Audit DB Tables

R/app_server.R

@@ -44,6 +44,9 @@ app_server <- function(input, output, session) {
 
 
   observeEvent(res_auth$user, {
+    dbUpdate("DELETE FROM _variables")
+    dbUpdate("INSERT INTO _variables (user) VALUES ({res_auth$user})")
+
     req(res_auth$admin == TRUE | "weight_adjust" %in% approved_roles[[res_auth$role]])
 
       appendTab("apptabs",

R/mod_decision_automation.R

@@ -542,7 +542,8 @@ mod_decision_automation_server <- function(id, user, approved_roles){
       req("auto_decision_adjust" %in% approved_roles[[user$role]])
 
       out_lst <- purrr::compact(reactiveValuesToList(auto_decision))
-      dbUpdate("UPDATE decision_categories SET lower_limit = NULL, upper_limit = NULL")
+      null_lst <- setdiff(names(auto_decision_update()), names(out_lst))
+      purrr::walk(null_lst, ~ dbUpdate("UPDATE decision_categories SET lower_limit = NULL, upper_limit = NULL WHERE decision = {.x}"))
       purrr::iwalk(out_lst, ~ dbUpdate("UPDATE decision_categories SET lower_limit = {.x[1]}, upper_limit = {.x[2]} WHERE decision = {.y}"))
       auto_decision_update(out_lst)
 
@@ -574,10 +575,10 @@ mod_decision_automation_server <- function(id, user, approved_roles){
         decision_lst %>%
         purrr::map_chr(~ input[[glue::glue("{risk_lbl(.x, input = FALSE)}_col")]]) %>%
         purrr::set_names(decision_lst)
-      purrr::iwalk(selected_colors, ~ {
+      purrr::iwalk(selected_colors, ~ if (!.x %in% color_current()[.y]) {
         dbUpdate("UPDATE decision_categories SET color = {.x} WHERE decision = {.y}")
         shinyjs::runjs(glue::glue("document.documentElement.style.setProperty('--{risk_lbl(.y, input = FALSE)}-color', '{.x}');"))
-        })
+      })
       loggit::loggit("INFO", glue::glue("The decision category display colors were modified by {user$name} ({user$role})"))
       color_current(selected_colors)
 

R/mod_decision_automation_utils.R

@@ -13,6 +13,7 @@ assign_decisions <- function(decision_list, package) {
   decision <- paste0(names(decision_list)[purrr::map_lgl(decision_list, ~ .x[1] < score && score <= .x[2])], "")
   decision_id <- dbSelect("SELECT id FROM decision_categories WHERE decision = {decision}")
   if (decision != "") {
+    dbUpdate("INSERT INTO _variables (user) VALUES ('SYSTEM')")
     dbUpdate("UPDATE package SET decision_id = {decision_id},
                         decision_by = 'Auto Assigned', decision_date = {Sys.Date()}
                          WHERE name = {package}")
@@ -23,6 +24,7 @@ assign_decisions <- function(decision_list, package) {
       "INSERT INTO comments
           VALUES ({package}, 'Auto Assigned', 'admin',
           {comment}, 'o', {getTimeStamp()})")
+    dbUpdate("DELETE FROM _variables WHERE id IN (SELECT id FROM _variables ORDER BY id DESC LIMIT 1)")
   }
 
   return(decision)

R/utils_startup.R

@@ -22,10 +22,10 @@ create_db <- function(db_name){
 
   # Queries needed to run the first time the db is created.
   queries <- c(
+    "create_variable_table.sql",
     "create_decision_table.sql",
     "create_package_table.sql",
     "create_metric_table.sql",
-    "initialize_metric_table.sql",
     "create_package_metrics_table.sql",
     "create_community_usage_metrics_table.sql",
     "create_comments_table.sql"
@@ -34,13 +34,17 @@ create_db <- function(db_name){
   # Append path to the queries.
   queries <- file.path(path, queries)
 
+  queries <- purrr::map(queries, ~ scan(.x, sep = "\n", what = "character", blank.lines.skip = FALSE, quiet = TRUE) %>%
+                          {split(.[nzchar(.)], cumsum(!nzchar(.))[nzchar(.)])} %>%
+                          purrr::map(~ paste(.x, collapse = " "))) %>% 
+    unlist()
   # Apply each query.
   sapply(queries, function(x){
 
     tryCatch({
       rs <- DBI::dbSendStatement(
         con,
-        paste(scan(x, sep = "\n", what = "character"), collapse = ""))
+        x)
     }, error = function(err) {
       message <- paste("dbSendStatement",err)
       message(message, .loggit = FALSE)

