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added tests for new bash jobs, and removed extra hash definition in job dict

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This commit is contained in:
PatchOfScotland
2023-03-30 14:20:29 +02:00
parent 311c98f7f2
commit 18d579da22
9 changed files with 528 additions and 54 deletions
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498
tests/test_conductors.py
View File

@ -1,35 +1,40 @@
import os
import stat
import unittest
from datetime import datetime
from typing import Dict
from meow_base.core.correctness.vars import JOB_TYPE_PYTHON, SHA256, \
JOB_PARAMETERS, JOB_HASH, PYTHON_FUNC, JOB_ID, BACKUP_JOB_ERROR_FILE, \
JOB_PARAMETERS, PYTHON_FUNC, JOB_ID, BACKUP_JOB_ERROR_FILE, \
JOB_EVENT, META_FILE, PARAMS_FILE, JOB_STATUS, JOB_ERROR, JOB_TYPE, \
JOB_PATTERN, STATUS_DONE, JOB_TYPE_PAPERMILL, JOB_RECIPE, JOB_RULE, \
JOB_CREATE_TIME, JOB_REQUIREMENTS, EVENT_PATH, EVENT_RULE, EVENT_TYPE, \
EVENT_TYPE_WATCHDOG, get_base_file, get_result_file, get_job_file
from meow_base.conductors import LocalPythonConductor
EVENT_TYPE_WATCHDOG, JOB_TYPE_BASH, \
get_base_file, get_result_file, get_job_file
from meow_base.conductors import LocalPythonConductor, LocalBashConductor
from meow_base.functionality.file_io import read_file, read_yaml, write_file, \
write_notebook, write_yaml, lines_to_string, make_dir
from meow_base.functionality.hashing import get_file_hash
from meow_base.functionality.meow import create_watchdog_event, create_job, \
create_rule
from meow_base.functionality.parameterisation import parameterize_bash_script
from meow_base.patterns.file_event_pattern import FileEventPattern
from meow_base.recipes.jupyter_notebook_recipe import JupyterNotebookRecipe, \
papermill_job_func
from meow_base.recipes.python_recipe import PythonRecipe, python_job_func
from meow_base.recipes.bash_recipe import BashRecipe, assemble_bash_job_script
from shared import TEST_MONITOR_BASE, APPENDING_NOTEBOOK, TEST_JOB_OUTPUT, \
TEST_JOB_QUEUE, COMPLETE_PYTHON_SCRIPT, BAREBONES_PYTHON_SCRIPT, \
BAREBONES_NOTEBOOK, setup, teardown
BAREBONES_NOTEBOOK, COMPLETE_BASH_SCRIPT, BAREBONES_BASH_SCRIPT, \
setup, teardown
def failing_func():
raise Exception("bad function")
class MeowTests(unittest.TestCase):
class PythonTests(unittest.TestCase):
def setUp(self)->None:
super().setUp()
setup()
@ -96,7 +101,6 @@ class MeowTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
PYTHON_FUNC:python_job_func
}
)
@ -184,7 +188,6 @@ class MeowTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
PYTHON_FUNC:papermill_job_func
}
)
@ -271,8 +274,7 @@ class MeowTests(unittest.TestCase):
file_hash
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
JOB_PARAMETERS:params_dict
}
)
@ -313,7 +315,6 @@ class MeowTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
PYTHON_FUNC:papermill_job_func
}
)
@ -395,7 +396,6 @@ class MeowTests(unittest.TestCase):
"infile":file_path,
"outfile":result_path
},
JOB_HASH: file_hash,
PYTHON_FUNC:failing_func,
}
)
@ -463,7 +463,6 @@ class MeowTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params,
JOB_HASH: file_hash,
PYTHON_FUNC:failing_func,
}
)
@ -533,7 +532,6 @@ class MeowTests(unittest.TestCase):
"infile":file_path,
"outfile":result_path
},
JOB_HASH: file_hash,
PYTHON_FUNC:failing_func,
}
)
@ -602,7 +600,6 @@ class MeowTests(unittest.TestCase):
"infile":file_path,
"outfile":result_path
},
