From 37faa1c1ef79835c538929a778920ef81ea3cdfc Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Fri, 9 Feb 2024 13:58:24 +0100 Subject: [PATCH 01/18] prepare v4.0.0b4 --- CHANGELOG.md | 2 ++ autosubmit_api/__init__.py | 2 +- setup.py | 2 +- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 978cdfd..ef0cfcd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,7 @@ # CHANGELOG +### Pre-release v4.0.0b4 - Release date: TBD + ### Pre-release v4.0.0b3 - Release date: 2023-02-09 * Fix HPC value in the running endpoint diff --git a/autosubmit_api/__init__.py b/autosubmit_api/__init__.py index 8226b2e..31671cf 100644 --- a/autosubmit_api/__init__.py +++ b/autosubmit_api/__init__.py @@ -17,6 +17,6 @@ # You should have received a copy of the GNU General Public License # along with Autosubmit. If not, see . -__version__ = "4.0.0b3" +__version__ = "4.0.0b4" __author__ = "Luiggi Tenorio, Bruno P. Kinoshita, Cristian Gutiérrez, Julian Berlin, Wilmer Uruchi" __credits__ = "Barcelona Supercomputing Center" \ No newline at end of file diff --git a/setup.py b/setup.py index 8a648a8..87d42ee 100644 --- a/setup.py +++ b/setup.py @@ -61,7 +61,7 @@ setup( "Intended Audience :: Developers", "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: POSIX :: Linux", - "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", ], entry_points={ "console_scripts": [ -- GitLab From b98d3558f8e07494fdae078823613a93aecef379 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Mon, 12 Feb 2024 16:03:29 +0100 Subject: [PATCH 02/18] refactor Experiment Status Worker --- autosubmit_api/bgtasks/bgtask.py | 103 ++--- autosubmit_api/bgtasks/scheduler.py | 8 +- .../bgtasks/tasks/status_updater.py | 119 +++++ autosubmit_api/builders/experiment_builder.py | 16 +- autosubmit_api/database/common.py | 60 ++- autosubmit_api/database/models.py | 2 +- autosubmit_api/experiment/old_code.txt | 412 ------------------ .../experiment_status_db_manager.py | 155 ------- .../history/database_managers/test.py | 261 ----------- autosubmit_api/history/experiment_status.py | 81 ---- .../history/experiment_status_manager.py | 89 ---- autosubmit_api/persistance/__init__.py | 0 autosubmit_api/persistance/experiment.py | 33 ++ .../workers/populate_running_experiments.py | 4 +- autosubmit_api/workers/test.py | 18 - tests/bgtasks/test_status_updater.py | 26 ++ tests/experiments/as_times.db | Bin 20480 -> 20480 bytes 17 files changed, 288 insertions(+), 1099 deletions(-) create mode 100644 autosubmit_api/bgtasks/tasks/status_updater.py delete mode 100644 autosubmit_api/experiment/old_code.txt delete mode 100644 autosubmit_api/history/database_managers/experiment_status_db_manager.py delete mode 100644 autosubmit_api/history/database_managers/test.py delete mode 100644 autosubmit_api/history/experiment_status.py delete mode 100644 autosubmit_api/history/experiment_status_manager.py create mode 100644 autosubmit_api/persistance/__init__.py create mode 100644 autosubmit_api/persistance/experiment.py delete mode 100644 autosubmit_api/workers/test.py create mode 100644 tests/bgtasks/test_status_updater.py diff --git a/autosubmit_api/bgtasks/bgtask.py b/autosubmit_api/bgtasks/bgtask.py index 30698b6..eeefa36 100644 --- a/autosubmit_api/bgtasks/bgtask.py +++ b/autosubmit_api/bgtasks/bgtask.py @@ -1,91 +1,82 @@ from abc import ABC, abstractmethod +import traceback +from autosubmit_api.logger import logger from autosubmit_api.experiment import common_requests -from autosubmit_api.history.experiment_status_manager import ExperimentStatusManager from autosubmit_api.config.basicConfig import APIBasicConfig from autosubmit_api.workers.business import populate_times, process_graph_drawings from autosubmit_api.workers.populate_details.populate import DetailsProcessor -class BackgroundTask(ABC): - @staticmethod +class BackgroundTaskTemplate(ABC): + """ + Interface to define Background Tasks. + Do not override the run method. + """ + logger = logger + + @classmethod + def run(cls): + """ + Not blocking exceptions + """ + try: + cls.procedure() + except Exception as exc: + cls.logger.error(f"Exception on Background Task {cls.id}: {exc}") + cls.logger.error(traceback.print_exc()) + + @classmethod @abstractmethod - def run(): + def procedure(cls): raise NotImplementedError - + @property @abstractmethod def id(self) -> dict: raise NotImplementedError - + @property @abstractmethod def trigger_options(self) -> dict: raise NotImplementedError - -class PopulateDetailsDB(BackgroundTask): + +class PopulateDetailsDB(BackgroundTaskTemplate): id = "TASK_POPDET" - trigger_options = { - "trigger": "interval", - "hours": 4 - } + trigger_options = {"trigger": "interval", "hours": 4} - @staticmethod - def run(): + @classmethod + def procedure(cls): APIBasicConfig.read() return DetailsProcessor(APIBasicConfig).process() - -class PopulateQueueRuntimes(BackgroundTask): + +class PopulateQueueRuntimes(BackgroundTaskTemplate): id = "TASK_POPQUE" - trigger_options = { - "trigger": "interval", - "minutes": 3 - } - - @staticmethod - def run(): - """ Process and updates queuing and running times. """ - populate_times.process_completed_times() - + trigger_options = {"trigger": "interval", "minutes": 3} -class PopulateRunningExperiments(BackgroundTask): - id = "TASK_POPRUNEX" - trigger_options = { - "trigger": "interval", - "minutes": 5 - } + @classmethod + def procedure(cls): + """Process and updates queuing and running times.""" + populate_times.process_completed_times() - @staticmethod - def run(): - """ - Updates STATUS of experiments. - """ - ExperimentStatusManager().update_running_experiments() - -class VerifyComplete(BackgroundTask): +class VerifyComplete(BackgroundTaskTemplate): id = "TASK_VRFCMPT" - trigger_options = { - "trigger": "interval", - "minutes": 10 - } + trigger_options = {"trigger": "interval", "minutes": 10} + + @classmethod + def procedure(cls): + common_requests.verify_last_completed(1800) - @staticmethod - def run(): - common_requests.verify_last_completed(1800) - -class PopulateGraph(BackgroundTask): +class PopulateGraph(BackgroundTaskTemplate): id = "TASK_POPGRPH" - trigger_options = { - "trigger": "interval", - "hours": 24 - } + trigger_options = {"trigger": "interval", "hours": 24} - @staticmethod - def run(): + @classmethod + def procedure(cls): """ Process coordinates of nodes in a graph drawing and saves them. """ - process_graph_drawings.process_active_graphs() \ No newline at end of file + process_graph_drawings.process_active_graphs() diff --git a/autosubmit_api/bgtasks/scheduler.py b/autosubmit_api/bgtasks/scheduler.py index 2c667c1..a941e39 100644 --- a/autosubmit_api/bgtasks/scheduler.py +++ b/autosubmit_api/bgtasks/scheduler.py @@ -1,13 +1,13 @@ from typing import List from flask_apscheduler import APScheduler from autosubmit_api.bgtasks.bgtask import ( - BackgroundTask, + BackgroundTaskTemplate, PopulateDetailsDB, PopulateQueueRuntimes, - PopulateRunningExperiments, VerifyComplete, PopulateGraph, ) +from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater from autosubmit_api.config import ( DISABLE_BACKGROUND_TASKS, RUN_BACKGROUND_TASKS_ON_START, @@ -15,10 +15,10 @@ from autosubmit_api.config import ( from autosubmit_api.logger import logger, with_log_run_times -REGISTERED_TASKS: List[BackgroundTask] = [ +REGISTERED_TASKS: List[BackgroundTaskTemplate] = [ PopulateDetailsDB, PopulateQueueRuntimes, - PopulateRunningExperiments, + StatusUpdater, VerifyComplete, PopulateGraph, ] diff --git a/autosubmit_api/bgtasks/tasks/status_updater.py b/autosubmit_api/bgtasks/tasks/status_updater.py new file mode 100644 index 0000000..91eb99f --- /dev/null +++ b/autosubmit_api/bgtasks/tasks/status_updater.py @@ -0,0 +1,119 @@ +from datetime import datetime +import os +import time +from typing import List + +from sqlalchemy import select +from autosubmit_api.bgtasks.bgtask import BackgroundTaskTemplate +from autosubmit_api.database import tables +from autosubmit_api.database.common import ( + create_autosubmit_db_engine, + create_as_times_db_engine, + create_main_db_conn, +) +from autosubmit_api.database.models import ExperimentModel +from autosubmit_api.experiment.common_requests import _is_exp_running +from autosubmit_api.history.database_managers.database_models import RunningStatus +from autosubmit_api.persistance.experiment import ExperimentPaths + + +class StatusUpdater(BackgroundTaskTemplate): + id = "TASK_STTSUPDTR" + trigger_options = {"trigger": "interval", "minutes": 5} + + @classmethod + def _clear_missing_experiments(cls): + """ + Clears the experiments that are not in the experiments table + """ + with create_main_db_conn() as conn: + try: + del_stmnt = tables.experiment_status_table.delete().where( + tables.experiment_status_table.c.exp_id.not_in( + select(tables.experiment_table.c.id) + ) + ) + conn.execute(del_stmnt) + conn.commit() + except Exception as exc: + conn.rollback() + cls.logger.error( + f"[{cls.id}] Error while clearing missing experiments status: {exc}" + ) + + @classmethod + def _get_experiments(cls) -> List[ExperimentModel]: + """ + Get the experiments list + """ + with create_autosubmit_db_engine().connect() as conn: + query_result = conn.execute(tables.experiment_table.select()).all() + return [ExperimentModel.model_validate(row._mapping) for