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added standardised job creation

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This commit is contained in:
PatchOfScotland
2023-04-22 21:48:33 +02:00
parent f306d8b6f2
commit d3eb2dbf9f
15 changed files with 515 additions and 1281 deletions
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326
tests/test_recipes.py
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@ -1,38 +1,28 @@
import jsonschema
import os
import stat
import subprocess
import unittest
from multiprocessing import Pipe
from typing import Dict
from meow_base.core.meow import valid_job
from meow_base.core.vars import EVENT_TYPE, WATCHDOG_BASE, \
EVENT_RULE, EVENT_TYPE_WATCHDOG, EVENT_PATH, SHA256, WATCHDOG_HASH, \
JOB_ID, JOB_TYPE_PYTHON, JOB_PARAMETERS, PYTHON_FUNC, \
JOB_STATUS, META_FILE, JOB_ERROR, PARAMS_FILE, SWEEP_STOP, SWEEP_JUMP, \
SWEEP_START, JOB_TYPE_PAPERMILL, JOB_TYPE_BASH, \
get_base_file, get_job_file, get_result_file
JOB_PARAMETERS, JOB_FILE, META_FILE, SWEEP_STOP, SWEEP_JUMP, \
SWEEP_START
from meow_base.core.rule import Rule
from meow_base.functionality.file_io import lines_to_string, make_dir, \
read_yaml, write_file, write_notebook, write_yaml
from meow_base.functionality.file_io import read_yaml, write_notebook, \
threadsafe_read_status
from meow_base.functionality.hashing import get_hash
from meow_base.functionality.meow import create_job, create_rules, \
create_rule, create_watchdog_event
from meow_base.functionality.parameterisation import parameterize_bash_script
from meow_base.functionality.meow import create_rules, create_rule
from meow_base.patterns.file_event_pattern import FileEventPattern
from meow_base.recipes.bash_recipe import BashRecipe, BashHandler, \
assemble_bash_job_script
from meow_base.recipes.bash_recipe import BashRecipe, BashHandler
from meow_base.recipes.jupyter_notebook_recipe import JupyterNotebookRecipe, \
PapermillHandler, papermill_job_func, get_recipe_from_notebook
from meow_base.recipes.python_recipe import PythonRecipe, PythonHandler, \
python_job_func
PapermillHandler, get_recipe_from_notebook
from meow_base.recipes.python_recipe import PythonRecipe, PythonHandler
from shared import BAREBONES_PYTHON_SCRIPT, COMPLETE_PYTHON_SCRIPT, \
TEST_JOB_QUEUE, TEST_MONITOR_BASE, TEST_JOB_OUTPUT, BAREBONES_NOTEBOOK, \
APPENDING_NOTEBOOK, COMPLETE_NOTEBOOK, BAREBONES_BASH_SCRIPT, \
COMPLETE_BASH_SCRIPT, \
COMPLETE_NOTEBOOK, BAREBONES_BASH_SCRIPT, COMPLETE_BASH_SCRIPT, \
setup, teardown
class JupyterNotebookTests(unittest.TestCase):
@ -338,94 +328,6 @@ class PapermillHandlerTests(unittest.TestCase):
values.remove(val)
self.assertEqual(len(values), 0)
# Test jobFunc performs as expected
def testJobFunc(self)->None:
file_path = os.path.join(TEST_MONITOR_BASE, "test")
result_path = os.path.join(TEST_MONITOR_BASE, "output", "test")
with open(file_path, "w") as f:
f.write("Data")
file_hash = get_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"extra":"A line from a test Pattern",
"outfile":result_path
})
recipe = JupyterNotebookRecipe(
"recipe_one", APPENDING_NOTEBOOK)
rule = create_rule(pattern, recipe)
params_dict = {
"extra":"extra",
"infile":file_path,
"outfile":result_path
}
job_dict = create_job(
JOB_TYPE_PAPERMILL,
create_watchdog_event(
file_path,
rule,
TEST_MONITOR_BASE,
file_hash
),
extras={
JOB_PARAMETERS:params_dict,
PYTHON_FUNC:papermill_job_func
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_file = os.path.join(job_dir, META_FILE)
write_yaml(job_dict, meta_file)
param_file = os.path.join(job_dir, PARAMS_FILE)
