NikolajDanger/meow_base
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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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3
recipes/__init__.py
View File

@ -1,4 +1,5 @@
from .jupyter_notebook_recipe import JupyterNotebookRecipe, PapermillHandler, \
get_recipe_from_notebook
from .python_recipe import PythonRecipe, PythonHandler
from .python_recipe import PythonRecipe, PythonHandler
from .bash_recipe import BashRecipe, BashHandler

6
recipes/bash_recipe.py
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@ -12,9 +12,8 @@ from meow_base.core.correctness.validation import check_type, valid_dict, \
valid_string, valid_dir_path
from meow_base.core.correctness.vars import DEBUG_INFO, DEFAULT_JOB_QUEUE_DIR, \
VALID_VARIABLE_NAME_CHARS, EVENT_PATH, EVENT_RULE, EVENT_TYPE, JOB_ID, \
EVENT_TYPE_WATCHDOG, JOB_TYPE_BASH, JOB_PARAMETERS, JOB_HASH, \
WATCHDOG_HASH, WATCHDOG_BASE, META_FILE, PARAMS_FILE, STATUS_QUEUED, \
JOB_STATUS, \
EVENT_TYPE_WATCHDOG, JOB_TYPE_BASH, JOB_PARAMETERS, WATCHDOG_HASH, \
WATCHDOG_BASE, META_FILE, STATUS_QUEUED, JOB_STATUS, \
get_base_file, get_job_file
from meow_base.functionality.debug import setup_debugging, print_debug
from meow_base.functionality.file_io import valid_path, make_dir, write_yaml, \
@ -138,7 +137,6 @@ class BashHandler(BaseHandler):
event,
extras={
JOB_PARAMETERS:yaml_dict,
JOB_HASH: event[WATCHDOG_HASH],
# CONTROL_SCRIPT:python_job_func
}
)

12
recipes/jupyter_notebook_recipe.py
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@ -17,7 +17,7 @@ from meow_base.core.correctness.meow import valid_event
from meow_base.core.correctness.validation import check_type, valid_string, \
valid_dict, valid_path, valid_dir_path, valid_existing_file_path
from meow_base.core.correctness.vars import VALID_VARIABLE_NAME_CHARS, \
PYTHON_FUNC, DEBUG_INFO, EVENT_TYPE_WATCHDOG, JOB_HASH, \
PYTHON_FUNC, DEBUG_INFO, EVENT_TYPE_WATCHDOG, \
DEFAULT_JOB_QUEUE_DIR, EVENT_PATH, JOB_TYPE_PAPERMILL, WATCHDOG_HASH, \
JOB_PARAMETERS, JOB_ID, WATCHDOG_BASE, META_FILE, PARAMS_FILE, \
JOB_STATUS, STATUS_QUEUED, EVENT_RULE, EVENT_TYPE, EVENT_RULE, \
@ -142,7 +142,6 @@ class PapermillHandler(BaseHandler):
event,
extras={
JOB_PARAMETERS:yaml_dict,
JOB_HASH: event[WATCHDOG_HASH],
PYTHON_FUNC:papermill_job_func,
}
)
@ -206,7 +205,7 @@ def papermill_job_func(job_dir):
from datetime import datetime
from meow_base.core.correctness.vars import JOB_EVENT, JOB_ID, \
EVENT_PATH, META_FILE, PARAMS_FILE, \
JOB_STATUS, JOB_HASH, SHA256, STATUS_SKIPPED, JOB_END_TIME, \
JOB_STATUS, SHA256, STATUS_SKIPPED, JOB_END_TIME, \
JOB_ERROR, STATUS_FAILED, get_job_file, \
get_result_file
from meow_base.functionality.file_io import read_yaml, write_notebook, write_yaml
@ -228,19 +227,20 @@ def papermill_job_func(job_dir):
# Check the hash of the triggering file, if present. This addresses
# potential race condition as file could have been modified since
# triggering event
if JOB_HASH in job:
if JOB_EVENT in job and WATCHDOG_HASH in job[JOB_EVENT]:
# get current hash
triggerfile_hash = get_file_hash(job[JOB_EVENT][EVENT_PATH], SHA256)
# If hash doesn't match, then abort the job. If its been modified, then
# another job will have been scheduled anyway.
if not triggerfile_hash \
or triggerfile_hash != job[JOB_HASH]:
or triggerfile_hash != job[JOB_EVENT][WATCHDOG_HASH]:
job[JOB_STATUS] = STATUS_SKIPPED
job[JOB_END_TIME] = datetime.now()
msg = "Job was skipped as triggering file " + \
f"'{job[JOB_EVENT][EVENT_PATH]}' has been modified since " + \
"scheduling. Was expected to have hash " + \
f"'{job[JOB_HASH]}' but has '{triggerfile_hash}'."
f"'{job[JOB_EVENT][WATCHDOG_HASH]}' but has '" + \
f"{triggerfile_hash}'."
job[JOB_ERROR] = msg
write_yaml(job, meta_file)
return