row in query_result] + + @classmethod + def _check_exp_running(cls, expid: str) -> bool: + """ + Decide if the experiment is running + """ + MAX_PKL_AGE = 600 # 10 minutes + MAX_PKL_AGE_EXHAUSTIVE = 3600 # 1 hour + + is_running = False + try: + pkl_path = ExperimentPaths(expid).job_list_pkl + pkl_age = int(time.time()) - int(os.stat(pkl_path).st_mtime) + + if pkl_age < MAX_PKL_AGE: # First running check + is_running = True + elif pkl_age < MAX_PKL_AGE_EXHAUSTIVE: # Exhaustive check + _, _, _flag, _, _ = _is_exp_running(expid) # Exhaustive validation + if _flag: + is_running = True + except Exception as exc: + cls.logger.error( + f"[{cls.id}] Error while checking experiment {expid}: {exc}" + ) + + return is_running + + @classmethod + def _update_experiment_status(cls, experiment: ExperimentModel, is_running: bool): + with create_as_times_db_engine().connect() as conn: + try: + del_stmnt = tables.experiment_status_table.delete().where( + tables.experiment_status_table.c.exp_id == experiment.id + ) + ins_stmnt = tables.experiment_status_table.insert().values( + exp_id=experiment.id, + name=experiment.name, + status=( + RunningStatus.RUNNING + if is_running + else RunningStatus.NOT_RUNNING + ), + seconds_diff=0, + modified=datetime.now().isoformat(timespec="seconds"), + ) + conn.execute(del_stmnt) + conn.execute(ins_stmnt) + conn.commit() + except Exception as exc: + conn.rollback() + cls.logger.error( + f"[{cls.id}] Error while doing database operations on experiment {experiment.name}: {exc}" + ) + + @classmethod + def procedure(cls): + """ + Updates STATUS of experiments. + """ + cls._clear_missing_experiments() + + # Read experiments table + exp_list = cls._get_experiments() + + # Check every experiment status & update + for experiment in exp_list: + is_running = cls._check_exp_running(experiment.name) + cls._update_experiment_status(experiment, is_running) diff --git a/autosubmit_api/builders/experiment_builder.py b/autosubmit_api/builders/experiment_builder.py index 5a3b5a6..7bf5c48 100644 --- a/autosubmit_api/builders/experiment_builder.py +++ b/autosubmit_api/builders/experiment_builder.py @@ -4,16 +4,16 @@ from autosubmit_api.builders.configuration_facade_builder import ( ConfigurationFacadeDirector, ) from autosubmit_api.database import tables -from autosubmit_api.database.common import create_main_db_conn -from autosubmit_api.database.models import Experiment +from autosubmit_api.database.common import create_autosubmit_db_engine, create_main_db_conn +from autosubmit_api.database.models import ExperimentModel class ExperimentBuilder(BaseBuilder): def produce_base_from_dict(self, obj: dict): - self._product = Experiment.model_validate(obj) + self._product = ExperimentModel.model_validate(obj) def produce_base(self, expid): - with create_main_db_conn() as conn: + with create_autosubmit_db_engine().connect() as conn: result = conn.execute( tables.experiment_table.select().where( tables.experiment_table.c.name == expid @@ -21,7 +21,7 @@ class ExperimentBuilder(BaseBuilder): ).one() # Set new product - self._product = Experiment( + self._product = ExperimentModel( id=result.id, name=result.name, description=result.description, @@ -30,12 +30,12 @@ class ExperimentBuilder(BaseBuilder): def produce_details(self): exp_id = self._product.id - with create_main_db_conn() as conn: + with create_autosubmit_db_engine().connect()() as conn: result = conn.execute( tables.details_table.select().where( tables.details_table.c.exp_id == exp_id ) - ).one_or_none + ).one_or_none() # Set details props if result: @@ -63,5 +63,5 @@ class ExperimentBuilder(BaseBuilder): ) @property - def product(self) -> Experiment: + def product(self) -> ExperimentModel: return super().product \ No newline at end of file diff --git a/autosubmit_api/database/common.py b/autosubmit_api/database/common.py index c39b76d..6891df5 100644 --- a/autosubmit_api/database/common.py +++ b/autosubmit_api/database/common.py @@ -1,27 +1,63 @@ import os from typing import Any -from sqlalchemy import Connection, Select, create_engine, select, text, func +from sqlalchemy import Connection, Engine, Select, create_engine, select, text, func +from autosubmit_api.builders import BaseBuilder from autosubmit_api.logger import logger from autosubmit_api.config.basicConfig import APIBasicConfig -def create_main_db_conn(): - APIBasicConfig.read() - autosubmit_db_path = os.path.abspath(APIBasicConfig.DB_PATH) - as_times_db_path = os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB) - engine = create_engine("sqlite://") - conn = engine.connect() - conn.execute(text(f"attach database '{autosubmit_db_path}' as autosubmit;")) - conn.execute(text(f"attach database '{as_times_db_path}' as as_times;")) - return conn +class AttachedDatabaseConnBuilder(BaseBuilder): + """ + SQLite utility to build attached databases. + """ + + def __init__(self) -> None: + super().__init__(False) + APIBasicConfig.read() + self.engine = create_engine("sqlite://") + self._product = self.engine.connect() + + def attach_db(self, path: str, name: str): + self._product.execute(text(f"attach database '{path}' as {name};")) + def attach_autosubmit_db(self): + autosubmit_db_path = os.path.abspath(APIBasicConfig.DB_PATH) + self.attach_db(autosubmit_db_path, "autosubmit") -def create_autosubmit_db_engine(): + def attach_as_times_db(self): + as_times_db_path = os.path.join( + APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB + ) + self.attach_db(as_times_db_path, "as_times") + + @property + def product(self) -> Connection: + return super().product + + +def create_main_db_conn() -> Connection: + """ + Connection with the autosubmit and as_times DDBB. + """ + builder = AttachedDatabaseConnBuilder() + builder.attach_autosubmit_db() + builder.attach_as_times_db() + + return builder.product + + +def create_autosubmit_db_engine() -> Engine: + """ + Create an engine for the autosubmit DDBB. Usually named autosubmit.db + """ APIBasicConfig.read() return create_engine(f"sqlite:///{ os.path.abspath(APIBasicConfig.DB_PATH)}") -def create_as_times_db_engine(): +def create_as_times_db_engine() -> Engine: + """ + Create an engine for the AS_TIMES DDBB. Usually named as_times.db + """ APIBasicConfig.read() db_path = os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB) return create_engine(f"sqlite:///{ os.path.abspath(db_path)}") diff --git a/autosubmit_api/database/models.py b/autosubmit_api/database/models.py index db4a3e0..c63b2b0 100644 --- a/autosubmit_api/database/models.py +++ b/autosubmit_api/database/models.py @@ -2,7 +2,7 @@ from typing import Optional from pydantic import BaseModel -class Experiment(BaseModel): +class ExperimentModel(BaseModel): id: int name: str description: str diff --git a/autosubmit_api/experiment/old_code.txt b/autosubmit_api/experiment/old_code.txt deleted file mode 100644 index d9cac6a..0000000 --- a/autosubmit_api/experiment/old_code.txt +++ /dev/null @@ -1,412 +0,0 @@ -def get_experiment_metrics(expid): - """ - Gets metrics - """ - error = False - error_message = "" - SYPD = ASYPD = CHSY = JPSY = RSYPD = Parallelization = 0 - seconds_in_a_day = 86400 - list_considered = [] - core_hours_year = [] - warnings_job_data = [] - total_run_time = 0 - total_queue_time = total_CHSY = total_JPSY = energy_count = 0 - - try: - # Basic info - BasicConfig.read() - path = BasicConfig.LOCAL_ROOT_DIR + '/' + expid + '/pkl' - tmp_path = os.path.join( - BasicConfig.LOCAL_ROOT_DIR, expid, BasicConfig.LOCAL_TMP_DIR) - pkl_filename = "job_list_" + str(expid) + ".pkl" - path_pkl = path + "/" + pkl_filename - - as_conf = AutosubmitConfig( - expid, BasicConfig, ConfigParserFactory()) - if not as_conf.check_conf_files(): - # Log.critical('Can not run with invalid configuration') - raise Exception( - 'Autosubmit GUI might not have permission to access necessary configuration files.') - - # Chunk Information - chunk_unit = as_conf.get_chunk_size_unit() - chunk_size = as_conf.get_chunk_size() - year_per_sim = datechunk_to_year(chunk_unit, chunk_size) - if year_per_sim <= 0: - raise Exception("The system couldn't calculate year per SIM value " + str(year_per_sim) + - ", for chunk size " + str(chunk_size) + " and chunk unit " + str(chunk_unit)) - - # From database - # db_file = os.path.join(BasicConfig.LOCAL_ROOT_DIR, "ecearth.db") - # conn = DbRequests.create_connection(db_file) - # job_times = DbRequests.get_times_detail_by_expid(conn, expid) - - # Job time information - # Try to get packages - job_to_package = {} - package_to_jobs = {} - job_to_package, package_to_jobs, _, _ = JobList.retrieve_packages( - BasicConfig, expid) - # Basic data - job_running_to_seconds = {} - # SIM POST TRANSFER jobs (COMPLETED) in experiment - sim_jobs_in_pkl = [] - post_jobs_in_pkl = [] - transfer_jobs_in_pkl = [] - clean_jobs_in_pkl = [] - sim_jobs_info = [] - post_jobs_info = [] - transfer_jobs_info = [] - clean_jobs_info = [] - sim_jobs_info_asypd = [] - sim_jobs_info_rsypd = [] - outlied = [] - # Get pkl information - if os.path.exists(path_pkl): - fd = open(path_pkl, 'r') - pickle_content = pickle.load(fd) - # pickle 0: Name, 2: StatusCode - sim_jobs_in_pkl = [item[0] - for item in pickle_content if 'SIM' in item[0].split('_') and int(item[2]) == Status.COMPLETED] - post_jobs_in_pkl = [item[0] - for