write_yaml(params_dict, param_file)
base_file = os.path.join(job_dir, get_base_file(JOB_TYPE_PAPERMILL))
write_notebook(APPENDING_NOTEBOOK, base_file)
papermill_job_func(job_dir)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
self.assertTrue(os.path.exists(job_dir))
meta_path = os.path.join(job_dir, META_FILE)
self.assertTrue(os.path.exists(meta_path))
status = read_yaml(meta_path)
self.assertIsInstance(status, Dict)
self.assertIn(JOB_STATUS, status)
self.assertEqual(status[JOB_STATUS], job_dict[JOB_STATUS])
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_base_file(JOB_TYPE_PAPERMILL))))
self.assertTrue(os.path.exists(os.path.join(job_dir, PARAMS_FILE)))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_job_file(JOB_TYPE_PAPERMILL))))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_result_file(JOB_TYPE_PAPERMILL))))
self.assertTrue(os.path.exists(result_path))
# Test jobFunc doesn't execute with no args
def testJobFuncBadArgs(self)->None:
try:
papermill_job_func({})
except Exception:
pass
self.assertEqual(len(os.listdir(TEST_JOB_QUEUE)), 0)
self.assertEqual(len(os.listdir(TEST_JOB_OUTPUT)), 0)
# Test handling criteria function
def testValidHandleCriteria(self)->None:
ph = PapermillHandler()
@ -840,100 +742,6 @@ class PythonHandlerTests(unittest.TestCase):
values.remove(val)
self.assertEqual(len(values), 0)
# Test jobFunc performs as expected
def testJobFunc(self)->None:
file_path = os.path.join(TEST_MONITOR_BASE, "test")
result_path = os.path.join(TEST_MONITOR_BASE, "output")
with open(file_path, "w") as f:
f.write("250")
file_hash = get_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"extra":"A line from a test Pattern",
"outfile": result_path
})
recipe = PythonRecipe(
"recipe_one", COMPLETE_PYTHON_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"extra":"extra",
"infile":file_path,
"outfile": result_path
}
job_dict = create_job(
JOB_TYPE_PYTHON,
create_watchdog_event(
file_path,
rule,
TEST_MONITOR_BASE,
file_hash
),
extras={
JOB_PARAMETERS:params_dict,
PYTHON_FUNC:python_job_func
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_file = os.path.join(job_dir, META_FILE)
write_yaml(job_dict, meta_file)
param_file = os.path.join(job_dir, PARAMS_FILE)
write_yaml(params_dict, param_file)
base_file = os.path.join(job_dir, get_base_file(JOB_TYPE_PYTHON))
write_notebook(APPENDING_NOTEBOOK, base_file)
write_file(lines_to_string(COMPLETE_PYTHON_SCRIPT), base_file)
python_job_func(job_dir)
self.assertTrue(os.path.exists(job_dir))
meta_path = os.path.join(job_dir, META_FILE)
self.assertTrue(os.path.exists(meta_path))
status = read_yaml(meta_path)
self.assertIsInstance(status, Dict)
self.assertIn(JOB_STATUS, status)
self.assertEqual(status[JOB_STATUS], job_dict[JOB_STATUS])
self.assertNotIn(JOB_ERROR, status)
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_base_file(JOB_TYPE_PYTHON))))
self.assertTrue(os.path.exists(os.path.join(job_dir, PARAMS_FILE)))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_job_file(JOB_TYPE_PYTHON))))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_result_file(JOB_TYPE_PYTHON))))
self.assertTrue(os.path.exists(result_path))
with open(result_path, "r") as f:
result = f.read()
self.assertEqual(result, "124937.5")
# Test jobFunc doesn't execute with no args
def testJobFuncBadArgs(self)->None:
try:
python_job_func({})
except Exception:
pass
self.assertEqual(len(os.listdir(TEST_JOB_QUEUE)), 0)
self.assertEqual(len(os.listdir(TEST_JOB_OUTPUT)), 0)
# Test handling criteria function
def testValidHandleCriteria(self)->None:
