge(private$commit.interactions, commit.data.subset,
by.x = "base.hash", by.y = "hash", all.x = TRUE)
author.index = match("author.name", colnames(commit.interaction.data))
colnames(commit.interaction.data)[[author.index]] = "base.author"
commit.interaction.data = merge(commit.interaction.data, commit.data.subset,
by.x = "commit.hash", by.y = "hash", all.x = TRUE)
author.index = match("author.name", colnames(commit.interaction.data))
colnames(commit.interaction.data)[[author.index]] = "interacting.author"
## warning if we have interactions without authors
if (anyNA(commit.interaction.data[["base.author"]]) ||
anyNA(commit.interaction.data[["interacting.author"]])) {
logging::logwarn("There are commits in the commit-interactions that are not in
the commit data, possibly due to incomplete commit data or deleted users.
This results in the commit-interactions having empty entries.
To clean up these entries, call cleanup.commit.interactions.")
}
private$commit.interactions = commit.interaction.data
}
},
## * * Gender data --------------------------------------------------
#' Update the gender related fields of: \code{authors}
#'
#' This method should be called whenever the field \code{gender} is changed.
update.gender.data = function() {
logging::logdebug("update.gender.data: starting.")
## update author data by attaching gender data
if (!is.null(private$authors)) {
## remove previous gender data
private$authors["gender"] = NULL
## merge gender data
private$authors = merge(private$authors, private$gender,
by = "author.name", all.x = TRUE, sort = FALSE)
}
logging::logdebug("update.gender.data: finished.")
},
## * * PaStA data --------------------------------------------------
#' Use the information about the deleted patchstack mails that are stored in the field \code{patchstack.mails}
#' to also filter out PaStA information that relates to the deleted mails.
#'
#' The PaStA information is not discarded completely however but instead is gathered for each patchstack and is
#' assigned to the first mail in each patchstack because this very first mail has not been filtered and
#' represents the patchstack.
#'
#' @return the filtered PaStA data
filter.pasta.data = function() {
logging::logdebug("filter.pasta.data: starting.")
new.pasta = parallel::mclapply(private$mails.patchstacks, function(patchstack) {
## get all PaStA data that relates to the current patchstack (do not drop data.frame structure!)
pasta.tmp = private$pasta[private$pasta[["message.id"]] %in% patchstack[["message.id"]], , drop = FALSE]
## override all old message IDs with the message ID of the first mail in the patchstack since it
## is the only one that is kept (if any data is available in 'pasta.tmp')
if (nrow(pasta.tmp) > 0) {
pasta.tmp["message.id"] = patchstack[1, "message.id"]
}
return(pasta.tmp)
})
## combine new re-written PaStA data
new.pasta = plyr::rbind.fill(new.pasta)
## remove potential duplicates
new.pasta = unique(new.pasta)
## remove old items from PaStA data
## 1) flatten the list of mail-dataframes (i.e. patchstacks) to a single mail-dataframe
patchstack.mails = plyr::rbind.fill(private$mails.patchstacks)
## 2) delete any PaStA information that relate to message IDs of mails that will be discarded
pasta = private$pasta[!(private$pasta[["message.id"]] %in% patchstack.mails[["message.id"]]), ]
## append the new pasta data to the old pasta data
pasta = plyr::rbind.fill(pasta, new.pasta)
## reestablish ordering using the 'revision.set.id' column of the PaStA data
pasta = pasta[order(pasta[["revision.set.id"]]), ]
logging::logdebug("filter.pasta.data: finished.")
return(pasta)
},
#' Aggregate PaStA data for convenient merging to main data sources.
#'
#' In detail, the given PaStA data is independently aggregated by both the
#' columns \code{commit.hash} and \code{message.id}. The resulting data.frames
#' are stored in the fields \code{pasta.commits} and \code{pasta.mails},
#' respectively.
#'
#' **Note**: The column \code{commit.hash} gets renamed to \code{hash} to match
#' the corresponding column in the commit data (see \code{read.commits}).
aggregate.pasta.data = function() {
logging::logdebug("aggregate.pasta.data: starting.")