item in pickle_content if 'POST' in item[0].split('_') and int(item[2]) == Status.COMPLETED] - transfer_member = [item[0] - for item in pickle_content if item[0].find('TRANSFER_MEMBER') > 0 and int(item[2]) == Status.COMPLETED] - transfer_jobs_in_pkl = [item[0] - for item in pickle_content if 'TRANSFER' in item[0].split('_') and int(item[2]) == Status.COMPLETED and item[0] not in transfer_member] - clean_member = [item[0] - for item in pickle_content if item[0].find('CLEAN_MEMBER') > 0 and int(item[2]) == Status.COMPLETED] - clean_jobs_in_pkl = [item[0] - for item in pickle_content if 'CLEAN' in item[0].split('_') and int(item[2]) == Status.COMPLETED and item[0] not in clean_member] - - # print(transfer_jobs_in_pkl) - fakeAllJobs = [SimpleJob(item[0], tmp_path, int(item[2])) - for item in pickle_content] - del pickle_content - job_running_to_seconds, _, warnings_job_data = JobList.get_job_times_collection( - BasicConfig, fakeAllJobs, expid, job_to_package, package_to_jobs, timeseconds=True) - # ASYPD - RSYPD warnings - if len(post_jobs_in_pkl) == 0: - warnings_job_data.append( - "ASYPD | There are no (COMPLETED) POST jobs in the experiment, ASYPD cannot be computed.") - if len(transfer_jobs_in_pkl) == 0 and len(clean_jobs_in_pkl) == 0: - warnings_job_data.append( - "RSYPD | There are no TRANSFER nor CLEAN (COMPLETED) jobs in the experiment, RSYPD cannot be computed.") - if len(transfer_jobs_in_pkl) == 0 and len(clean_jobs_in_pkl) > 0: - warnings_job_data.append( - "RSYPD | There are no TRANSFER (COMPLETED) jobs in the experiment, we resort to use (COMPLETED) CLEAN jobs to compute RSYPD.") - - Parallelization = 0 - try: - processors_value = as_conf.get_processors("SIM") - if processors_value.find(":") >= 0: - # It is an expression - components = processors_value.split(":") - Parallelization = int(sum( - [math.ceil(float(x) / 36.0) * 36.0 for x in components])) - warnings_job_data.append("Parallelization parsing | {0} was interpreted as {1} cores.".format( - processors_value, Parallelization)) - else: - # It is int - Parallelization = int(processors_value) - except Exception as exp: - # print(exp) - warnings_job_data.append( - "CHSY Critical | Autosubmit API could not parse the number of processors for the SIM job.") - pass - - # ASYPD - # Main Loop - # Times exist - if len(job_running_to_seconds) > 0: - # job_info attributes: ['name', 'queue_time', 'run_time', 'status', 'energy', 'submit', 'start', 'finish', 'ncpus'] - sim_jobs_info = [job_running_to_seconds[job_name] - for job_name in sim_jobs_in_pkl if job_running_to_seconds.get(job_name, None) is not None] - sim_jobs_info.sort(key=lambda x: tostamp(x.finish), reverse=True) - - # SIM outlier detection - data_run_times = [job.run_time for job in sim_jobs_info] - mean_1 = np.mean(data_run_times) if len(data_run_times) > 0 else 0 - std_1 = np.std(data_run_times) if len(data_run_times) > 0 else 0 - threshold = 2 - - # ASYPD Pre - post_jobs_info = [job_running_to_seconds[job_name] - for job_name in post_jobs_in_pkl if job_running_to_seconds.get(job_name, None) is not None and job_running_to_seconds[job_name].finish is not None] - post_jobs_info.sort(key=lambda x: tostamp(x.finish), reverse=True) - # End ASYPD Pre - for job_info in sim_jobs_info: - # JobRow object - z_score = (job_info.run_time - mean_1) / \ - std_1 if std_1 > 0 else 0 - # print("{} : {}".format(job_info.name, z_score, threshold)) - if np.abs(z_score) <= threshold and job_info.run_time > 0: - status = job_info.status if job_info else "UNKNOWN" - # Energy - energy = round(job_info.energy, 2) if job_info else 0 - if energy == 0: - warnings_job_data.append( - "Considered | Job {0} (Package {1}) has no energy information and is not going to be considered for energy calculations.".format(job_info.name, job_to_package.get(job_info.name, ""))) - total_queue_time += max(int(job_info.queue_time), 0) - total_run_time += max(int(job_info.run_time), 0) - seconds_per_year = (Parallelization * - job_info.run_time) / year_per_sim - job_JPSY = round(energy / year_per_sim, - 2) if year_per_sim > 0 else 0 - job_SYPD = round((year_per_sim * seconds_in_a_day) / - max(int(job_info.run_time), 0), 2) if job_info.run_time > 0 else 0 - job_ASYPD = round((year_per_sim * seconds_in_a_day) / (int(job_info.queue_time) + int(job_info.run_time) + sum( - job.queue_time + job.run_time for job in post_jobs_info) / len(post_jobs_info)) if len(post_jobs_info) > 0 else 0, 2) - - # Maximum finish time - # max_sim_finish = tostamp(job_info.finish) if job_info.finish is not None and tostamp( - # job_info.finish) > max_sim_finish else max_sim_finish - # sim_count += 1 - total_CHSY += round(seconds_per_year / 3600, 2) - total_JPSY += job_JPSY - if job_JPSY > 0: - # Ignore for mean calculation - energy_count += 1 - # core_hours_year.append(year_seconds/3600) - list_considered.append( - {"name": job_info.name, - "queue": int(job_info.queue_time), - "running": int(job_info.run_time), - "CHSY": round(seconds_per_year / 3600, 2), - "SYPD": job_SYPD, - "ASYPD": job_ASYPD, - "JPSY": job_JPSY, - "energy": energy}) - else: - # print("Outlied {}".format(job_info.name)) - outlied.append(job_info.name) - warnings_job_data.append( - "Outlier | Job {0} (Package {1} - Running time {2} seconds) has been considered an outlier (mean {3}, std {4}, z_score {5}) and will be ignored for performance calculations.".format(job_info.name, job_to_package.get(job_info.name, "NA"), str(job_info.run_time), str(round(mean_1, 2)), str(round(std_1, 2)), str(round(z_score, 2)))) - - # ASYPD Pre - sim_jobs_info_asypd = [job for job in sim_jobs_info if job.name not in outlied] if len( - post_jobs_info) > 0 else [] - sim_jobs_info_asypd.sort( - key=lambda x: tostamp(x.finish), reverse=True) - - # RSYPD - transfer_jobs_info = [job_running_to_seconds[job_name] - for job_name in transfer_jobs_in_pkl if job_running_to_seconds.get(job_name, None) is not None and job_running_to_seconds[job_name].finish is not None] - transfer_jobs_info.sort( - key=lambda x: tostamp(x.finish), reverse=True) - if len(transfer_jobs_info) <= 0: - clean_jobs_info = [job_running_to_seconds[job_name] - for job_name in clean_jobs_in_pkl if job_running_to_seconds.get(job_name, None) is not None and job_running_to_seconds[job_name].finish is not None] - clean_jobs_info.sort( - key=lambda x: tostamp(x.finish), reverse=True) - sim_jobs_info_rsypd = [job for job in sim_jobs_info if job.name not in outlied and tostamp(job.finish) <= tostamp( - clean_jobs_info[0].finish)] if len(clean_jobs_info) > 0 else [] - else: - sim_jobs_info_rsypd = [job for job in sim_jobs_info if job.name not in outlied and tostamp(job.finish) <= tostamp( - transfer_jobs_info[0].finish)] - sim_jobs_info_rsypd.sort( - key=lambda x: tostamp(x.finish), reverse=True) - - SYPD = ((year_per_sim * len(list_considered) * seconds_in_a_day) / - (total_run_time)) if total_run_time > 0 else 0 - SYPD = round(SYPD, 2) - # Old - # ASYPD = ((year_per_sim * len(list_considered) * seconds_in_a_day) / - # (total_run_time + total_queue_time) if (total_run_time + - # total_queue_time) > 0 else 0) - # Paper Implementation - # ASYPD = ((year_per_sim * len(list_considered) * seconds_in_a_day) / (max_sim_finish - - # min_submit)) if (max_sim_finish - min_submit) > 0 else 0 - # ASYPD New Implementation - ASYPD = (year_per_sim * len(sim_jobs_info_asypd) * seconds_in_a_day) / (sum(job.queue_time + job.run_time for job in sim_jobs_info_asypd) + - sum(job.queue_time + job.run_time for job in post_jobs_info) / len(post_jobs_info)) if len(sim_jobs_info_asypd) > 0 and len(post_jobs_info) > 0 else 0 - - # RSYPD - RSYPD = 0 - if len(transfer_jobs_info) > 0: - RSYPD = (year_per_sim * len(sim_jobs_info_rsypd) * seconds_in_a_day) / (tostamp(transfer_jobs_info[0].finish) - tostamp(sim_jobs_info_rsypd[-1].start)) if len( - sim_jobs_info_rsypd) > 0 and len(transfer_jobs_info) > 0 and (tostamp(transfer_jobs_info[0].finish) - tostamp(sim_jobs_info_rsypd[-1].start)) > 0 else 0 - else: - RSYPD = (year_per_sim * len(sim_jobs_info_rsypd) * seconds_in_a_day) / (tostamp(clean_jobs_info[0].finish) - tostamp(sim_jobs_info_rsypd[-1].start)) if len( - sim_jobs_info_rsypd) > 0 and len(clean_jobs_info) > 0 and (tostamp(clean_jobs_info[0].finish) - tostamp(sim_jobs_info_rsypd[-1].start)) > 0 else 0 - - ASYPD = round(ASYPD, 4) - RSYPD = round(RSYPD, 4) - CHSY = round(total_CHSY / len(list_considered), - 2) if len(list_considered) > 0 else total_CHSY - JPSY = round( - total_JPSY / energy_count, 2) if energy_count > 0 else total_JPSY - except Exception as ex: - print(traceback.format_exc()) - error = True - error_message = str(ex) - pass - - return {"SYPD": SYPD, - "ASYPD": ASYPD, - "RSYPD": RSYPD, - "CHSY": CHSY, - "JPSY": JPSY, - "Parallelization": Parallelization, - "considered": list_considered, - "error": error, - "error_message": error_message, - "warnings_job_data": warnings_job_data, - } - -def get_experiment_graph_format_test(expid): - """ - Some testing. Does not serve any purpose now, but the code might be useful. - """ - base_list = dict() - pkl_timestamp = 10000000 - try: - notransitive = False - print("Received " + str(expid)) - BasicConfig.read() - exp_path = os.path.join(BasicConfig.LOCAL_ROOT_DIR, expid) - tmp_path = os.path.join(exp_path, BasicConfig.LOCAL_TMP_DIR) - as_conf = AutosubmitConfig( - expid, BasicConfig, ConfigParserFactory()) - if not as_conf.check_conf_files(): - # Log.critical('Can not run with invalid configuration') - raise Exception( - 'Autosubmit GUI might not have permission to access necessary configuration files.') - - job_list = Autosubmit.load_job_list( - expid, as_conf, notransitive=notransitive) - - job_list.sort_by_id() - base_list = job_list.get_graph_representation(BasicConfig) - except Exception as e: - return {'nodes': [], - 'edges': [], - 'error': True, - 'error_message': str(e), - 'graphviz': False, - 'max_children': 0, - 'max_parents': 0, - 'total_jobs': 0, - 'pkl_timestamp': 0} - name_to_id = dict() - # name_to_weight = dict() - list_nodes = list() - list_edges = list() - i = 0 - with open('/home/Earth/wuruchi/Documents/Personal/spectralgraph/data/graph_' + expid + '.txt', 'w') as the_file: - for item in base_list['nodes']: - # the_file.write(str(i) + "\n") - name_to_id[item['id']] = i - list_nodes.append(i) - i += 1 - for item in base_list['edges']: - the_file.write(str(name_to_id[item['from']]) + " " + str( - name_to_id[item['to']]) + " " + ("10" if item['is_wrapper'] == True else "1") + "\n") - list_edges.append( - (name_to_id[item['from']], name_to_id[item['to']])) - for item in base_list['fake_edges']: - the_file.write(str(name_to_id[item['from']]) + " " + str( - name_to_id[item['to']]) + " " + ("10" if item['is_wrapper'] == True else "1") + "\n") - list_edges.append( - (name_to_id[item['from']], name_to_id[item['to']])) - return list_nodes, list_edges - - - -def update_running_experiments(time_condition=600): - """ - Tests if an experiment is running and updates database as_times.db accordingly.\n - :return: Nothing - """ - t0 = time.time() - experiment_to_modified_ts = dict() # type: Dict[str, int] - try: - BasicConfig.read() - path = BasicConfig.LOCAL_ROOT_DIR - # List of experiments from pkl - tp0 = time.time() - currentDirectories = subprocess.Popen(['ls', '-t', path], - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT) if (os.path.exists(path)) else None - stdOut, stdErr = currentDirectories.communicate( - ) if currentDirectories else (None, None) - - # Build connection to ecearth.db - db_file = os.path.join(path, "ecearth.db") - conn = DbRequests.create_connection(db_file) - current_table = DbRequests.prepare_status_db() - readingpkl = stdOut.split() if stdOut else [] - - tp1 = time.time() - for expid in readingpkl: - pkl_path = os.path.join(path, expid, "pkl", "job_list_{0}.pkl".format(expid)) - if not len(expid) == 4 or not os.path.exists(pkl_path): - continue - t1 = time.time() - # Timer safeguard - if (t1 - t0) > SAFE_TIME_LIMIT_STATUS: - raise Exception( - "Time limit reached {0:06.2f} seconds on update_running_experiments while processing {1}. \ - Time spent on reading data {2:06.2f} seconds.".format((t1 - t0), expid, (tp1 - tp0))) - current_stat = os.stat(pkl_path) - time_diff = int(time.time()) - int(current_stat.st_mtime) - if (time_diff < time_condition): - experiment_to_modified_ts[expid] = time_diff - if current_table.get(expid, None) is not None: - # UPDATE RUNNING - _exp_id, _status, _seconds = current_table[expid] - if _status != "RUNNING": - DbRequests.update_exp_status( - expid, "RUNNING", time_diff) - else: - # Insert new experiment - current_id = DbRequests.insert_experiment_status( - conn, expid, time_diff) - current_table[expid] = ( - current_id, 'RUNNING', time_diff) - elif (time_diff <= 3600): - # If it has been running in the last 1 hour - # It must have been added before - error, error_message, is_running, timediff, _ = _is_exp_running( - expid) - if is_running == True: - if current_table.get(expid, None): - _exp_id, _status, _seconds = current_table[expid] - if _status != "RUNNING" and is_running == True: - DbRequests.update_exp_status( - expid, "RUNNING", _seconds) - else: - current_id = DbRequests.insert_experiment_status( - conn, expid, time_diff) - current_table[expid] = ( - current_id, 'RUNNING', time_diff) - - for expid in current_table: - exp_id, status, seconds = current_table[expid] - if status == "RUNNING" and experiment_to_modified_ts.get(expid, None) is None: - # Perform exhaustive check - error, error_message, is_running, timediff, _ = _is_exp_running( - expid) - # UPDATE NOT RUNNING - if (is_running == False): - # print("Update NOT RUNNING for " + expid) - DbRequests.update_exp_status( - expid, "NOT RUNNING", timediff) - except Exception as e: - # print(expid) - print(e.message) - # print(traceback.format_exc()) - -def get_experiment_run_detail(expid, run_id): - error = False - error_message = "" - result = None - try: - result = JobDataStructure(expid).get_current_run_job_data_json(run_id) - tags = {"source": JobList.get_sourcetag(), "target": JobList.get_targettag(), "sync": JobList.get_synctag(), "check": JobList.get_checkmark( - ), "completed": JobList.get_completed_tag(), "running_tag": JobList.get_running_tag(), "queuing_tag": JobList.get_queuing_tag(), "failed_tag": JobList.get_failed_tag()} - except Exception as exp: - error = True - error_message = str(exp) - pass - return {"error": error, "error_message": error_message, "rundata": result} \ No newline at end of file diff --git a/autosubmit_api/history/database_managers/experiment_status_db_manager.py b/autosubmit_api/history/database_managers/experiment_status_db_manager.py deleted file mode 100644 index b7092a4..0000000 --- a/autosubmit_api/history/database_managers/experiment_status_db_manager.py +++ /dev/null @@ -1,155 +0,0 @@ -#!/usr/bin/env python - - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import os -import textwrap -import time - -from autosubmit_api.experiment.common_db_requests import prepare_status_db -from .database_manager import DatabaseManager, DEFAULT_LOCAL_ROOT_DIR -from ...config.basicConfig import APIBasicConfig -from ...history import utils as HUtils -from ...history.database_managers import database_models as Models -from typing import List - -class ExperimentStatusDbManager(DatabaseManager): - """ Manages the actions on the status database """ - def __init__(self, expid, basic_config): - # type: (str, APIBasicConfig) -> None - super(ExperimentStatusDbManager, self).__init__(expid, basic_config) - self._as_times_file_path = os.path.join(APIBasicConfig.DB_DIR, self.AS_TIMES_DB_NAME) - self._ecearth_file_path = os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.DB_FILE) - self._pkl_file_path = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, self.expid, "pkl", "job_list_{0}.pkl".format(self.expid)) - self.default_experiment_status_row = Models.ExperimentStatusRow(0, "DEFAULT", "NOT RUNNING", 0, "") - - - def validate_status_database(self): - """ Creates experiment_status table if it does not exist """ - prepare_status_db() - # Redundant code - # create_table_query = textwrap.dedent( - # '''CREATE TABLE - # IF NOT EXISTS experiment_status ( - # exp_id integer PRIMARY KEY, - # name text NOT NULL, - # status text NOT NULL, - # seconds_diff integer NOT NULL, - # modified text NOT NULL - # );''' - # ) - # self.execute_statement_on_dbfile(self._as_times_file_path, create_table_query) - - def print_current_table(self): - for experiment in self._get_experiment_status_content(): - print(experiment) - if self.current_experiment_status_row: - print(("Current Row:\n\t" + self.current_experiment_status_row.name + "\n\t" + - str(self.current_experiment_status_row.exp_id) + "\n\t" + self.current_experiment_status_row.status)) - - def get_experiment_table_content(self): - # type: () -> List[Models.ExperimentStatusRow] - return self._get_experiment_status_content() - - def is_running(self, time_condition=600): - # type : (int) -> bool - """ True if experiment is running, False otherwise. """ - if (os.path.exists(self._pkl_file_path)): - current_stat = os.stat(self._pkl_file_path) - timest = int(current_stat.st_mtime) - timesys = int(time.time()) - time_diff = int(timesys - timest) - if (time_diff < time_condition): - return True - else: - return False - return False - - def set_existing_experiment_status_as_running(self, expid): - """ Set the experiment_status row as running. """ - self.update_exp_status(expid, Models.RunningStatus.RUNNING) - - def create_experiment_status_as_running(self, experiment): - """ Create a new experiment_status row for the Models.Experiment item.""" - self.create_exp_status(experiment.id, experiment.name, Models.RunningStatus.RUNNING) - - - def get_experiment_status_row_by_expid(self, expid): - # type: (str) -> Models.ExperimentStatusRow | None - """ - Get Models.ExperimentStatusRow by expid. Uses exp_id (int id) as an intermediate step and validation. - """ - experiment_row = self.get_experiment_row_by_expid(expid) - return self.get_experiment_status_row_by_exp_id(experiment_row.id) if experiment_row else None - - def get_experiment_row_by_expid(self, expid): - # type: (str) -> Models.ExperimentRow | None - """ - Get the experiment from ecearth.db by expid as Models.ExperimentRow. - """ - statement = self.get_built_select_statement("experiment", "name=?") - current_rows = self.get_from_statement_with_arguments(self._ecearth_file_path, statement, (expid,)) - if len(current_rows) <= 0: - return None - # raise ValueError("Experiment {0} not found in {1}".format(expid, self._ecearth_file_path)) - return Models.ExperimentRow(*current_rows[0]) - - def _get_experiment_status_content(self): - # type: () -> List[Models.ExperimentStatusRow] - """ - Get all registers from experiment_status as List of Models.ExperimentStatusRow.