ph = PythonHandler()
@ -1336,97 +1144,61 @@ class BashHandlerTests(unittest.TestCase):
values.remove(val)
self.assertEqual(len(values), 0)
# Test jobFunc performs as expected
def testJobFunc(self)->None:
file_path = os.path.join(TEST_MONITOR_BASE, "test")
result_path = os.path.join(TEST_MONITOR_BASE, "output")
def testJobSetup(self)->None:
from_handler_to_runner_reader, from_handler_to_runner_writer = Pipe()
bh = BashHandler(job_queue_dir=TEST_JOB_QUEUE)
bh.to_runner_job = from_handler_to_runner_writer
with open(os.path.join(TEST_MONITOR_BASE, "A"), "w") as f:
f.write("Data")
with open(file_path, "w") as f:
f.write("250")
file_hash = get_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"extra":"A line from a test Pattern",
"outfile": result_path
})
pattern_one = FileEventPattern(
"pattern_one", "A", "recipe_one", "file_one")
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"extra":"extra",
"infile":file_path,
"outfile": result_path
patterns = {
pattern_one.name: pattern_one,
}
recipes = {
recipe.name: recipe,
}
job_dict = create_job(
JOB_TYPE_BASH,
create_watchdog_event(
file_path,
rule,
TEST_MONITOR_BASE,
file_hash
),
extras={
JOB_PARAMETERS:params_dict
}
)
rules = create_rules(patterns, recipes)
self.assertEqual(len(rules), 1)
_, rule = rules.popitem()
self.assertIsInstance(rule, Rule)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
self.assertEqual(len(os.listdir(TEST_JOB_OUTPUT)), 0)
meta_file = os.path.join(job_dir, META_FILE)
write_yaml(job_dict, meta_file)
event = {
EVENT_TYPE: EVENT_TYPE_WATCHDOG,
EVENT_PATH: os.path.join(TEST_MONITOR_BASE, "A"),
WATCHDOG_BASE: TEST_MONITOR_BASE,
EVENT_RULE: rule,
WATCHDOG_HASH: get_hash(
os.path.join(TEST_MONITOR_BASE, "A"), SHA256
)
}
base_script = parameterize_bash_script(
COMPLETE_BASH_SCRIPT, params_dict
)
base_file = os.path.join(job_dir, get_base_file(JOB_TYPE_BASH))
write_file(lines_to_string(base_script), base_file)
st = os.stat(base_file)
os.chmod(base_file, st.st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
params_dict = {
"file_one": os.path.join(TEST_MONITOR_BASE, "A")
}
job_script = assemble_bash_job_script()
job_file = os.path.join(job_dir, get_job_file(JOB_TYPE_BASH))
write_file(lines_to_string(job_script), job_file)
st = os.stat(job_file)
os.chmod(job_file, st.st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
bh.setup_job(event, params_dict)
print(os.listdir(job_dir))
print(os.getcwd())
result = subprocess.call(job_file, cwd=".")
self.assertEqual(result, 0)
if from_handler_to_runner_reader.poll(3):
job_dir = from_handler_to_runner_reader.recv()
self.assertIsInstance(job_dir, str)
self.assertTrue(os.path.exists(job_dir))
meta_path = os.path.join(job_dir, META_FILE)
self.assertTrue(os.path.exists(meta_path))
status = read_yaml(meta_path)
self.assertIsInstance(status, Dict)
self.assertIn(JOB_STATUS, status)
self.assertEqual(status[JOB_STATUS], job_dict[JOB_STATUS])
self.assertNotIn(JOB_ERROR, status)
self.assertTrue(len(os.listdir(job_dir)), 3)
for f in [META_FILE, "recipe.sh", JOB_FILE]:
self.assertTrue(os.path.exists(os.path.join(job_dir, f)))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_base_file(JOB_TYPE_BASH))))
self.assertTrue(os.path.exists(
os.path.join(job_dir, get_job_file(JOB_TYPE_BASH))))
self.assertTrue(os.path.exists(result_path))
with open(result_path, "r") as f:
result = f.read()
self.assertEqual(result, "124937\n")
job = threadsafe_read_status(os.path.join(job_dir, META_FILE))
valid_job(job)
# Test handling criteria function
def testValidHandleCriteria(self)->None: