def verify_paths(params):
"""verify paths exist as either relational or absolute paths, modifying them if necessary"""
# under one shot mode, only care about 1 result file
if params.one_shot:
if not os.path.isfile(params.result_file):
print(params.task_dir, " one_shot result file does not exist")
return
# normally want to check each run in the directory
if os.path.isdir(params.task_dir):
walk_runs(params, check_result_exists)
else:
print(params.task_dir, " directory does not exist")
def update_db(params, db):
# check if table for task exists; if not then create it
task_table_name = params.task_table_name
create_table(params, db, task_table_name)
# load up latest run and parsed date for task
def check_last_runs_table(runs):
natural_sort(runs)
cursor = db.cursor()
cursor.execute("SELECT MAX({}), MAX({}) FROM {}".format(
"parsed_date", "run", params.task_table_name))
row = cursor.fetchone()
if row[0]:
# storing in database truncates decimal, so add 1 second
last_parsed_date = row[0] + 1
last_run = row[1]
print("last parsed date", last_parsed_date)
print("last run", last_run)
params.last_parsed_date = last_parsed_date
params.last_run = last_run
else:
print("first population")
params.last_run = 0
# else first run, nothing in table yet
def add_run_to_db(params, run):
run_number = get_trailing_num(run)
resfilename = get_result_file(params, params.run_prefix, run_number)
try:
parsed_date = os.path.getmtime(resfilename)
# throw away unless newer than latest or run number greater than maximum
if parsed_date <= params.last_parsed_date and run_number <= params.last_run:
return
except OSError:
print("file {} not found; skipping".format(resfilename))
return
params.last_run += 1
print("run {} added ({}) ({})".format(run_number, params.last_run,
parsed_date))
with open(resfilename, 'r') as res:
# make sure table is compatible with run data by inserting any new columns
# always called "run" in table (converted from whatever prefix users use)
result_params = ["run", "parsed_date"]
result_params.extend(res.readline().split('\t'))
if result_params[-1] == '\n':
result_params.pop()
result_params = [
"".join(('\"', p.strip(), '\"')) for p in result_params
]
pre_sample_pos = res.tell()
result_params_sample = res.readline().split('\t')
# go back to presample location for normal line iteration
res.seek(pre_sample_pos, os.SEEK_SET)
# add new column to table
for c in range(len(result_params)):
if result_params[c] not in params.tracked_columns:
print("ADDING {} as new column".format(result_params[c]))
add_column_to_table(
params, db, result_params[c], result_params_sample[
c - 2]) # -2 accounts for run and parsed date
# add value rows
rows_to_add = []
for line in res:
# run number and parsed_date are always recorded
result_params_val = [params.last_run, parsed_date]
result_params_val.extend(line.split('\t'))
if result_params_val[-1] == '\n':
result_params_val.pop()
# something must be wrong here
if len(result_params_val) > len(result_params):
print(
"There are {} values for only {} parameters in run {}; \
skipping run".format(len(result_params_val),
len(result_params), run_number))
# skip this run
params.last_run -= 1
return
# for when the last column value is the empty string
while len(result_params_val) < len(result_params):
result_params_val.append('')
rows_to_add.append(
tuple(
convert_strictest(param) if param != nullval else None
for param in result_params_val))
param_placeholders = ("?," * len(result_params)).rstrip(',')
# specify columns to insert into since ordering of columns in file may not match table
insert_rows_command = "INSERT OR IGNORE INTO {} ({}) VALUES ({})".format(
params.task_table_name, ','.join(result_params),
param_placeholders)
cursor = db.cursor()
cursor.executemany(insert_rows_command, rows_to_add)
walk_runs(params, add_run_to_db, check_last_runs_table)
db.commit()
def verify_paths(params):
"""verify paths exist as either relational or absolute paths, modifying them if necessary"""
if os.path.isdir(params.task_dir):
walk_runs(params, check_result_exists)
else:
print(params.task_dir, " directory does not exist")
def update_db(params, db):
# check if table for task exists; if not then create it
task_table_name = params.task_table_name
create_table(params, db, task_table_name)
# verify that the max runs in the task_dir is >= to the max runs in the database
def check_runs_match_table(runs):
natural_sort(runs)
highest_run = get_trailing_num(runs[-1])
cursor = db.cursor()
cursor.execute("SELECT MAX({}) FROM {}".format(params.run_prefix, params.task_table_name))
row = cursor.fetchone()
if row[0]:
if highest_run < row[0]:
print("stored run ({}) is higher than existing run ({}); \
consider running with --clean to remake task table".format(row[0], highest_run))
# else first run, nothing in table yet
def add_run_to_db(params, run):
resfilename = get_result_file(params, run)
run_number = get_trailing_num(run)
try:
parsed_date = os.path.getmtime(resfilename)
except OSError:
print("file {} not found; skipping".format(resfilename))
return
with open(resfilename, 'r') as res:
# make sure table is compatible with run data by inserting any new columns
# always called "run" in table (converted from whatever prefix users use)
result_params = ["run", "parsed_date"]
result_params.extend(res.readline().split('\t'))
if result_params[-1] == '\n':
result_params.pop()
result_params = ["".join(('\"',p.strip(),'\"')) for p in result_params]