## check for data first
if (!self$is.data.source.cached("pasta")) {
## take (empty) input data and no rows from it
private$pasta.mails = create.empty.pasta.list()
private$pasta.commits = create.empty.pasta.list()
} else {
## compute aggregated data.frames for easier merging
## 1) define group function (determines result in aggregated data.frame cells)
group.fun = unname # unique
## 2) aggregate by message ID
group.col = "message.id"
private$pasta.mails = aggregate(
as.formula(sprintf(". ~ %s", group.col)), private$pasta,
group.fun, na.action = na.pass
)
## 3) aggregate by commit hash
group.col = "commit.hash"
private$pasta.commits = aggregate(
as.formula(sprintf(". ~ %s", group.col)), private$pasta,
group.fun, na.action = na.pass
)
}
## set column names consistent to main data
colnames(private$pasta.mails) = c("message.id", "pasta", "revision.set.id")
colnames(private$pasta.commits) = c("hash", "pasta", "revision.set.id")
logging::logdebug("aggregate.pasta.data: finished.")
},
#' Update the PaStA-related columns \code{pasta} and \code{revision.set.id} that are appended to \code{commits}
#' using the currently available PaStA data from the field \code{pasta.commits}.
update.pasta.commit.data = function() {
logging::logdebug("update.pasta.commit.data: starting.")
## remove previous PaStA data
private$commits.unfiltered["pasta"] = NULL
private$commits.unfiltered["revision.set.id"] = NULL
## only merge new data if pasta has been configured (it could also be changed to 'FALSE' in which case
## we want to just remove the columns above)
if (private$project.conf$get.value("pasta")) {
## merge PaStA data
private$commits.unfiltered = merge(private$commits.unfiltered, private$pasta.commits,
by = "hash", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$commits.unfiltered = private$commits.unfiltered[order(private$commits.unfiltered[["date"]], decreasing = FALSE), ]
## remove duplicated revision set ids
private$commits.unfiltered[["revision.set.id"]] = lapply(private$commits.unfiltered[["revision.set.id"]], function(rev.id) {
return(unique(rev.id))
})
}
## remove previous PaStA data
private$commits["pasta"] = NULL
private$commits["revision.set.id"] = NULL
## only merge new data if pasta has been configured (it could also be changed to 'FALSE' in which case
## we want to just remove the columns above)
if (private$project.conf$get.value("pasta")) {
## merge PaStA data
private$commits = merge(private$commits, private$pasta.commits,
by = "hash", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$commits = private$commits[order(private$commits[["date"]], decreasing = FALSE), ]
## remove duplicated revision set ids
private$commits[["revision.set.id"]] = lapply(private$commits[["revision.set.id"]], function(rev.id) {
return(unique(rev.id))
})
}
logging::logdebug("update.pasta.commit.data: finished.")
},
#' Update the PaStA-related columns \code{pasta} and \code{revision.set.id} that are appended to \code{mails}
#' using the currently available PaStA data from the field \code{pasta.mails}.
update.pasta.mail.data = function() {
logging::logdebug("update.pasta.mail.data: starting.")
## remove previous PaStA data
private$mails.unfiltered["pasta"] = NULL
private$mails.unfiltered["revision.set.id"] = NULL
## only merge new data if pasta has been configured (it could also be changed to 'FALSE' in which case
## we want to just remove the columns above)
if (private$project.conf$get.value("pasta")) {
## merge PaStA data
private$mails.unfiltered = merge(private$mails.unfiltered, private$pasta.mails,
by = "message.id", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$mails.unfiltered = private$mails.unfiltered[order(private$mails.unfiltered[["date"]],
decreasing = FALSE), ]
## remove duplicated revision set ids
private$mails.unfiltered[["revision.set.id"]] = lapply(private$mails.unfiltered[["revision.set.id"]],
function(rev.id) {
return(unique(rev.id))
})
}
## remove previous PaStA data
private$mails["pasta"] = NULL
private$mails["revision.set.id"] = NULL
## only merge new data if pasta has been configured (it could also be changed to 'FALSE' in which case
## we want to just remove the columns above)
if (private$project.conf$get.value("pasta")) {
## merge PaStA data
private$mails = merge(private$mails, private$pasta.mails,
by = "message.id", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$mails = private$mails[order(private$mails[["date"]], decreasing = FALSE), ]
## remove duplicated revision set ids
private$mails[["revision.set.id"]] = lapply(private$mails[["revision.set.id"]], function(rev.id) {
return(unique(rev.id))
})
}
logging::logdebug("update.pasta.mail.data: finished.")
