def __init__(self):
# Load the configuration for the filters
try:
filter_list_from_config = Config.filters()
except Exception as e:
log("ERROR", "Filter configuration error: " + str(e))
sys.exit() # Configuration errors should prevent execution
# Create (and empty if needed) base filter path
self.filter_base_dir = os.path.join(Config.get('Saved_Log_Dir'),
'temp_filter_processing')
if os.path.isdir(self.filter_base_dir):
shutil.rmtree(self.filter_base_dir)
# Create staging (all original files go here) and final (all filtered files end up here) directories
os.makedirs(os.path.join(self.filter_base_dir, 'staging'),
exist_ok=True)
os.makedirs(os.path.join(self.filter_base_dir, 'final'), exist_ok=True)
# Build the filter instance list
for filter_from_config in filter_list_from_config:
self.instance_list.append(
FilterInstance(filter_from_config.get("name"),
filter_from_config.get("exe"),
filter_from_config.get("type"),
filter_from_config.get("timeout"),
self.filter_base_dir))
log(
"INFO",
str(len(filter_list_from_config)) +
" valid filters have been found")
def cleanup(self):
# Executes when there are no more jobs
if self.status is True:
log("ERROR", "Filter cleanup when filters are still running")
# Delete all temp filter input/output folders
# (which should be empty unless there was an error in a filter's termination)
try:
shutil.rmtree(self.filter_base_dir)
except OSError as e:
log(
"ERROR",
"When deleting the temporary filter processing folder, encountered an error: "
+ str(e))
def needs_update(self, job):
# Checks if a job exists in the database and if it needs updating
cur = self.conn.cursor()
# Do directory/file names need to be sanitized?
cur.execute(
"SELECT FrontendUsername, InstanceName, FileSize FROM file_index WHERE JobID='{}' and EntryName='{}'".format(
job["job_id"], job["entry_name"]))
response = cur.fetchone()
if response is None:
# Does not exist in db
return True
else:
# Does exist in db
if response[0] != job["frontend_user"] or response[1] != job["instance_name"]:
log("ERROR", "Duplicate job found for either another Frontend Username or an Instance Name")
return TabError
elif int(job["err_file_size"] + job["out_file_size"]) > int(response[2]):
# File size is greater, therefore update the job
return True
else:
# Already added without a file size difference
return False
def main():
# Parse command line arguments (if any)
parser = argparse.ArgumentParser(
description=
"GlideinMonitor's indexing script for GlideIn .out & .err files")
parser.add_argument('-c', help="Path to Config File")
parser.add_argument('-f',
help="Ignore the lock file and force an index anyway",
action='store_true')
args = parser.parse_args()
# Process config file
Config.init(args.c)
# Check for index job lock
lock_location = os.path.join(Config.get('Saved_Log_Dir'), "index_lock")
if not pathlib.Path(lock_location).exists():
try:
os.mkdir(Config.get('Saved_Log_Dir'))
log("INFO", "Creating new directory for index_lock")
except FileExistsError:
pass
pathlib.Path(lock_location).touch()
else:
# Job index already running/did not complete
if not args.f:
log("ERROR", "Lock file present in saved log directory")
return
# Connect to the database
db = Database()
# Get list of job data that should be indexed
job_index_list = determine_indexing(db)
# Archive the original files
archive_files(db, job_index_list)
# Indexing & filtering complete
db.commit()
log("INFO", "Indexing Complete")
# Delete the lock file
os.remove(pathlib.Path(lock_location))
def begin_indexing(args):
# Check for index job lock
lock_location = os.path.join(Config.get('Saved_Log_Dir'), "index_lock")
if not pathlib.Path(lock_location).exists():
pathlib.Path(lock_location).touch()
else:
# Job index already running/did not complete
if not args.f:
log("ERROR", "Lock file present in saved log directory")
return
# Entry point for indexing
db = Database()
jobs_updated = 0
saved_dir_name = Config.get('Saved_Log_Dir')
datetime_name = datetime.datetime.now().strftime("%Y-%m-%d")
log("INFO", "Begin Indexing")
# Get a dictionary of jobs from the GWMS_Log_Dir directory
tree = directory_jobs(Config.get('GWMS_Log_Dir'))
log("INFO", "Directory Listing Completion")