\n - """ - statement = self.get_built_select_statement("experiment_status") - current_rows = self.get_from_statement(self._as_times_file_path, statement) - return [Models.ExperimentStatusRow(*row) for row in current_rows] - - def get_experiment_status_row_by_exp_id(self, exp_id): - # type: (int) -> Models.ExperimentStatusRow - """ Get Models.ExperimentStatusRow from as_times.db by exp_id (int)""" - statement = self.get_built_select_statement("experiment_status", "exp_id=?") - arguments = (exp_id,) - current_rows = self.get_from_statement_with_arguments(self._as_times_file_path, statement, arguments) - if len(current_rows) <= 0: - return None - return Models.ExperimentStatusRow(*current_rows[0]) - - - def create_exp_status(self, exp_id, expid, status): - # type: (int, str, str) -> None - """ - Create experiment status - """ - statement = ''' INSERT INTO experiment_status(exp_id, name, status, seconds_diff, modified) VALUES(?,?,?,?,?) ''' - arguments = (exp_id, expid, status, 0, HUtils.get_current_datetime()) - return self.insert_statement_with_arguments(self._as_times_file_path, statement, arguments) - - def update_exp_status(self, expid, status="RUNNING"): - # type: (str, str) -> None - """ - Update status, seconds_diff, modified in experiment_status. - """ - statement = ''' UPDATE experiment_status SET status = ?, seconds_diff = ?, modified = ? WHERE name = ? ''' - arguments = (status, 0, HUtils.get_current_datetime(), expid) - self.execute_statement_with_arguments_on_dbfile(self._as_times_file_path, statement, arguments) - - def delete_exp_status(self, expid): - # type: (str) -> None - """ Deletes experiment_status row by expid. Useful for testing purposes. """ - statement = ''' DELETE FROM experiment_status where name = ? ''' - arguments = (expid,) - self.execute_statement_with_arguments_on_dbfile(self._as_times_file_path, statement, arguments) \ No newline at end of file diff --git a/autosubmit_api/history/database_managers/test.py b/autosubmit_api/history/database_managers/test.py deleted file mode 100644 index 1b88b37..0000000 --- a/autosubmit_api/history/database_managers/test.py +++ /dev/null @@ -1,261 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import unittest -import time -import random -import os -from shutil import copy2 -from autosubmit_api.history.database_managers.experiment_history_db_manager import ExperimentHistoryDbManager -from autosubmit_api.history.database_managers.experiment_status_db_manager import ExperimentStatusDbManager -# from experiment_status_db_manager import ExperimentStatusDbManager -from autosubmit_api.history.data_classes.experiment_run import ExperimentRun -from autosubmit_api.history.data_classes.job_data import JobData -import autosubmit_api.history.database_managers.database_models as Models -from autosubmit_api.config.basicConfig import APIBasicConfig -import autosubmit_api.history.utils as HUtils - -EXPID_TT00_SOURCE = "test_database.db~" -EXPID_TT01_SOURCE = "test_database_no_run.db~" -EXPID = "t024" -EXPID_NONE = "t027" -# BasicConfig.read() -JOBDATA_DIR = APIBasicConfig.JOBDATA_DIR -LOCAL_ROOT_DIR = APIBasicConfig.LOCAL_ROOT_DIR - -class TestExperimentStatusDatabaseManager(unittest.TestCase): - """ Covers Experiment Status Database Manager """ - def setUp(self): - APIBasicConfig.read() - self.exp_status_db = ExperimentStatusDbManager(EXPID, APIBasicConfig) - if self.exp_status_db.get_experiment_status_row_by_expid(EXPID) == None: - self.exp_status_db.create_exp_status(7375, "t024", "NOT RUNNING") - - - def test_get_current_experiment_status_row(self): - exp_status_row = self.exp_status_db.get_experiment_status_row_by_expid(EXPID) - self.assertIsNotNone(exp_status_row) - exp_status_row_none = self.exp_status_db.get_experiment_status_row_by_expid(EXPID_NONE) - self.assertIsNone(exp_status_row_none) - exp_row_direct = self.exp_status_db.get_experiment_status_row_by_exp_id(exp_status_row.exp_id) - self.assertTrue(exp_status_row.exp_id == exp_row_direct.exp_id) - - - def test_update_exp_status(self): - self.exp_status_db.update_exp_status(EXPID, "RUNNING") - exp_status_row_current = self.exp_status_db.get_experiment_status_row_by_expid(EXPID) - self.assertTrue(exp_status_row_current.status == "RUNNING") - self.exp_status_db.update_exp_status(EXPID, "NOT RUNNING") - exp_status_row_current = self.exp_status_db.get_experiment_status_row_by_expid(EXPID) - self.assertTrue(exp_status_row_current.status == "NOT RUNNING") - - def test_create_exp_status(self): - experiment = self.exp_status_db.get_experiment_row_by_expid(EXPID_NONE) - self.exp_status_db.create_experiment_status_as_running(experiment) - experiment_status = self.exp_status_db.get_experiment_status_row_by_expid(EXPID_NONE) - self.assertIsNotNone(experiment_status) - self.exp_status_db.delete_exp_status(EXPID_NONE) - experiment_status = self.exp_status_db.get_experiment_status_row_by_expid(EXPID_NONE) - self.assertIsNone(experiment_status) - - -class TestExperimentHistoryDbManager(unittest.TestCase): - """ Covers Experiment History Database Manager and Data Models """ - def setUp(self): - APIBasicConfig.read() - source_path_tt00 = os.path.join(JOBDATA_DIR, EXPID_TT00_SOURCE) - self.target_path_tt00 = os.path.join(JOBDATA_DIR, "job_data_{0}.db".format(EXPID)) - copy2(source_path_tt00, self.target_path_tt00) - source_path_tt01 = os.path.join(JOBDATA_DIR, EXPID_TT01_SOURCE) - self.target_path_tt01 = os.path.join(JOBDATA_DIR, "job_data_{0}.db".format(EXPID_NONE)) - copy2(source_path_tt01, self.target_path_tt01) - self.experiment_database = ExperimentHistoryDbManager(EXPID, APIBasicConfig) - self.experiment_database.initialize() - - def tearDown(self): - os.remove(self.target_path_tt00) - os.remove(self.target_path_tt01) - - def test_get_max_id(self): - max_item = self.experiment_database.get_experiment_run_dc_with_max_id() - self.assertTrue(max_item.run_id > 0) - self.assertTrue(max_item.run_id >= 18) # Max is 18 - - def test_pragma(self): - self.assertTrue(self.experiment_database._get_pragma_version() == Models.DatabaseVersion.CURRENT_DB_VERSION.value) # Update version on changes - - def test_get_job_data(self): - job_data = self.experiment_database._get_job_data_last_by_name("a29z_20000101_fc0_1_SIM") - self.assertTrue(len(job_data) > 0) - self.assertTrue(job_data[0].last == 1) - self.assertTrue(job_data[0].job_name == "a29z_20000101_fc0_1_SIM") - - job_data = self.experiment_database.get_job_data_dcs_by_name("a29z_20000101_fc0_1_SIM") - self.assertTrue(job_data[0].job_name == "a29z_20000101_fc0_1_SIM") - - job_data = self.experiment_database._get_job_data_last_by_run_id(18) # Latest - self.assertTrue(len(job_data) > 0) - - job_data = self.experiment_database._get_job_data_last_by_run_id_and_finished(18) - self.assertTrue(len(job_data) > 0) - - job_data = self.experiment_database.get_job_data_all() - self.assertTrue(len(job_data) > 0) - - def test_insert_and_delete_experiment_run(self): - new_run = ExperimentRun(19) - new_id = self.experiment_database._insert_experiment_run(new_run) - self.assertIsNotNone(new_id) - last_experiment_run = self.experiment_database.get_experiment_run_dc_with_max_id() - self.assertTrue(new_id == last_experiment_run.run_id) - self.experiment_database.delete_experiment_run(new_id) - last_experiment_run = self.experiment_database.get_experiment_run_dc_with_max_id() - self.assertTrue(new_id != last_experiment_run.run_id) - - def test_insert_and_delete_job_data(self): - max_run_id = self.experiment_database.get_experiment_run_dc_with_max_id().run_id - new_job_data_name = "test_001_name_{0}".format(int(time.time())) - new_job_data = JobData(_id=1, job_name=new_job_data_name, run_id=max_run_id) - new_job_data_id = self.experiment_database._insert_job_data(new_job_data) - self.assertIsNotNone(new_job_data_id) - self.experiment_database.delete_job_data(new_job_data_id) - job_data = self.experiment_database.get_job_data_dcs_by_name(new_job_data_name) - self.assertTrue(len(job_data) == 0) - - - def test_update_experiment_run(self): - experiment_run_data_class = self.experiment_database.get_experiment_run_dc_with_max_id() # 18 - backup_run = self.experiment_database.get_experiment_run_dc_with_max_id() - experiment_run_data_class.chunk_unit = "unouno" - experiment_run_data_class.running = random.randint(1, 100) - experiment_run_data_class.queuing = random.randint(1, 100) - experiment_run_data_class.suspended = random.randint(1, 100) - self.experiment_database._update_experiment_run(experiment_run_data_class) - last_experiment_run = self.experiment_database.get_experiment_run_dc_with_max_id() # 18 - self.assertTrue(self.experiment_database.db_version == Models.DatabaseVersion.CURRENT_DB_VERSION.value) - self.assertTrue(last_experiment_run.chunk_unit == experiment_run_data_class.chunk_unit) - self.assertTrue(last_experiment_run.running == experiment_run_data_class.running) - self.assertTrue(last_experiment_run.queuing == experiment_run_data_class.queuing) - self.assertTrue(last_experiment_run.suspended == experiment_run_data_class.suspended) - self.experiment_database._update_experiment_run(backup_run) - - def test_job_data_from_model(self): - job_data_rows = self.experiment_database._get_job_data_last_by_name("a29z_20000101_fc0_1_SIM") - job_data_row_first = job_data_rows[0] - job_data_data_class = JobData.from_model(job_data_row_first) - self.assertTrue(job_data_row_first.job_name == job_data_data_class.job_name) - - def test_update_job_data_processed(self): - current_time = time.time() - job_data_rows = self.experiment_database._get_job_data_last_by_name("a29z_20000101_fc0_1_SIM") - job_data_row_first = job_data_rows[0] - job_data_data_class = JobData.from_model(job_data_row_first) - backup_job_dc = JobData.from_model(job_data_row_first) - job_data_data_class.nnodes = random.randint(1, 1000) - job_data_data_class.ncpus = random.randint(1, 1000) - job_data_data_class.status = "DELAYED" - job_data_data_class.finish = current_time - self.experiment_database._update_job_data_by_id(job_data_data_class) - job_data_rows_current = self.experiment_database._get_job_data_last_by_name("a29z_20000101_fc0_1_SIM") - job_data_row_first = job_data_rows_current[0] - self.assertTrue(job_data_row_first.nnodes == job_data_data_class.nnodes) - self.assertTrue(job_data_row_first.ncpus == job_data_data_class.ncpus) - self.assertTrue(job_data_row_first.status == job_data_data_class.status) - self.assertTrue(job_data_row_first.finish == job_data_data_class.finish) - self.experiment_database._update_job_data_by_id(backup_job_dc) - - def test_bulk_update(self): - current_time = time.time() - all_job_data_rows = self.experiment_database.get_job_data_all() - job_data_rows_test = [job for job in all_job_data_rows if job.run_id == 3] - backup = [JobData.from_model(job) for job in job_data_rows_test] - list_job_data_class = [JobData.from_model(job) for job in job_data_rows_test] - backup_changes = [(HUtils.get_current_datetime(), job.status, job.rowstatus, job._id) for job in list_job_data_class] - changes = [(HUtils.get_current_datetime(), "DELAYED", job.rowstatus, job._id) for job in list_job_data_class] - self.experiment_database.update_many_job_data_change_status(changes) - all_job_data_rows = self.experiment_database.get_job_data_all() - job_data_rows_validate = [job for job in all_job_data_rows if job.run_id == 3] - for (job_val, change_item) in zip(job_data_rows_validate, changes): - modified, status, rowstatus, _id = change_item - # self.assertTrue(job_val.finish == finish) - self.assertTrue(job_val.modified == modified) - self.assertTrue(job_val.status == status) - self.assertTrue(job_val.rowstatus == rowstatus) - self.assertTrue(job_val.id == _id) - self.experiment_database.update_many_job_data_change_status(backup_changes) - - def test_job_data_maxcounter(self): - new_job_data = ExperimentHistoryDbManager(EXPID_NONE, APIBasicConfig) - new_job_data.initialize() - max_empty_table_counter = new_job_data.get_job_data_max_counter() - self.assertTrue(max_empty_table_counter == 0) - max_existing_counter = self.experiment_database.get_job_data_max_counter() - self.assertTrue(max_existing_counter > 0) - - def test_register_submitted_job_data_dc(self): - job_data_dc = self.experiment_database.get_job_data_dc_unique_latest_by_job_name("a29z_20000101_fc0_1_SIM") - max_counter = self.experiment_database.get_job_data_max_counter() - self.assertTrue(max_counter > 0) - self.assertTrue(job_data_dc.counter > 0) - next_counter = max(max_counter, job_data_dc.counter + 1) - self.assertTrue(next_counter >= max_counter) - self.assertTrue(next_counter >= job_data_dc.counter + 1) - job_data_dc.counter = next_counter - job_data_dc_current = self.experiment_database.register_submitted_job_data_dc(job_data_dc) - self.assertTrue(job_data_dc._id < job_data_dc_current._id) - job_data_last_list = self.experiment_database._get_job_data_last_by_name(job_data_dc.job_name) - self.assertTrue(len(job_data_last_list) == 1) - self.experiment_database.delete_job_data(job_data_last_list[0].id) - job_data_dc.last = 1 - updated_job_data_dc = self.experiment_database.update_job_data_dc_by_id(job_data_dc) - self.assertTrue(job_data_dc._id == updated_job_data_dc._id) - job_data_dc = self.experiment_database.get_job_data_dc_unique_latest_by_job_name("a29z_20000101_fc0_1_SIM") - self.assertTrue(job_data_dc._id == updated_job_data_dc._id) - - def test_update_children_and_platform_output(self): - job_data_dc = self.experiment_database.get_job_data_dc_unique_latest_by_job_name("a29z_20000101_fc0_1_SIM") - children_str = "a00, a01, a02" - platform_output_str = " SLURM OUTPUT " - job_data_dc.children = children_str - job_data_dc.platform_output = platform_output_str - self.assertTrue(self.experiment_database.db_version == Models.DatabaseVersion.CURRENT_DB_VERSION.value) - self.experiment_database.update_job_data_dc_by_id(job_data_dc) - job_data_dc_updated = self.experiment_database.get_job_data_dc_unique_latest_by_job_name("a29z_20000101_fc0_1_SIM") - self.assertTrue(job_data_dc_updated.children == children_str) - self.assertTrue(job_data_dc_updated.platform_output == platform_output_str) - # Back to normal - job_data_dc.children = "" - job_data_dc.platform_output = "NO OUTPUT" - self.experiment_database.update_job_data_dc_by_id(job_data_dc) - job_data_dc_updated = self.experiment_database.get_job_data_dc_unique_latest_by_job_name("a29z_20000101_fc0_1_SIM") - self.assertTrue(job_data_dc_updated.children == "") - self.assertTrue(job_data_dc_updated.platform_output == "NO OUTPUT") - - - - def test_experiment_run_dc(self): - experiment_run = self.experiment_database.get_experiment_run_dc_with_max_id() - self.assertIsNotNone(experiment_run) - - def test_if_database_not_exists(self): - exp_manager = ExperimentHistoryDbManager("0000", APIBasicConfig) - self.assertTrue(exp_manager.my_database_exists() == False) - - -if __name__ == '__main__': - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/history/experiment_status.py b/autosubmit_api/history/experiment_status.py deleted file mode 100644 index d9046aa..0000000 --- a/autosubmit_api/history/experiment_status.py +++ /dev/null @@ -1,81 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import traceback -from .database_managers.experiment_status_db_manager import ExperimentStatusDbManager -from .database_managers.database_manager import DEFAULT_LOCAL_ROOT_DIR, DEFAULT_HISTORICAL_LOGS_DIR -from .internal_logging import Logging -from ..config.basicConfig import APIBasicConfig -from typing import List -from .database_managers.database_models import ExperimentStatusRow - -class ExperimentStatus(): - """ Represents the Experiment Status Mechanism that keeps track of currently active experiments """ - def __init__(self, expid): - # type: (str) -> None - self.expid = expid # type: str - print(expid) - APIBasicConfig.read() - try: - self.manager = ExperimentStatusDbManager(self.expid, APIBasicConfig) - except Exception as exp: - message = "Error while trying to update {0} in experiment_status.".format(str(self.expid)) - print(message) - print(str(exp)) - print() - Logging(self.expid, APIBasicConfig).log(message, traceback.format_exc()) - self.manager = None - - def validate_database(self): - # type: () -> None - self.manager.validate_status_database() - - def get_current_table_content(self): - # type: () -> List[ExperimentStatusRow] - return self.manager.get_experiment_table_content() - - def set_as_running(self): - # type: () -> ExperimentStatusRow - """ Set the status of the experiment in experiment_status of as_times.db as RUNNING. Inserts row if necessary.""" - if not self.manager: - raise Exception("ExperimentStatus: The database manager is not available.") - exp_status_row = self.manager.get_experiment_status_row_by_expid(self.expid) - if exp_status_row: - self.manager.set_existing_experiment_status_as_running(exp_status_row.name) - return self.manager.get_experiment_status_row_by_expid(self.expid) - else: - exp_row = self.manager.get_experiment_row_by_expid(self.expid) - if exp_row: - self.manager.create_experiment_status_as_running(exp_row) - return self.manager.get_experiment_status_row_by_expid(self.expid) - else: - print(("Couldn't find {} in the main database. There is not enough information to set it as running.".format(self.expid))) - return self.manager.default_experiment_status_row - - - def set_as_not_running(self): - # type: () -> None - """ Deletes row by expid. """ - if not self.manager: - raise Exception("ExperimentStatus: The database manager is not available.") - exp_status_row = self.manager.get_experiment_status_row_by_expid(self.expid) - if not exp_status_row: - # raise Exception("ExperimentStatus: Query error, experiment {} not found in status table.".format(self.expid)) - pass # If it is not in the status table, we don't need to worry about it. - else: - self.manager.delete_exp_status(exp_status_row.name) diff --git a/autosubmit_api/history/experiment_status_manager.py b/autosubmit_api/history/experiment_status_manager.py deleted file mode 100644 index 8a79477..0000000 --- a/autosubmit_api/history/experiment_status_manager.py +++ /dev/null @@ -1,89 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import os -import time -import subprocess -from .experiment_status import ExperimentStatus -from ..config.basicConfig import APIBasicConfig -from ..experiment.common_requests import _is_exp_running -from ..common.utils import get_experiments_from_folder -from typing import Dict, Set -from .utils import SAFE_TIME_LIMIT_STATUS -from . import utils as HUtils - - - -class ExperimentStatusManager(object): - """ Manages the update of the status table. """ - def __init__(self): - APIBasicConfig.read() - self._basic_config = APIBasicConfig - self._experiments_updated = set() - self._local_root_path = self._basic_config.LOCAL_ROOT_DIR - self._base_experiment_status = ExperimentStatus("0000") - self._base_experiment_status.validate_database() - self._validate_configuration() - self._creation_timestamp = int(time.time()) - - def _validate_configuration(self): - # type: () -> None - if not os.path.exists(self._local_root_path): - raise Exception("Experiment Status Manager: LOCAL ROOT DIR not found.") - - def update_running_experiments(self, time_condition=600): - # type: (int) -> None - """ - Tests if an experiment is running and updates database as_times.db accordingly.