inst/sql_queries/create_comments_table.sql

@@ -5,4 +5,70 @@ CREATE TABLE IF NOT EXISTS comments (
    comment 		 CHAR,
    comment_type CHAR,
    added_on 	 DATE
-);
+);
+
+CREATE TABLE IF NOT EXISTS comments_audit_log (
+   id             INTEGER PRIMARY KEY AUTOINCREMENT,
+   comment_id     CHAR NOT NULL, 
+   old_row_data   JSON,
+   new_row_data   JSON,
+   dml_type       CHAR NOT NULL,
+   dml_timestamp  DATETIME DEFAULT UTC_TIMESTAMP,
+   dml_created_by CHAR
+);
+
+CREATE TRIGGER comments_update_audit_trigger
+AFTER UPDATE ON comments FOR EACH ROW
+BEGIN
+  INSERT INTO comments_audit_log (
+    comment_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    NEW.id,
+    JSON_OBJECT(
+      "user_name", OLD.user_name,
+      "user_role", OLD.user_role,
+      "comment", OLD.comment,
+      "comment_type", OLD.comment_type,
+      "added_on", OLD.added_on
+    ),
+    JSON_OBJECT(
+      "user_name", NEW.user_name,
+      "user_role", NEW.user_role,
+      "comment", NEW.comment,
+      "comment_type", NEW.comment_type,
+      "added_on", NEW.added_on
+    ),
+    'UPDATE',
+    (SELECT user FROM _variables LIMIT 1)
+  );
+END
+
+CREATE TRIGGER comments_delete_audit_trigger
+AFTER DELETE ON comments FOR EACH ROW
+BEGIN
+  INSERT INTO comments_audit_log (
+    comment_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    OLD.id,
+    JSON_OBJECT(
+      "user_name", OLD.user_name,
+      "user_role", OLD.user_role,
+      "comment", OLD.comment,
+      "comment_type", OLD.comment_type,
+      "added_on", OLD.added_on
+    ),
+    NULL,
+    'DELETE',
+    (SELECT user FROM _variables LIMIT 1)
+  );
+END

inst/sql_queries/create_decision_table.sql

@@ -4,4 +4,43 @@ CREATE TABLE IF NOT EXISTS decision_categories (
    color        CHAR,
    lower_limit 	DECIMAL(3, 2) NULL,
    upper_limit 	DECIMAL(3, 2) NULL
-);
+);
+
+CREATE TABLE IF NOT EXISTS decision_categories_audit_log (
+   id                     INTEGER PRIMARY KEY AUTOINCREMENT,
+   decision_categories_id INTEGER NOT NULL,
+   old_row_data           JSON,
+   new_row_data           JSON,
+   dml_type               CHAR NOT NULL,
+   dml_timestamp          DATETIME DEFAULT UTC_TIMESTAMP,
+   dml_created_by         CHAR
+);
+
+CREATE TRIGGER decision_categories_update_audit_trigger
+AFTER UPDATE ON decision_categories FOR EACH ROW
+BEGIN
+  INSERT INTO decision_categories_audit_log (
+    decision_categories_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    NEW.id,
+    JSON_OBJECT(
+      "decision", OLD.decision,
+      "color", OLD.color,
+      "lower_limit", OLD.lower_limit,
+      "upper_limit", OLD.upper_limit
+    ),
+    JSON_OBJECT(
+      "decision", NEW.decision,
+      "color", NEW.color,
+      "lower_limit", NEW.lower_limit,
+      "upper_limit", NEW.upper_limit
+    ),
+    'UPDATE',
+    (SELECT user FROM _variables ORDER BY id DESC LIMIT 1)
+  );
+END

inst/sql_queries/create_metric_table.sql

@@ -7,4 +7,53 @@ CREATE TABLE IF NOT EXISTS metric (
    description  CHAR,
    class        CHAR,    /* class = maintenance or test */
    weight       REAL
-);
+);
+
+INSERT INTO metric 
+  (name, long_name, description, is_perc, is_url, class, weight)
+VALUES 
+  ('has_vignettes',       'Vignettes',         'Number of vignettes',              0, 0, 'maintenance', 1),
+  ('has_news',            'NEWS file',         'Number of NEWS files',             0, 0, 'maintenance', 1),
+  ('news_current',        'NEWS current',      'NEWS contains current version',    0, 0, 'maintenance', 1),
+  ('has_bug_reports_url', 'Report Bugs',       'URL to report bugs exists',    0, 0, 'maintenance', 1),
+  ('has_website',         'Website',           'Package public website',           0, 1, 'maintenance', 1),
+  ('has_maintainer',      'Maintainer',        'Package maintainers',              0, 0, 'maintenance', 1),
+  ('has_source_control',  'Source Control',    'Package source control url',       0, 1, 'maintenance', 1),
+  ('export_help',         'Documentation',     '% of documented objects',          1, 0, 'maintenance', 1),
+  ('bugs_status',         'Bugs Closure Rate', '% of the last 30 bugs closed',     1, 0, 'maintenance', 1),
+  ('license',             'License',           "Package's license",                0, 0, 'maintenance', 1),
+  ('covr_coverage',       'Test Coverage',     '% of objects tested',     1, 0, 'maintenance', 1),
+  ('downloads_1yr',       'Downloads',         'Number of package downloads in the last year', 0, 0, 'community', 1)
+;
+
+CREATE TABLE IF NOT EXISTS metric_audit_log (
+   id             INTEGER PRIMARY KEY AUTOINCREMENT,
+   metric_id      INTEGER NOT NULL,
+   metric_name    CHAR,
+   old_weight     REAL,
+   new_weight     REAL,
+   dml_type       CHAR NOT NULL,
+   dml_timestamp  DATETIME DEFAULT UTC_TIMESTAMP,
+   dml_created_by CHAR
+);
+
+CREATE TRIGGER metric_update_audit_trigger
+AFTER UPDATE ON metric FOR EACH ROW
+BEGIN
+  INSERT INTO metric_audit_log (
+    metric_id,
+    metric_name,
+    old_weight,
+    new_weight,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    NEW.id,
+    NEW.name,
+    OLD.weight,
+    NEW.weight,
+    'UPDATE',
+    (SELECT user FROM _variables ORDER BY id DESC LIMIT 1)
+  );
+END