JOB_HASH: file_hash,
PYTHON_FUNC:failing_func,
}
)
@ -724,3 +721,476 @@ class MeowTests(unittest.TestCase):
self.assertTrue(status)
# TODO test job status funcs
class BashTests(unittest.TestCase):
def setUp(self)->None:
super().setUp()
setup()
def tearDown(self)->None:
super().tearDown()
teardown()
# Test LocalBashConductor creation
def testLocalBashConductorCreation(self)->None:
LocalBashConductor()
# Test LocalBashConductor naming
def testLocalBashConductorNaming(self)->None:
test_name = "test_name"
conductor = LocalBashConductor(name=test_name)
self.assertEqual(conductor.name, test_name)
conductor = LocalBashConductor()
self.assertTrue(conductor.name.startswith("conductor_"))
# Test LocalBashConductor executes valid bash jobs
def testLocalBashConductorValidBashJob(self)->None:
lpc = LocalBashConductor(
job_queue_dir=TEST_JOB_QUEUE,
job_output_dir=TEST_JOB_OUTPUT
)
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("150")
file_hash = get_file_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"num":450,
"outfile":result_path
})
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"num":450,
"infile":file_path,
"outfile":result_path
}
job_dict = create_job(
JOB_TYPE_BASH,
create_watchdog_event(
file_path,
rule,
TEST_MONITOR_BASE,
file_hash
),
extras={
JOB_PARAMETERS:params_dict,
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_path = os.path.join(job_dir, META_FILE)
write_yaml(job_dict, meta_path)
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)
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)
lpc.execute(job_dir)
self.assertFalse(os.path.exists(job_dir))
job_output_dir = os.path.join(TEST_JOB_OUTPUT, job_dict[JOB_ID])
self.assertTrue(os.path.exists(job_output_dir))
meta_path = os.path.join(job_output_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], STATUS_DONE)
self.assertNotIn(JOB_ERROR, status)
self.assertTrue(os.path.exists(
os.path.join(job_output_dir, get_base_file(JOB_TYPE_BASH))))
self.assertTrue(os.path.exists(
os.path.join(job_output_dir, get_job_file(JOB_TYPE_BASH))))
self.assertTrue(os.path.exists(result_path))
# Test LocalBashConductor does not execute jobs with missing metafile
def testLocalBashConductorMissingMetafile(self)->None:
lpc = LocalBashConductor(
job_queue_dir=TEST_JOB_QUEUE,
job_output_dir=TEST_JOB_OUTPUT
)
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("150")
file_hash = get_file_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"num":450,
"outfile":result_path
})
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"num":450,
"infile":file_path,
"outfile":result_path
}
job_dict = create_job(
JOB_TYPE_BASH,
create_watchdog_event(
file_path,
rule,
TEST_MONITOR_BASE,
file_hash
),
extras={
JOB_PARAMETERS: params_dict
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
lpc.execute(job_dir)
output_dir = os.path.join(TEST_JOB_OUTPUT, job_dict[JOB_ID])
self.assertFalse(os.path.exists(job_dir))
self.assertTrue(os.path.exists(output_dir))
error_file = os.path.join(output_dir, BACKUP_JOB_ERROR_FILE)
self.assertTrue(os.path.exists(error_file))
error = read_file(error_file)
self.assertEqual(error,
"Recieved incorrectly setup job.\n\n[Errno 2] No such file or "
f"directory: 'test_job_queue_dir{os.path.sep}{job_dict[JOB_ID]}{os.path.sep}job.yml'")
# Test LocalBashConductor does not execute jobs with bad script
def testLocalBashConductorBadScript(self)->None:
lpc = LocalBashConductor(
job_queue_dir=TEST_JOB_QUEUE,
job_output_dir=TEST_JOB_OUTPUT
)
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("150")
file_hash = get_file_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"num":450,
"outfile":result_path
})
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"num":450,
"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:failing_func,
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_path = os.path.join(job_dir, META_FILE)
write_yaml(job_dict, meta_path)
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)
job_script = [
"#!/bin/bash",
"echo Does Nothing"
]
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)
lpc.execute(job_dir)
output_dir = os.path.join(TEST_JOB_OUTPUT, job_dict[JOB_ID])
self.assertFalse(os.path.exists(job_dir))
self.assertTrue(os.path.exists(output_dir))
meta_path = os.path.join(output_dir, META_FILE)
self.assertTrue(os.path.exists(meta_path))
job = read_yaml(meta_path)
self.assertIsInstance(job, dict)
# Test LocalBashConductor does not execute jobs with invalid metafile
def testLocalBashConductorInvalidMetafile(self)->None:
lpc = LocalBashConductor(
job_queue_dir=TEST_JOB_QUEUE,
job_output_dir=TEST_JOB_OUTPUT
)
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("150")
file_hash = get_file_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"num":450,
"outfile":result_path
})
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"num":450,
"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
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_path = os.path.join(job_dir, META_FILE)
write_file("This is not a metafile dict", meta_path)
lpc.execute(job_dir)
output_dir = os.path.join(TEST_JOB_OUTPUT, job_dict[JOB_ID])
self.assertFalse(os.path.exists(job_dir))
self.assertTrue(os.path.exists(output_dir))
error_file = os.path.join(output_dir, BACKUP_JOB_ERROR_FILE)
self.assertTrue(os.path.exists(error_file))
error = read_file(error_file)
self.assertEqual(error,
"Recieved incorrectly setup job.\n\nExpected type(s) are "
"'[typing.Dict]', got <class 'str'>")
# Test LocalBashConductor does not execute jobs with mangled metafile
def testLocalBashConductorMangledMetafile(self)->None:
lpc = LocalBashConductor(
job_queue_dir=TEST_JOB_QUEUE,
job_output_dir=TEST_JOB_OUTPUT
)
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("150")
file_hash = get_file_hash(file_path, SHA256)
pattern = FileEventPattern(
"pattern",
file_path,
"recipe_one",
"infile",
parameters={
"num":450,
"outfile":result_path
})
recipe = BashRecipe(
"recipe_one", COMPLETE_BASH_SCRIPT)
rule = create_rule(pattern, recipe)
params_dict = {
"num":450,
"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
}
)
job_dir = os.path.join(TEST_JOB_QUEUE, job_dict[JOB_ID])
make_dir(job_dir)
meta_path = os.path.join(job_dir, META_FILE)
write_yaml({
"This": "is",
"a": "dictionary",
"but": "not",
"valid": "job",
"definitons": "file"
}, meta_path)
lpc.execute(job_dir)
output_dir = os.path.join(TEST_JOB_OUTPUT, job_dict[JOB_ID])
self.assertFalse(os.path.exists(job_dir))
self.assertTrue(os.path.exists(output_dir))
error_file = os.path.join(output_dir, BACKUP_JOB_ERROR_FILE)
self.assertTrue(os.path.exists(error_file))
error = read_file(error_file)
self.assertEqual(error,
"Recieved incorrectly setup job.\n\n\"Job require key "
"'job_type'\"")
# Test execute criteria function
def testValidExecuteCriteria(self)->None:
lpc = LocalBashConductor()
pattern_bash = FileEventPattern(
