preparing for data load tomorrow

cleaning_scripts/get_weekly_commit_counts.R

@@ -5,41 +5,145 @@ library(dplyr)
 library(lubridate)
 
 #for a given file we want to get the count data and produce a csv
-test_file <- "/gscratch/comdata/users/mjilg/program_testing/core_2012-01-01_to_2014-12-31.csv"
+readme_pub_info <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/13125_test_README_publication_commits.csv"
-test_dir <- "/gscratch/comdata/users/mjilg/program_testing/"
+contributing_pub_info <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/13125_test_CONTRIBUTING_publication_commits.csv"
+readme_dir <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/main_commit_data/readme/"
+contributing_dir <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/main_commit_data/contributing/"
 
-transform_commit_data <- function(filepath){
+test_file <- "/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/main_commit_data/contributing/_voxpupuli_beaker_commits.csv"
+
+transform_commit_data <- function(filepath, ref_df){
+  #basic, loading in the file 
   df = read.csv(filepath, header = TRUE) 
+  temp_df <- df
   dir_path = dirname(filepath)
   file_name = basename(filepath)
   
-  # transform the rows of commit data to weekly count data
+  # isolate project id
-  project_name <- sub("_[0-9]{4}-[0-9]{2}-[0-9]{2}_to_[0-9]{4}-[0-9]{2}-[0-9]{2}.csv$", "", file_name)
+  project_id <- sub("_commits\\.csv$", "", file_name)
+  project_id <- sub("^_", "", project_id)
   
+  #make sure the dates are formatted correctly and state the project_id
   df <- df |>
     mutate(commit_date = ymd_hms(commit_date)) |>
-    mutate(project_name = project_name)
+    mutate(project_id = project_id)
   
+  #find the publication entry, in the specified df
+  matched_entry <- ref_df |>
+    filter(repo_id == project_id)
+  commit_date <- as.Date(matched_entry$commit_date)
+  
+  #get information about project age either in the "present" 
+  #or at the time of first commit
+  oldest_commit_date <- min(as.Date(df$commit_date))
+  project_age <- as.numeric(as.Date("2024-06-24") - oldest_commit_date)
+  age_at_commit <- as.numeric(commit_date - oldest_commit_date)
+  
+  #add that to the data 
+  df <- df |> 
+    mutate(age = project_age,
+           age_at_commit = age_at_commit)
+  
+  #we are looking at weekly data, 6m before and 6m after
+  start_date <- commit_date %m-% months(6)
+  end_date <- commit_date %m+% months(6)
+  introduction_week <- floor_date(commit_date, "week")
+  
+  #filler for when there are weeks without commits
+  all_weeks <- seq.Date(floor_date(start_date, "week"), floor_date(end_date, "week"), by = "week")
+  complete_weeks_df <- expand.grid(week = all_weeks, 
+                                   project_id = project_id,
+                                   age = project_age,
+                                   age_at_commit = age_at_commit)
+  
+  #add a column with the floored week
+  df <- df |>
+    mutate(week = floor_date(commit_date, "week"))
+  
+  #for each week, get the list of unique authors that committed
+  cumulative_authors <- df %>%
+    arrange(week) %>%
+    group_by(week) %>%
+    summarize(cumulative_author_emails = list(unique(author_email)), .groups = 'drop')
+  #same for each committer
+  cumulative_committers <- df %>%
+    arrange(week) %>%
+    group_by(week) %>%
+    summarize(cumulative_committer_emails = list(unique(committer_email)), .groups = 'drop')
+  
+  #now cut out the commit data that we don't care about 
+  df <- df |>
+    filter(as.Date(commit_date) >= start_date & as.Date(commit_date) <= end_date)
+  
+  #in order:
+  # - we group by project, week, ages
+  # - and we summarize commit and authorship details
+  # - we then fill in information for missingness
+  # - and add in vars for before/after
+  # - and weekly index
   weekly_commits <- df |>
-    mutate(week = floor_date(commit_date, "week")) |>
+    group_by(project_id, week, age, age_at_commit) |>
-    group_by(week, project_name) |>
+    summarise(commit_count = n(),
-    summarise(commit_count = n(), .groups = 'drop')
+              author_emails = list(unique(author_email)),
+              committer_emails = list(unique(committer_email)),
+              .groups = 'drop') |>
+    right_join(complete_weeks_df, by=c("week", "project_id", "age", "age_at_commit")) |>
+    replace_na(list(commit_count = 0)) |>
+    mutate(before_after = if_else(week < floor_date(commit_date, "week"), 0, 1)) |>
+    mutate(week_index = as.integer(difftime(week,
+                                            introduction_week, 
+                                            units = "weeks"))) 
+  # then, to get the authorship details in
+  # we check if the email data is present, if not we fill in blank 
+  # we bring in the information about authorship lists that we already had 
+  # then comparing the current week's author list with the previous week's cumulative list, or empty
+  #  ---- the length of that difference is the 'new' value
+  # then we delete out the author list information
+  weekly_with_authorship <- weekly_commits |>
+    mutate(
+      author_emails = ifelse(is.na(author_emails), list(character()), author_emails),
+      committer_emails = ifelse(is.na(committer_emails), list(character()), committer_emails)
+    ) |>
+    left_join(cumulative_authors, by = "week") |>
+    left_join(cumulative_committers, by = "week") |>
+    mutate(new_author_emails = mapply(function(x, y) length(setdiff(x, y)), author_emails, lag(cumulative_author_emails, default = list(character(1)))),
+           new_committer_emails = mapply(function(x, y) length(setdiff(x, y)), committer_emails, lag(cumulative_committer_emails, default = list(character(1))))) |>
+    select(-author_emails, -committer_emails, -cumulative_author_emails, -cumulative_committer_emails)
   