},
#' Recompute the values of the cached fields \code{pasta.mails} and \code{pasta.commits} using the currrently
#' available PaStA information of the field \code{pasta} and also assign/update this PaStA information to
#' \code{mails} and \code{commits}.
#'
#' This method should be called whenever the field \code{pasta} is changed.
update.pasta.data = function() {
logging::logdebug("update.pasta.data: starting.")
## filter patchstack mails from PaStA data if configured
if (private$project.conf$get.value("mails.filter.patchstack.mails")) {
private$pasta = private$filter.pasta.data()
}
## aggregate by message IDs and commit hashes
private$aggregate.pasta.data()
## update mail data by attaching PaStA data
private$update.pasta.mail.data()
## update commit data by attaching PaStA data
private$update.pasta.commit.data()
## get the caller function as a string
stacktrace = get.stacktrace(sys.calls())
caller = get.second.last.element(stacktrace)
## only print warning if this function has not been called by 'cleanup.pasta.data' including the case
## that it is called manually, i.e. the stack is too short.
if (all(is.na(caller)) || paste(caller, collapse = " ") != "cleanup.pasta.data()") {
logging::logwarn("There might be PaStA data that does not appear in the mail or commit data.
To clean this up you can call the function 'cleanup.pasta.data()'.")
}
logging::logdebug("update.pasta.data: finished.")
},
## * * synchronicity data ------------------------------------------
#' Update the column \code{synchronicity} that is appended to commits using the currently available
#' synchronicity data from the field \code{synchronicity}.
#'
#' This method should be called whenever the field \code{synchronicity} is changed.
update.synchronicity.data = function() {
logging::logdebug("update.synchronicity.data: starting.")
## update commit data by attaching synchronicity data
## do not check whether synchronicity is available in order to remove the columns if it is not
## remove previous synchronicity data
private$commits.unfiltered["synchronicity"] = NULL
## only merge new data if synchronicity has been configured (it could also be changed to 'FALSE' in
## which case we want to just remove the columns above)
if (private$project.conf$get.value("synchronicity")) {
## merge synchronicity data
private$commits.unfiltered = merge(private$commits.unfiltered, private$synchronicity,
by = "hash", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$commits.unfiltered = private$commits.unfiltered[order(private$commits.unfiltered[["date"]],
decreasing = FALSE), ]
}
## remove previous synchronicity data
private$commits["synchronicity"] = NULL
## only merge new data if synchronicity has been configured (it could also be changed to 'FALSE' in
## which case we want to just remove the columns above)
if (private$project.conf$get.value("synchronicity")) {
## merge synchronicity data
private$commits = merge(private$commits, private$synchronicity,
by = "hash", all.x = TRUE, sort = FALSE)
## sort by date again because 'merge' disturbs the order
private$commits = private$commits[order(private$commits[["date"]], decreasing = FALSE), ]
}
## get the caller function as a string
stacktrace = get.stacktrace(sys.calls())
caller = get.second.last.element(stacktrace)
## only print warning if this function has not been called by 'cleanup.synchronicity.data' including the
## case that it is called manually, i.e. the stack is too short.
if (all(is.na(caller)) || paste(caller, collapse = " ") != "cleanup.synchronicity.data()") {
logging::logwarn("There might be synchronicity data that does not appear in the commit data.
To clean this up you can call the function 'cleanup.synchronicity.data()'.")
}
logging::logdebug("update.synchronicity.data: finished.")