12
recipes/python_recipe.py
View File

@ -16,7 +16,7 @@ from meow_base.core.correctness.meow import valid_event
from meow_base.core.correctness.validation import check_script, valid_string, \
valid_dict, valid_dir_path
from meow_base.core.correctness.vars import VALID_VARIABLE_NAME_CHARS, \
PYTHON_FUNC, DEBUG_INFO, EVENT_TYPE_WATCHDOG, JOB_HASH, \
PYTHON_FUNC, DEBUG_INFO, EVENT_TYPE_WATCHDOG, \
DEFAULT_JOB_QUEUE_DIR, EVENT_RULE, EVENT_PATH, JOB_TYPE_PYTHON, \
WATCHDOG_HASH, JOB_PARAMETERS, JOB_ID, WATCHDOG_BASE, META_FILE, \
PARAMS_FILE, JOB_STATUS, STATUS_QUEUED, EVENT_TYPE, EVENT_RULE, \
@ -132,7 +132,6 @@ class PythonHandler(BaseHandler):
event,
extras={
JOB_PARAMETERS:yaml_dict,
JOB_HASH: event[WATCHDOG_HASH],
PYTHON_FUNC:python_job_func
}
)
@ -182,7 +181,7 @@ def python_job_func(job_dir):
from io import StringIO
from meow_base.core.correctness.vars import JOB_EVENT, JOB_ID, \
EVENT_PATH, META_FILE, PARAMS_FILE, \
JOB_STATUS, JOB_HASH, SHA256, STATUS_SKIPPED, JOB_END_TIME, \
JOB_STATUS, SHA256, STATUS_SKIPPED, JOB_END_TIME, \
JOB_ERROR, STATUS_FAILED, get_base_file, \
get_job_file, get_result_file
from meow_base.functionality.file_io import read_yaml, write_yaml
@ -203,19 +202,20 @@ def python_job_func(job_dir):
# Check the hash of the triggering file, if present. This addresses
# potential race condition as file could have been modified since
# triggering event
if JOB_HASH in job:
if JOB_EVENT in job and WATCHDOG_HASH in job[JOB_EVENT]:
# get current hash
triggerfile_hash = get_file_hash(job[JOB_EVENT][EVENT_PATH], SHA256)
# If hash doesn't match, then abort the job. If its been modified, then
# another job will have been scheduled anyway.
if not triggerfile_hash \
or triggerfile_hash != job[JOB_HASH]:
or triggerfile_hash != job[JOB_EVENT][WATCHDOG_HASH]:
job[JOB_STATUS] = STATUS_SKIPPED
job[JOB_END_TIME] = datetime.now()
msg = "Job was skipped as triggering file " + \
f"'{job[JOB_EVENT][EVENT_PATH]}' has been modified since " + \
"scheduling. Was expected to have hash " + \
f"'{job[JOB_HASH]}' but has '{triggerfile_hash}'."
f"'{job[JOB_EVENT][WATCHDOG_HASH]}' but has '" + \
f"{triggerfile_hash}'."
job[JOB_ERROR] = msg
write_yaml(job, meta_file)
return