# Iterate through each job checking the database if it needs to be updated
for job_name, job_data in tree.items():
# Skip entries that are missing an err/out file
if "err_file_path" not in job_data or "out_file_path" not in job_data:
log(
"INFO", "Missing ERR/OUT file for entry - jobID: " +
job_data["entry_name"] + " - " + str(job_data["job_id"]))
continue
# Check if the current instance is in the database, if not then add it
final_dir_name = os.path.join(saved_dir_name,
job_data["instance_name"],
job_data["frontend_user"], datetime_name)
if db.needs_update(job_data):
# Create the directory if it does not exist
if not os.path.exists(final_dir_name):
os.makedirs(final_dir_name)
# Check if the file has certain logs within it
found_logs = {
"MasterLog": False,
"StartdLog": False,
"StarterLog": False,
"StartdHistoryLog": False,
"glidein_activity": False
}
if job_data['err_file_size'] != 0:
with open(job_data["err_file_path"], 'rb',
0) as file, mmap.mmap(file.fileno(),
0,
access=mmap.ACCESS_READ) as s:
if s.find(b'MasterLog\n========') != -1:
found_logs["MasterLog"] = True
if s.find(b'StartdLog\n========') != -1:
found_logs["StartdLog"] = True
if s.find(b'StarterLog\n========') != -1:
found_logs["StarterLog"] = True
if s.find(b'StartdHistoryLog\n========') != -1:
found_logs["StartdHistoryLog"] = True
if s.find(
b'=== Encoded XML description of glidein activity ==='
) != -1:
found_logs["glidein_activity"] = True
# Tar the output and error file
curr_job_path = os.path.join(
final_dir_name, job_name[0] + "_" + job_name[1] + "_" +
job_name[2] + ".tar.gz")
with tarfile.open(curr_job_path, "w:gz") as tar:
tar.add(job_data["out_file_path"],
arcname=os.path.basename(job_data["out_file_path"]))
tar.add(job_data["err_file_path"],
arcname=os.path.basename(job_data["err_file_path"]))
tar.close()
# Add/Update it in the database
db.add_job(job_data, curr_job_path, found_logs)
# Job added/updated
jobs_updated += 1
# Indexing complete
db.commit()
# Delete the lock file
os.remove(pathlib.Path(lock_location))
log("INFO", "Jobs added/updated " + str(jobs_updated))
log("INFO", "Indexing Complete")
def filter_runner(base_directory, instance_list, job_queue, messageQueue):
# Variables within runner
master_jobs_list = {}
unpacked_expectations = {}
staging_dir = os.path.join(base_directory, 'staging')
final_dir = os.path.join(base_directory, 'final')
timeout_stepper = 0
timeout_start = None
completion_check = False
# The thread runner method, runs until cleanup method
while len(instance_list) != 0:
# Check for messages
for i in range(0, messageQueue.qsize()):
# Get the message
the_message = messageQueue.get()
# Check for timeout
if the_message == 'TIMEOUT_START':
# Timeout received
timeout_start = time.time()
# Should this pass check for completion
if timeout_start:
completion_check = True
# Process any new jobs
for i in range(0, job_queue.qsize()):
# Get the next job passed from the indexer
completion_check = False
next_job = job_queue.get()
# Generate a unique ID for the job
job_uuid = str(uuid.uuid1())
while job_uuid in master_jobs_list:
job_uuid = uuid.uuid1()
# Add it to the list (used at the end to build the archive
# (Archive path, .out file name, .err file name)
master_jobs_list[job_uuid] = (
next_job[0],
os.path.basename(next_job[1]["out_file_path"]),
os.path.basename(next_job[1]["err_file_path"]))
# New job, move all files to the staging directory
shutil.copyfile(next_job[1]['err_file_path'],
os.path.join(staging_dir, job_uuid + '.err'))
shutil.copyfile(next_job[1]['out_file_path'],
os.path.join(staging_dir, job_uuid + '.out'))
# Go through each filter from the top**, moving files as necessary
for i in range(len(instance_list)):
# Check for new files and move/convert if needed depending on the type
if i == 0:
# Check the staging directory if it's on the first filter
if instance_list[i].type == 'whole':
new_files = Filter.move_files(
staging_dir, instance_list[i].input_directory)
else:
new_files, updating_expectations = Filter.type_moving(
staging_dir, instance_list[i].input_directory,
instance_list[i].type, unpacked_expectations)
unpacked_expectations.update(updating_expectations)
else:
if instance_list[i].type == instance_list[i - 1].type:
new_files = Filter.move_files(