pre_sample_pos = res.tell()
result_params_sample = res.readline().split('\t')
# go back to presample location for normal line iteration
res.seek(pre_sample_pos, os.SEEK_SET)
# add new column to table
for c in range(len(result_params)):
if result_params[c] not in params.tracked_columns:
print("ADDING {} as new column".format(result_params[c]))
add_column_to_table(params, db, result_params[c], result_params_sample[c-2]) # -2 accounts for run and parsed date
# add value rows
rows_to_add = []
for line in res:
# run number and parsed_date are always recorded
result_params_val = [run_number, parsed_date]
result_params_val.extend(line.split('\t'))
if result_params_val[-1] == '\n':
result_params_val.pop()
# something must be wrong here
if len(result_params_val) > len(result_params):
print("There are {} values for only {} parameters in run {}; \
skipping run".format(len(result_params_val), len(result_params), run_number))
# skip this run
return
# for when the last column value is the empty string
while len(result_params_val) < len(result_params):
result_params_val.append('')
rows_to_add.append(tuple(convert_strictest(param) if param != nullval else None for param in result_params_val))
param_placeholders = ("?,"*len(result_params)).rstrip(',')
# specify columns to insert into since ordering of columns in file may not match table
insert_rows_command = "INSERT OR IGNORE INTO {} ({}) VALUES ({})".format(
params.task_table_name,
','.join(result_params),
param_placeholders)
cursor = db.cursor()
cursor.executemany(insert_rows_command, rows_to_add)
walk_runs(params, add_run_to_db, check_runs_match_table)
db.commit()
def verify_paths(params):
"""verify paths exist as either relational or absolute paths, modifying them if necessary"""
if os.path.isdir(params.task_dir):
walk_runs(params, check_result_exists)
else:
print(params.task_dir, " directory does not exist")
def update_db(params, db):
# check if table for task exists; if not then create it
create_table(params, db)
# load up latest run and parsed date for task
def check_last_runs_table(runs):
natural_sort(runs)
cursor = db.cursor()
cursor.execute("SELECT MAX({}), MAX({}) FROM {}".format("parsed_date", "run", params.task_table_name))
row = cursor.fetchone()
if row[0]:
# storing in database truncates decimal, so add 1 second
last_parsed_date = row[0] + 1
last_run = row[1]
print("last parsed date", last_parsed_date)
print("last run", last_run)
params.last_parsed_date = last_parsed_date
params.last_run = last_run
else:
print("first population")
params.last_run = 0
# else first run, nothing in table yet
def add_run_to_db(params, run):
resfilename = get_result_file(params, run)
run_number = get_trailing_num(run)
try:
parsed_date = os.path.getmtime(resfilename)
# throw away unless newer than latest or run number greater than maximum
if parsed_date <= params.last_parsed_date and run_number <= params.last_run:
return
except OSError:
print("file {} not found; skipping".format(resfilename))
return
params.last_run += 1
print("run {} added ({}) ({})".format(run_number, params.last_run, parsed_date))
with open(resfilename, 'rb') as res:
# make sure table is compatible with run data by inserting any new columns
# always called "run" in table (converted from whatever prefix users use)
csvreader = csv.reader(res, delimiter=params.delimiter)
result_params = ["run", "parsed_date"]
result_params.extend(csvreader.next())
empty_end = False
if not result_params[-1]: # empty or None
empty_end = True
result_params.pop()
result_params = ["".join(('\"',p.strip(),'\"')) for p in result_params]
print(result_params)
result_params_sample = [params.last_run, parsed_date]
result_params_sample.extend(csvreader.next())
if empty_end:
result_params_sample.pop()
while len(result_params_sample) < len(result_params):
result_params_sample.append('')
# add new column to table
for c in range(len(result_params)):
if result_params[c] not in params.tracked_columns:
print("ADDING {} as new column".format(result_params[c]))
add_column_to_table(params, db, result_params[c], result_params_sample[c])
# add value rows
rows_to_add = [tuple(convert_strictest(param) if param != nullval else None for param in result_params_sample)]
for line in csvreader:
# run number and parsed_date are always recorded
result_params_val = [params.last_run, parsed_date]
result_params_val.extend(line)
if empty_end:
result_params_val.pop()
# something must be wrong here
if len(result_params_val) > len(result_params):
print("There are {} values for only {} parameters in run {}; \
skipping run".format(len(result_params_val), len(result_params), run_number))
# skip this run
params.last_run -= 1
return
# for padding when columns have unequal depth
while len(result_params_val) < len(result_params):
result_params_val.append('')
rows_to_add.append(tuple(convert_strictest(param) if param != nullval else None for param in result_params_val))
print("rows to add")
print(rows_to_add)
param_placeholders = ("?,"*len(result_params)).rstrip(',')
# specify columns to insert into since ordering of columns in file may not match table
insert_rows_command = "INSERT OR IGNORE INTO {} ({}) VALUES ({})".format(
params.task_table_name,
','.join(result_params),
param_placeholders)
cursor = db.cursor()
cursor.executemany(insert_rows_command, rows_to_add)
walk_runs(params, add_run_to_db, check_last_runs_table)
db.commit()