inst/sql_queries/create_package_metrics_table.sql

@@ -8,4 +8,95 @@ CREATE TABLE IF NOT EXISTS package_metrics (
    encode       BLOB,
    FOREIGN KEY (package_id) REFERENCES package(id),
    FOREIGN KEY (metric_id) REFERENCES metric(id)
-);
+);
+
+CREATE TABLE IF NOT EXISTS package_metrics_audit_log (
+   id                 INTEGER PRIMARY KEY AUTOINCREMENT,
+   package_metrics_id INTEGER NOT NULL,
+   old_row_data       JSON,
+   new_row_data       JSON,
+   dml_type           CHAR NOT NULL,
+   dml_timestamp      DATETIME DEFAULT UTC_TIMESTAMP,
+   dml_created_by     CHAR
+);
+
+CREATE TRIGGER package_metrics_insert_audit_trigger
+AFTER INSERT ON package_metrics FOR EACH ROW
+BEGIN
+  INSERT INTO package_metrics_audit_log (
+    package_metrics_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    NEW.id,
+    NULL,
+    JSON_OBJECT(
+      "package_id", NEW.package_id,
+      "package_name", (SELECT name FROM package WHERE id = NEW.package_id LIMIT 1),
+      "metric_id", NEW.metric_id,
+      "metric_name", (SELECT name FROM metric WHERE id = NEW.metric_id LIMIT 1),
+      "value", NEW.value
+    ),
+    'INSERT',
+    (SELECT user FROM _variables ORDER BY id DESC LIMIT 1)
+  );
+END
+
+CREATE TRIGGER package_metrics_update_audit_trigger
+AFTER UPDATE ON package_metrics FOR EACH ROW
+BEGIN
+  INSERT INTO package_metrics_audit_log (
+    package_metrics_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    NEW.id,
+    JSON_OBJECT(
+      "package_id", OLD.package_id,
+      "package_name", (SELECT name FROM package WHERE id = OLD.package_id LIMIT 1),
+      "metric_id", OLD.metric_id,
+      "metric_name", (SELECT name FROM metric WHERE id = OLD.metric_id LIMIT 1),
+      "value", OLD.value
+    ),
+    JSON_OBJECT(
+      "package_id", NEW.package_id,
+      "package_name", (SELECT name FROM package WHERE id = NEW.package_id LIMIT 1),
+      "metric_id", NEW.metric_id,
+      "metric_name", (SELECT name FROM metric WHERE id = NEW.metric_id LIMIT 1),
+      "value", NEW.value
+    ),
+    'UPDATE',
+    (SELECT user FROM _variables ORDER BY id DESC LIMIT 1)
+  );
+END
+
+CREATE TRIGGER package_metrics_delete_audit_trigger
+AFTER DELETE ON package_metrics FOR EACH ROW
+BEGIN
+  INSERT INTO package_metrics_audit_log (
+    package_metrics_id,
+    old_row_data,
+    new_row_data,
+    dml_type,
+    dml_created_by
+  )
+  VALUES(
+    OLD.id,
+    JSON_OBJECT(
+      "package_id", OLD.package_id,
+      "package_name", (SELECT name FROM package WHERE id = OLD.package_id LIMIT 1),
+      "metric_id", OLD.metric_id,
+      "metric_name", (SELECT name FROM metric WHERE id = OLD.metric_id LIMIT 1),
+      "value", OLD.value
+    ),
+    NULL,
+    'DELETE',
+    (SELECT user FROM _variables ORDER BY id DESC LIMIT 1)
+  );
+END