-  #prepare to save the new, transformed file
+  #gracefully exit
-  count_path <- file.path(dir_path, "weekly_counts")
+  return(weekly_with_authorship)
-  count_file_name <- paste0("weeklycount_", file_name)
-  output_file_path <- file.path(count_path, count_file_name)
-  #save and gracefully exit
-  write.csv(weekly_commits, output_file_path, row.names = FALSE)
-  return(weekly_commits)
 }
 
 #then for all files in a directory
-transform_directory_of_commit_data <- function(dir_path) {
+transform_directory_of_commit_data <- function(is_readme) {
+  ref_df <- read.csv(contributing_pub_info)
+  dir_path <- contributing_dir
+  if (is_readme){
+    ref_df <- read.csv(readme_pub_info)
+    dir_path <- readme_dir
+  }
+  counted_list <- list()
   file_list <- list.files(path = dir_path, pattern = "*.csv", full.names = TRUE)
   for (filepath in file_list) {
-    transform_commit_data(filepath)
+    transformed_data <- transform_commit_data(filepath, ref_df)
+    counted_list <- append(counted_list, list(transformed_data))
   }
+  counted_df <- bind_rows(counted_list)
+  
+  return(counted_df)
 }
 
-transform_directory_of_commit_data(test_dir)
+#below is for contributing file 
+test_big_df <- transform_directory_of_commit_data(is_readme=FALSE)
+output_filepath <-"/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/013125_weekly_count_CONTRIBUTING.csv"
+#below is for readme
+#test_big_df <- transform_directory_of_commit_data(is_readme=TRUE)
+#output_filepath <-"/mmfs1/gscratch/comdata/users/mjilg/govdoc-cr-data/13125_hyak_test/013125_weekly_count_README.csv"
+
+#validation testing 
+#length(unique(test_big_df$project_id))
+#filtered_df <- test_big_df %>%
+#  filter(commit_count != 0, new_author_emails == 0, new_committer_emails == 0)
+
+#another graceful exit
+#test_big_df.to_csv(output_filepath, index=False)

rstudio-server.job

@@ -3,7 +3,7 @@
 #SBATCH --job-name=mg-govdoc-cr
 #SBATCH --partition=cpu-g2-mem2x  #update this line - use hyakalloc to find partitions you can use
 
-#SBATCH --time=03:00:00
+#SBATCH --time=04:00:00
 #SBATCH --nodes=1
 #SBATCH --ntasks=4
 #SBATCH --mem=64G