"pattern_bash", "A", "recipe_bash", "file_one")
recipe_bash = BashRecipe(
"recipe_bash", BAREBONES_BASH_SCRIPT
)
bash_rule = create_rule(pattern_bash, recipe_bash)
status, _ = lpc.valid_execute_criteria({})
self.assertFalse(status)
status, _ = lpc.valid_execute_criteria("")
self.assertFalse(status)
status, _ = lpc.valid_execute_criteria({
JOB_ID: "path",
JOB_EVENT: "type",
JOB_TYPE: "rule",
JOB_PATTERN: "pattern",
JOB_RECIPE: "recipe",
JOB_RULE: "rule",
JOB_STATUS: "status",
JOB_CREATE_TIME: "create",
JOB_REQUIREMENTS: "requirements"
})
self.assertFalse(status)
status, s = lpc.valid_execute_criteria({
JOB_ID: "path",
JOB_EVENT: {
EVENT_PATH: "path",
EVENT_TYPE: EVENT_TYPE_WATCHDOG,
EVENT_RULE: bash_rule
},
JOB_TYPE: "type",
JOB_PATTERN: bash_rule.pattern.name,
JOB_RECIPE: bash_rule.recipe.name,
JOB_RULE: bash_rule.name,
JOB_STATUS: "status",
JOB_CREATE_TIME: datetime.now(),
JOB_REQUIREMENTS: bash_rule.recipe.requirements
})
self.assertFalse(status)
status, s = lpc.valid_execute_criteria({
JOB_ID: "path",
JOB_EVENT: {
EVENT_PATH: "path",
EVENT_TYPE: EVENT_TYPE_WATCHDOG,
EVENT_RULE: bash_rule
},
JOB_TYPE: JOB_TYPE_BASH,
JOB_PATTERN: bash_rule.pattern.name,
JOB_RECIPE: bash_rule.recipe.name,
JOB_RULE: bash_rule.name,
JOB_STATUS: "status",
JOB_CREATE_TIME: datetime.now(),
JOB_REQUIREMENTS: bash_rule.recipe.requirements
})
self.assertTrue(status)
# TODO test job status funcs

3
tests/test_functionality.py
View File

@ -14,7 +14,7 @@ from typing import Dict
from meow_base.core.rule import Rule
from meow_base.core.correctness.vars import CHAR_LOWERCASE, CHAR_UPPERCASE, \
SHA256, EVENT_TYPE, EVENT_PATH, EVENT_TYPE_WATCHDOG, \
WATCHDOG_BASE, WATCHDOG_HASH, EVENT_RULE, JOB_PARAMETERS, JOB_HASH, \
WATCHDOG_BASE, WATCHDOG_HASH, EVENT_RULE, JOB_PARAMETERS, \
PYTHON_FUNC, JOB_ID, JOB_EVENT, \
JOB_TYPE, JOB_PATTERN, JOB_RECIPE, JOB_RULE, JOB_STATUS, JOB_CREATE_TIME, \
JOB_REQUIREMENTS, STATUS_QUEUED, JOB_TYPE_PAPERMILL
@ -443,7 +443,6 @@ class MeowTests(unittest.TestCase):
"infile":"file_path",
"outfile":"result_path"
},
JOB_HASH: "file_hash",
PYTHON_FUNC:max
}
)

18
tests/test_recipes.py
View File

@ -11,7 +11,7 @@ from typing import Dict
from meow_base.core.correctness.meow import valid_job
from meow_base.core.correctness.vars import EVENT_TYPE, WATCHDOG_BASE, \
EVENT_RULE, EVENT_TYPE_WATCHDOG, EVENT_PATH, SHA256, WATCHDOG_HASH, \
JOB_ID, JOB_TYPE_PYTHON, JOB_PARAMETERS, JOB_HASH, PYTHON_FUNC, \
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
@ -378,7 +378,6 @@ class PapermillHandlerTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
PYTHON_FUNC:papermill_job_func
}
)
@ -797,7 +796,6 @@ class PythonHandlerTests(unittest.TestCase):
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash,
PYTHON_FUNC:python_job_func
}
)
@ -1210,8 +1208,7 @@ class BashHandlerTests(unittest.TestCase):
file_hash
),
extras={
JOB_PARAMETERS:params_dict,
JOB_HASH: file_hash
JOB_PARAMETERS:params_dict
}
)
@ -1235,7 +1232,6 @@ class BashHandlerTests(unittest.TestCase):
st = os.stat(job_file)
os.chmod(job_file, st.st_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
print(os.listdir(job_dir))
print(os.getcwd())
@ -1265,16 +1261,6 @@ class BashHandlerTests(unittest.TestCase):
self.assertEqual(result, "124937\n")
# Test jobFunc doesn't execute with no args
def testJobFuncBadArgs(self)->None:
try:
Bash_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 = BashHandler()