},
## * * timestamps --------------------------------------------------
#' Call the getters of the specified data sources in order to
#' initialize the sources and extract the timestamps.
#'
#' @param data.sources the data sources to be prepared
prepare.timestamps = function(data.sources) {
for (source in data.sources) {
self[[ DATASOURCE.TO.UNFILTERED.ARTIFACT.FUNCTION[[source]] ]]()
}
},
#' Extract the earliest and the latest date from the specified data source
#' and store it to the timestamps data.frame.
#'
#' @param name the name the timestamps are registered as
#' @param source the specified data source
extract.timestamps = function(name, source) {
## initialize data structure for timestamp
if (is.null(private$data.timestamps)) {
## let this stay as a sanity-check; this is actually initialized this way when creating the object
private$data.timestamps = data.frame(start = numeric(0), end = numeric(0))
}
## collect minimum and maximum date for data source
## 1) if we have data available
if (nrow(private[[source]]) > 0) {
source.date.min = min(private[[source]][, "date"])
source.date.max = max(private[[source]][, "date"])
}
## NAs otherwise
else {
source.date.min = as.POSIXct(NA)
source.date.max = as.POSIXct(NA)
}
## remove old line if existing
private$data.timestamps = subset(
private$data.timestamps,
!(rownames(private$data.timestamps) == name)
)
## store the data in the timestamp data set
private$data.timestamps = rbind(
private$data.timestamps,
data.frame(
start = source.date.min,
end = source.date.max,
row.names = name
)
)
}
),
## * public ------------------------------------------------------------
public = list(
#' The constructor of the class.
#'
#' @param project.conf the given \code{ProjectConf} object for this instance of the class
initialize = function(project.conf) {
## check arguments
private$project.conf = verify.argument.for.parameter(project.conf, "ProjectConf", "ProjectData$new")
## if we have a direct subclass of ProjectData here,
## log this accordingly
if (class(self)[1] == "ProjectData") {
logging::loginfo("Initialized data object %s", self$get.class.name())
}
},
## * * printing ----------------------------------------------------
#' The toString method of the class.
get.class.name = function() {
return(
sprintf("ProjectData<%s>", private$project.conf$get.value("repo"))
)
},
## * * resetting environment ---------------------------------------
#' Reset the current environment in order to rebuild it.
#' Has to be called whenever the project configuration or data gets
#' changed.
reset.environment = function() {
private$authors = create.empty.authors.list()
private$commits.unfiltered = create.empty.commits.list()
private$commits = create.empty.commits.list()
private$commit.messages = create.empty.commit.message.list()
private$data.timestamps = data.frame(start = numeric(0), end = numeric(0))
private$issues = create.empty.issues.list()
private$issues.unfiltered = create.empty.issues.list()
private$mails.unfiltered = create.empty.mails.list()
private$mails = create.empty.mails.list()
private$mails.patchstacks = list()
private$pasta = create.empty.pasta.list()
private$pasta.mails = create.empty.pasta.list()
private$pasta.commits = create.empty.pasta.list()
private$gender = create.empty.gender.list()
private$synchronicity = create.empty.synchronicity.list()
private$commit.interactions = create.empty.commit.interaction.list()
},
## * * configuration -----------------------------------------------
#' Get the current project configuration.
#'
#' @return the \code{ProjectConf} object of the current instance of the class
get.project.conf = function() {
return(private$project.conf)
},
#' Set the current project configuration to the given one.
#'
#' @param project.conf the new project configuration.
#' @param reset.environment parameter to determine whether the environment
#' has to be reset or not [default: FALSE]
set.project.conf = function(project.conf, reset.environment = FALSE) {
private$project.conf = verify.argument.for.parameter(project.conf, "ProjectConf",
"ProjectData$set.project.conf")
if (reset.environment) {
self$reset.environment()
}
},
#' Get a value of the project configuration.
#'
#' @return the value of the given entry name
get.project.conf.entry = function(entry) {
return(private$project.conf$get.value(entry))
},
#' Set a value of the project configuration and, in some cases (i.e. when the parameters allow it)
#' resets the environment.
#'
#' @param entry the configuration option to set. The environment will not be reset, if and only if the entry to
#' change affects a parameter controlling whether or not to read additional data sources, that is,
#' if the parameter is one of the elements of the vector \code{CONF.PARAMETERS.NO.RESET.ENVIRONMENT}.
#' @param value the new value that is assigned to the configuration parameter
set.project.conf.entry = function(entry, value) {
private$project.conf$update.value(entry, value)
## only reset the environment when the 'entry' parameter is not one of the keys where it should not be reset
if (!(entry %in% CONF.PARAMETERS.NO.RESET.ENVIRONMENT)) {
self$reset.environment()
} else {
## if the 'commit.messages' parameter has been changed, update the commit message data, since we want to
## merge the data again if the parameter e.g. changed from "title" to "messages" or vice versa
if (entry == "commit.messages") {
private$update.commit.message.data()
}
## if the 'pasta' parameter has been changed, update the pasta data, since we want to
## merge the data again if the parameter changed
if (entry == "pasta") {
private$update.pasta.data()
}
## if the 'synchronicity' or 'synchronicity.time.window' parameter has been changed, update the
## synchronicity data, since we want to merge the data again if the parameter changed
if (entry == "synchronicity" || entry == "synchronicity.time.window") {
## re-read synchronicity data if the time window is changed and the data is cached because the
## change invalidates the cache
if (entry == "synchronicity.time.window" && self$is.data.source.cached("synchronicity")) {
self$set.synchronicity(NULL)
self$get.synchronicity()
} else {
private$update.synchronicity.data()
}
}
## if the 'custom.event.timestamps.file' parameter has changed, we want to clear them to trigger a re-read.
if (entry == "custom.event.timestamps.file") {
self$clear.custom.event.timestamps()
}
}
},
#' Update the project configuration based on the given list
#' of values and, in some cases (i.e. when the parameters allow it), reset the environment afterwards.
#'
#' @param updated.values the new values for the project configuration.
#' If at least one of the configuration parameters is not an element of the vector
#' \code{CONF.PARAMETERS.NO.RESET.ENVIRONMENT}, the environment will be reset.
#' [default: list()]
update.project.conf = function(updated.values = list()) {
private$project.conf$update.values(updated.values = updated.values)
## get the names of the parameters that are updated and a logical vector indicating whether the
## parameters cause a reset or not
params = names(updated.values)
params.keep.environment = params %in% CONF.PARAMETERS.NO.RESET.ENVIRONMENT
## only reset if at least one of them should cause a reset
if (!all(params.keep.environment)) {
self$reset.environment()
} else {
## if the 'commit.messages' parameter has been changed, update the commit message data, since we want to
## merge the data again if the parameter e.g. changed from "title" to "messages" or vice versa
if (c("commit.messages") %in% params) {
private$update.commit.message.data()
}
## if the 'pasta' parameter has been changed, update the pasta data, since we want to
## merge the data again if the parameter changed
if (c("pasta") %in% params) {
private$update.pasta.data()
}
## if the 'synchronicity' or 'synchronicity.time.window' parameter has been changed, update the
## synchronicity data, since we want to merge the data again if the parameter changed
if (c("synchronicity") %in% params || c("synchronicity.time.window") %in% params) {
## re-read synchronicity data if the time window is changed and the data is cached because the
## change invalidates the cache
if (c("synchronicity.time.window") %in% params && self$is.data.source.cached("synchronicity")) {
self$set.synchronicity(NULL)
self$get.synchronicity()
} else {
private$update.synchronicity.data()
}
}
## if the 'custom.event.timestamps.file' parameter has changed, we want to clear them to trigger a re-read.
if (c("custom.event.timestamps.file") %in% params) {
self$clear.custom.event.timestamps()
}
}
},
## * * backups -----------------------------------------------------
#' Backup the current environment to a file on the disk.
#'
#' @param file the path to the backup file
save.to.disk = function(file) {
save(self, file = file)
},