instance_list[i - 1].output_directory,
instance_list[i].input_directory)
else:
new_files, updating_expectations = Filter.type_moving(
instance_list[i - 1].output_directory,
instance_list[i].input_directory,
instance_list[i].type, unpacked_expectations)
unpacked_expectations.update(updating_expectations)
# If it didn't move any files, check if there are any files still in the input directory
if not new_files:
new_files = Filter.dir_empty_check(
instance_list[i].input_directory)
# Start the filter executable if not already running only if there are new files
if new_files:
completion_check = False
# Timeout check
if timeout_start is not None and timeout_stepper == i:
# The timeout has already started and current waiting on this filter
# Check if it needs to stop this filter
curr_filter_timeout = instance_list[i].exe_timeout
if time.time(
) - timeout_start > curr_filter_timeout != 0:
# Stopping this process if needed and deleting files from it's input directory
print("Timeout reached")
instance_list[i].exe_subprocess.terminate()
for root, dirs, files in os.walk(
instance_list[i].input_directory):
for f in files:
os.remove(os.path.join(root, f))
log(
"ERROR", "Filter \"" + instance_list[i].name +
"\" timeout reached")
if instance_list[i].exe_subprocess is None or instance_list[
i].exe_subprocess.poll() is not None:
# If the filter did run, check the return code
if instance_list[i].exe_subprocess is not None:
# Get the return code
return_code_from_filter_exe = instance_list[
i].exe_subprocess.poll()
# Check if the return code signals a failure
if return_code_from_filter_exe != 0:
# The filter exe errored out, submit the error to the log and terminate filters running
log(
"ERROR",
"The filter \"" + instance_list[i].name +
"\" encountered a return code of: " +
str(return_code_from_filter_exe) +
"\nTherefore the filters have been terminated, no filter archive created."
)
return
# Start the exe of the filter instance with the appropriate arguments
instance_list[i].exe_subprocess = subprocess.Popen([
instance_list[i].exe_full_path, "-i",
instance_list[i].input_directory, "-o",
instance_list[i].output_directory
])
else:
# Check if the timeout was waiting on this filter
if timeout_start is not None and timeout_stepper == i:
# It was waiting on this filter, and it finished processing files - move to the next filter
timeout_stepper += 1
timeout_start = time.time()
# Check the last filter's output folder and move any files to the final directory
if instance_list[len(instance_list) - 1].type == 'whole':
new_files = Filter.move_files(
instance_list[len(instance_list) - 1].output_directory,
final_dir)
else:
new_files, updating_expectations = new_files = Filter.type_moving(
instance_list[len(instance_list) - 1].output_directory,
final_dir, 'whole', unpacked_expectations)
unpacked_expectations.update(updating_expectations)
if new_files:
# New files, package them if both the .err and .out available
# Currently, jobs getting to the beginning of the filtering stage will have both .err and .out
# List all files in the final directory
final_dir_files = [
file for file in os.listdir(final_dir)
if os.path.isfile(os.path.join(final_dir, file))
]
final_dir_jobs = []
# Create a list containing complete jobs
for file in final_dir_files:
# Get the current file's uuid and extension
job_uuid, curr_ext = os.path.splitext(file)
# Check if the file's job has already been added
if job_uuid in final_dir_jobs:
continue
# Get the other job extension (if the current file is a .out, the other is .err and vice versa)
other_ext = '.out'
if curr_ext == '.out':
other_ext = '.err'
# Check if the other file is in the folder
if job_uuid + other_ext in final_dir_files:
# By far, the most efficient way to program this - Thomas Hein, programmer of the year here
final_dir_jobs.append(job_uuid)
# For all complete jobs, archive them
for completed_job_uuid in final_dir_jobs:
# Save the original immediately
with tarfile.open(master_jobs_list[completed_job_uuid][0],
"w:gz") as tar:
tar.add(os.path.join(final_dir,
completed_job_uuid + ".out"),
arcname=os.path.basename(
master_jobs_list[completed_job_uuid][1]))
tar.add(os.path.join(final_dir,
completed_job_uuid + ".err"),
arcname=os.path.basename(
master_jobs_list[completed_job_uuid][2]))
tar.close()
# Then delete the .out and .err files
os.remove(
os.path.join(final_dir, completed_job_uuid + ".out"))
os.remove(
os.path.join(final_dir, completed_job_uuid + ".err"))
# Check if filtering is complete
if completion_check:
log("INFO", "Filtering Complete")
return
# Thread sleep before checking again
time.sleep(0.5)
def determine_indexing(db):
# Entry point for indexing
jobs_updated = 0
log("INFO", "Begin Indexing")
# Get a dictionary of jobs from the GWMS_Log_Dir directory
tree = directory_jobs(Config.get('GWMS_Log_Dir'))
log("INFO", "Directory Listing Completion")
# List to be exported
job_index_list = []
# Iterate through each job checking the database if it needs to be updated
for job_name, job_data in tree.items():
# Skip entries that are missing an '.err'/'.out'. file
if "err_file_path" not in job_data or "out_file_path" not in job_data:
log(
"INFO", "Missing ERR/OUT file for entry - jobID: " +
job_data["entry_name"] + " - " + str(job_data["job_id"]))
continue
if db.needs_update(job_data):
# Check if the file has certain logs within it
found_logs = {
"MasterLog": False,
"StartdLog": False,
"StarterLog": False,
"StartdHistoryLog": False,
"glidein_activity": False
}
if job_data['err_file_size'] != 0:
with open(job_data["err_file_path"], 'rb',
0) as file, mmap.mmap(file.fileno(),
0,
access=mmap.ACCESS_READ) as s:
if s.find(b'MasterLog\n========') != -1:
found_logs["MasterLog"] = True
if s.find(b'StartdLog\n========') != -1:
found_logs["StartdLog"] = True
if s.find(b'StarterLog\n========') != -1:
found_logs["StarterLog"] = True
if s.find(b'StartdHistoryLog\n========') != -1:
found_logs["StartdHistoryLog"] = True
if s.find(
b'=== Encoded XML description of glidein activity ==='
) != -1:
found_logs["glidein_activity"] = True
# Add found logs into the job data
job_data.update(found_logs)
# Add the job to list to be indexed
job_index_list.append(job_data)
# Job added/updated
jobs_updated += 1
log("INFO", "Jobs to be added/updated " + str(jobs_updated))
return job_index_list
def __init__(self):
# Connect to SQLite unless specified otherwise in the config file
if Config.db("type") == "sqlite":
# SQLite Database
try:
os.mkdir(Config.db("dir"))
log("INFO", "Creating new directory for SQLite DB")
except FileExistsError:
pass
self.conn = sqlite3.connect(os.path.join(Config.db("dir"), "%s.sqlite" % Config.db("db_name")))
# Check if index table exists
db_cursor = self.conn.cursor()
db_cursor.execute("SELECT name FROM sqlite_master WHERE type='table' AND name='file_index';")
if db_cursor.fetchone() is None:
# It doesn't, create it
log("INFO", "Creating new SQLite database")
script_file = open(os.path.join(os.path.dirname(os.path.realpath(__file__)), "sqliteTableCreation.sql"),
'r')
script = script_file.read()
script_file.close()
db_cursor.executescript(script)
elif Config.db("type") == "mysql":
# MySQL Database
if not MYSQL_AVAILABLE:
log("ERROR", "MySQL database selected but there is no MySQL connector")
raise ImportError("Module not found: mysql.connector")
try:
self.conn = mysql.connector.connect(
host=Config.db("host"),
user=Config.db("user"),
passwd=Config.db("pass"),
database=Config.db("db_name")
)
mycursor = self.conn.cursor()
except mysql.connector.errors.ProgrammingError:
# Create the database
log("INFO", "Creating new MySQL Database")
mydb = mysql.connector.connect(
host=Config.db("host"),
user=Config.db("user"),
passwd=Config.db("pass")
)
mycursor = mydb.cursor()
mycursor.execute("CREATE DATABASE " + Config.db("db_name"))
self.conn = mysql.connector.connect(
host=Config.db("host"),
user=Config.db("user"),
passwd=Config.db("pass"),
database=Config.db("db_name")
)
mycursor = self.conn.cursor()
# Check if the table exists
mycursor.execute("SHOW TABLES")
if ('file_index',) not in mycursor:
# Create table
log("INFO", "Creating MySQL File Index table")
script_file = open(os.path.join(os.path.dirname(os.path.realpath(__file__)), "mysqlTableCreation.sql"),
'r')
script = script_file.read()
script_file.close()
mycursor.execute(script)
else:
log("ERROR", "No valid database selected (%s)" % Config.db("type"))
raise ImportError("Invalid ")