\n - :return: Nothing - """ - - # start_reading_folders = int(time.time()) - # currentDirectories = subprocess.Popen(['ls', '-t', self._local_root_path], stdout=subprocess.PIPE, stderr=subprocess.STDOUT) - # stdOut, _ = currentDirectories.communicate() - # readingpkl = stdOut.split() - # time_reading_folders = int(time.time()) - start_reading_folders - readingpkl = get_experiments_from_folder(self._local_root_path) - # Update those that are RUNNING - for expid in readingpkl: - pkl_path = os.path.join(self._local_root_path, str(expid), "pkl", "job_list_{0}.pkl".format(str(expid))) - if not len(expid) == 4 or not os.path.exists(pkl_path): - continue - time_spent = int(time.time()) - self._creation_timestamp - if time_spent > SAFE_TIME_LIMIT_STATUS: - raise Exception( - "Time limit reached {0} seconds on update_running_experiments while processing {1}. \ - Time spent on reading data {2} seconds.".format(time_spent, expid, time_reading_folders)) - time_diff = int(time.time()) - int(os.stat(pkl_path).st_mtime) - if (time_diff < time_condition): - self._experiments_updated.add(ExperimentStatus(expid).set_as_running().exp_id) - elif (time_diff <= 3600): - _, _ , is_running, _, _ = _is_exp_running(expid) # Exhaustive validation - if is_running == True: - self._experiments_updated.add(ExperimentStatus(expid).set_as_running().exp_id) - # Update those that were RUNNING - self._detect_and_delete_not_running() - - def _detect_and_delete_not_running(self): - # type: () -> None - current_rows = self._base_experiment_status.get_current_table_content() - for experiment_status_row in current_rows: - if experiment_status_row.status == "RUNNING" and experiment_status_row.exp_id not in self._experiments_updated: - _, _, is_running, _, _ = _is_exp_running(experiment_status_row.name) # Exhaustive validation - if is_running == False: - ExperimentStatus(experiment_status_row.name).set_as_not_running() \ No newline at end of file diff --git a/autosubmit_api/persistance/__init__.py b/autosubmit_api/persistance/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/autosubmit_api/persistance/experiment.py b/autosubmit_api/persistance/experiment.py new file mode 100644 index 0000000..71151ae --- /dev/null +++ b/autosubmit_api/persistance/experiment.py @@ -0,0 +1,33 @@ +import os +from autosubmit_api.config.basicConfig import APIBasicConfig + + +class ExperimentPaths: + """ + Helper class that builds related directories/files paths of an experiment + """ + + def __init__(self, expid: str) -> None: + self._expid = expid + + @property + def expid(self): + return self._expid + + @property + def exp_dir(self): + return os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, self.expid) + + @property + def pkl_dir(self): + return os.path.join(self.exp_dir, "pkl") + + @property + def job_list_pkl(self): + filename = f"job_list_{self.expid}.pkl" + return os.path.join(self.pkl_dir, filename) + + @property + def job_packages_db(self): + filename = f"job_packages_{self.expid}.db" + return os.path.join(self.pkl_dir, filename) diff --git a/autosubmit_api/workers/populate_running_experiments.py b/autosubmit_api/workers/populate_running_experiments.py index c0fe4ce..9355539 100644 --- a/autosubmit_api/workers/populate_running_experiments.py +++ b/autosubmit_api/workers/populate_running_experiments.py @@ -1,11 +1,11 @@ # import autosubmitAPIwu.experiment.common_requests as ExperimentUtils -from autosubmit_api.bgtasks.bgtask import PopulateRunningExperiments +from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater def main(): """ Updates STATUS of experiments. """ - PopulateRunningExperiments.run() + StatusUpdater.run() if __name__ == "__main__": diff --git a/autosubmit_api/workers/test.py b/autosubmit_api/workers/test.py deleted file mode 100644 index cd2a57b..0000000 --- a/autosubmit_api/workers/test.py +++ /dev/null @@ -1,18 +0,0 @@ -import unittest - -import workers.business.process_graph_drawings as ProcessGraph -from builders.configuration_facade_builder import ConfigurationFacadeDirector, AutosubmitConfigurationFacadeBuilder - -class TestGraphDraw(unittest.TestCase): - def setUp(self): - pass - - def test_graph_drawing_generator(self): - EXPID = "a29z" - autosubmit_configuration_facade = ConfigurationFacadeDirector(AutosubmitConfigurationFacadeBuilder(EXPID)).build_autosubmit_configuration_facade() - result = ProcessGraph._process_graph(EXPID, autosubmit_configuration_facade.chunk_size) - self.assertTrue(result == None) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff --git a/tests/bgtasks/test_status_updater.py b/tests/bgtasks/test_status_updater.py new file mode 100644 index 0000000..7e4db33 --- /dev/null +++ b/tests/bgtasks/test_status_updater.py @@ -0,0 +1,26 @@ +from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater +from autosubmit_api.database import tables +from autosubmit_api.database.common import ( + create_autosubmit_db_engine, + create_as_times_db_engine, +) +from autosubmit_api.history.database_managers.database_models import RunningStatus + +class TestStatusUpdater: + + def test_same_tables(self, fixture_mock_basic_config): + + StatusUpdater.run() + + with create_autosubmit_db_engine().connect() as conn: + experiments = conn.execute(tables.experiment_table.select()).all() + + with create_as_times_db_engine().connect() as conn: + exps_status = conn.execute(tables.experiment_status_table.select()).all() + + assert len(experiments) == len(exps_status) + assert set([x.id for x in experiments]) == set([x.exp_id for x in exps_status]) + assert set([x.name for x in experiments]) == set([x.name for x in exps_status]) + + for e_st in exps_status: + assert e_st.status in [RunningStatus.RUNNING, RunningStatus.NOT_RUNNING] diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index ef93733acc0d1b1e25f8f3577df6df68f498c66a..6f9bb2a2aaa0b33bf250e8e0ba4b93858abcc5bd 100644 GIT binary patch delta 166 zcmZozz}T>Wae_3X%tRSyRv8ApqD3217T9w!^EWZ@U*liH-?Uj!poG6pgPDy%RGGs# z(YPeZ&p$*VDAdo-)6d<=z{o_`z)087D8$gr%D~9V&`5&`s?xx~oPbJ3xJqOEDgjua BCR_jj delta 28 kcmZozz}T>Wae_1>`$QRMR(1xxyj>ep7T9lQ5%|Lo0Db2P4gdfE -- GitLab From c04fb95eaecdaac3fb2cc0b03431581815af0058 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Tue, 13 Feb 2024 11:15:36 +0100 Subject: [PATCH 03/18] moved job times updater --- autosubmit_api/bgtasks/bgtask.py | 10 --- autosubmit_api/bgtasks/scheduler.py | 4 +- .../bgtasks/tasks/job_times_updater.py | 60 ++++++++++++++++++ .../bgtasks/tasks/status_updater.py | 2 +- .../experiment/configuration_facade.py | 13 ++-- autosubmit_api/experiment/common_requests.py | 47 -------------- autosubmit_api/experiment/test.py | 45 ------------- autosubmit_api/persistance/experiment.py | 12 ++++ autosubmit_api/workers/verify_complete.py | 4 +- tests/experiments/as_times.db | Bin 20480 -> 20480 bytes 10 files changed, 85 insertions(+), 112 deletions(-) create mode 100644 autosubmit_api/bgtasks/tasks/job_times_updater.py delete mode 100644 autosubmit_api/experiment/test.py diff --git a/autosubmit_api/bgtasks/bgtask.py b/autosubmit_api/bgtasks/bgtask.py index eeefa36..c043c57 100644 --- a/autosubmit_api/bgtasks/bgtask.py +++ b/autosubmit_api/bgtasks/bgtask.py @@ -1,7 +1,6 @@ from abc import ABC, abstractmethod import traceback from autosubmit_api.logger import logger -from autosubmit_api.experiment import common_requests from autosubmit_api.config.basicConfig import APIBasicConfig from autosubmit_api.workers.business import populate_times, process_graph_drawings from autosubmit_api.workers.populate_details.populate import DetailsProcessor @@ -61,15 +60,6 @@ class PopulateQueueRuntimes(BackgroundTaskTemplate): populate_times.process_completed_times() -class VerifyComplete(BackgroundTaskTemplate): - id = "TASK_VRFCMPT" - trigger_options = {"trigger": "interval", "minutes": 10} - - @classmethod - def procedure(cls): - common_requests.verify_last_completed(1800) - - class PopulateGraph(BackgroundTaskTemplate): id = "TASK_POPGRPH" trigger_options = {"trigger": "interval", "hours": 24} diff --git a/autosubmit_api/bgtasks/scheduler.py b/autosubmit_api/bgtasks/scheduler.py index a941e39..7623f8a 100644 --- a/autosubmit_api/bgtasks/scheduler.py +++ b/autosubmit_api/bgtasks/scheduler.py @@ -4,9 +4,9 @@ from autosubmit_api.bgtasks.bgtask import ( BackgroundTaskTemplate, PopulateDetailsDB, PopulateQueueRuntimes, - VerifyComplete, PopulateGraph, ) +from autosubmit_api.bgtasks.tasks.job_times_updater import JobTimesUpdater from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater from autosubmit_api.config import ( DISABLE_BACKGROUND_TASKS, @@ -19,7 +19,7 @@ REGISTERED_TASKS: List[BackgroundTaskTemplate] = [ PopulateDetailsDB, PopulateQueueRuntimes, StatusUpdater, - VerifyComplete, + JobTimesUpdater, PopulateGraph, ] diff --git a/autosubmit_api/bgtasks/tasks/job_times_updater.py b/autosubmit_api/bgtasks/tasks/job_times_updater.py new file mode 100644 index 0000000..e47ca18 --- /dev/null +++ b/autosubmit_api/bgtasks/tasks/job_times_updater.py @@ -0,0 +1,60 @@ +import os +import time +from autosubmit_api.bgtasks.bgtask import BackgroundTaskTemplate +from autosubmit_api.common import utils as common_utils +from autosubmit_api.components.jobs import utils as JUtils +from autosubmit_api.config.basicConfig import APIBasicConfig +from autosubmit_api.experiment import common_db_requests as DbRequests +from autosubmit_api.experiment.common_requests import SAFE_TIME_LIMIT + + +def verify_last_completed(seconds=300): + """ + Verifying last 300 seconds by default + """ + # Basic info + t0 = time.time() + APIBasicConfig.read() + # Current timestamp + current_st = time.time() + # Current latest detail + td0 = time.time() + latest_detail = DbRequests.get_latest_completed_jobs(seconds) + t_data = time.time() - td0 + # Main Loop + for job_name, detail in list(latest_detail.items()): + tmp_path = os.path.join( + APIBasicConfig.LOCAL_ROOT_DIR, job_name[:4], APIBasicConfig.LOCAL_TMP_DIR) + detail_id, submit, start, finish, status = detail + submit_time, start_time, finish_time, status_text_res = JUtils.get_job_total_stats( + common_utils.Status.COMPLETED, job_name, tmp_path) + submit_ts = int(time.mktime(submit_time.timetuple())) if len( + str(submit_time)) > 0 else 0 + start_ts = int(time.mktime(start_time.timetuple())) if len( + str(start_time)) > 0 else 0 + finish_ts = int(time.mktime(finish_time.timetuple())) if len( + str(finish_time)) > 0 else 0 + if (finish_ts != finish): + #print("\tMust Update") + DbRequests.update_job_times(detail_id, + int(current_st), + submit_ts, + start_ts, + finish_ts, + status, + debug=False, + no_modify_time=True) + t1 = time.time() + # Timer safeguard + if (t1 - t0) > SAFE_TIME_LIMIT: + raise Exception( + "Time limit reached {0:06.2f} seconds on verify_last_completed while reading {1}. Time spent on reading data {2:06.2f} seconds.".format((t1 - t0), job_name, t_data)) + + +class JobTimesUpdater(BackgroundTaskTemplate): + id = "TASK_JBTMUPDTR" + trigger_options = {"trigger": "interval", "minutes": 10} + + @classmethod + def procedure(cls): + verify_last_completed(1800) \ No newline at end of file diff --git a/autosubmit_api/bgtasks/tasks/status_updater.py b/autosubmit_api/bgtasks/tasks/status_updater.py index 91eb99f..186be6f 100644 --- a/autosubmit_api/bgtasks/tasks/status_updater.py +++ b/autosubmit_api/bgtasks/tasks/status_updater.py @@ -92,7 +92,7 @@ class StatusUpdater(BackgroundTaskTemplate): else RunningStatus.NOT_RUNNING ), seconds_diff=0, - modified=datetime.now().isoformat(timespec="seconds"), + modified=datetime.now().isoformat(sep="-", timespec="seconds"), ) conn.execute(del_stmnt) conn.execute(ins_stmnt) diff --git a/autosubmit_api/components/experiment/configuration_facade.py b/autosubmit_api/components/experiment/configuration_facade.py index 47762a2..8ff5fad 100644 --- a/autosubmit_api/components/experiment/configuration_facade.py +++ b/autosubmit_api/components/experiment/configuration_facade.py @@ -11,6 +11,8 @@ from abc import ABCMeta, abstractmethod from autosubmit_api.common.utils import JobSection, parse_number_processors, timestamp_to_datetime_format, datechunk_to_year from typing import List +from autosubmit_api.persistance.experiment import ExperimentPaths + class ProjectType: GIT = "git" SVN = "svn" @@ -40,11 +42,12 @@ class ConfigurationFacade(metaclass=ABCMeta): def _process_basic_config(self): # type: () -> None - self.pkl_filename = "job_list_{0}.pkl".format(self.expid) - self.experiment_path = os.path.join(self.basic_configuration.LOCAL_ROOT_DIR, self.expid) - self.pkl_path = os.path.join(self.basic_configuration.LOCAL_ROOT_DIR, self.expid, "pkl", self.pkl_filename) - self.tmp_path = os.path.join(self.basic_configuration.LOCAL_ROOT_DIR, self.expid, self.basic_configuration.LOCAL_TMP_DIR) - self.log_path = os.path.join(self.basic_configuration.LOCAL_ROOT_DIR, self.expid, "tmp", "LOG_{0}".format(self.expid)) + exp_paths = ExperimentPaths(self.expid) + self.pkl_filename = os.path.basename(exp_paths.job_list_pkl) + self.experiment_path = exp_paths.exp_dir + self.pkl_path = exp_paths.job_list_pkl + self.tmp_path = exp_paths.tmp_dir + self.log_path = exp_paths.tmp_log_dir self.structures_path = self.basic_configuration.STRUCTURES_DIR if not os.path.exists(self.experiment_path): raise IOError("Experiment folder {0} not found".format(self.experiment_path)) if not os.path.exists(self.pkl_path): raise IOError("Required file {0} not found.".format(self.pkl_path)) diff --git a/autosubmit_api/experiment/common_requests.py b/autosubmit_api/experiment/common_requests.py index dce9f43..f963dad 100644 --- a/autosubmit_api/experiment/common_requests.py +++ b/autosubmit_api/experiment/common_requests.py @@ -769,53 +769,6 @@ def get_experiment_tree_structured(expid, log): return {'tree': [], 'jobs': [], 'total': 0, 'reference': [], 'error': True, 'error_message': str(e), 'pkl_timestamp': 0} -def verify_last_completed(seconds=300): - """ - Verifying last 300 seconds by default - """ - # Basic info - t0 = time.time() - APIBasicConfig.read() - # Current timestamp - current_st = time.time() - # Connection - path = APIBasicConfig.LOCAL_ROOT_DIR - db_file = os.path.join(path, DbRequests.DB_FILE_AS_TIMES) - conn = DbRequests.create_connection(db_file) - # Current latest detail - td0 = time.time() - latest_detail = DbRequests.get_latest_completed_jobs(seconds) - t_data = time.time() - td0 - # Main Loop - for job_name, detail in list(latest_detail.items()): - tmp_path = os.path.join( - APIBasicConfig.LOCAL_ROOT_DIR, job_name[:4], APIBasicConfig.LOCAL_TMP_DIR) - detail_id, submit, start, finish, status = detail - submit_time, start_time, finish_time, status_text_res = JUtils.get_job_total_stats( - common_utils.Status.COMPLETED, job_name, tmp_path) - submit_ts = int(time.mktime(submit_time.timetuple())) if len( - str(submit_time)) > 0 else 0 - start_ts = int(time.mktime(start_time.timetuple())) if len( - str(start_time)) > 0 else 0 - finish_ts = int(time.mktime(finish_time.timetuple())) if len( - str(finish_time)) > 0 else 0 - if (finish_ts != finish): - #print("\tMust Update") - DbRequests.update_job_times(detail_id, - int(current_st), - submit_ts, - start_ts, - finish_ts, - status, - debug=False, - no_modify_time=True) - t1 = time.time() - # Timer safeguard - if (t1 - t0) > SAFE_TIME_LIMIT: - raise Exception( - "Time limit reached {0:06.2f} seconds on verify_last_completed while reading {1}. Time spent on reading data {2:06.2f} seconds.".format((t1 - t0), job_name, t_data)) - - def get_experiment_counters(expid): """ Returns status counters of the experiment. diff --git a/autosubmit_api/experiment/test.py b/autosubmit_api/experiment/test.py deleted file mode 100644 index d3e98f7..0000000 --- a/autosubmit_api/experiment/test.py +++ /dev/null @@ -1,45 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015 Earth Sciences Department, BSC-CNS - -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import unittest - -from experiment.common_requests import get_job_history, get_experiment_data - -class TestCommonRequests(unittest.TestCase): - def setUp(self): - pass - - def test_get_history(self): - result = get_job_history("a3z4", "a3z4_19951101_fc8_1_SIM") - print(result) - self.assertTrue(result != None) - - def test_get_experiment_data(self): - result = get_experiment_data("a29z") - print(result) - result2 = get_experiment_data("a4a0") - print(result2) - result3 = get_experiment_data("a2am") - print(result3) - self.assertTrue(result != None) - self.assertTrue(result2 != None) - self.assertTrue(result3 != None) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/persistance/experiment.py b/autosubmit_api/persistance/experiment.py index 71151ae..d34370e 100644 --- a/autosubmit_api/persistance/experiment.py +++ b/autosubmit_api/persistance/experiment.py @@ -31,3 +31,15 @@ class ExperimentPaths: def job_packages_db(self): filename = f"job_packages_{self.expid}.db" return os.path.join(self.pkl_dir, filename) + + @property + def tmp_dir(self): + return os.path.join(self.exp_dir, APIBasicConfig.LOCAL_TMP_DIR) + + @property + def tmp_dir(self): + return os.path.join(self.exp_dir, APIBasicConfig.LOCAL_TMP_DIR) + + @property + def tmp_log_dir(self): + return os.path.join(self.tmp_dir, f"LOG_{self.expid}") \ No newline at end of file diff --git a/autosubmit_api/workers/verify_complete.py b/autosubmit_api/workers/verify_complete.py index a8e85a4..490b9d4 100644 --- a/autosubmit_api/workers/verify_complete.py +++ b/autosubmit_api/workers/verify_complete.py @@ -1,9 +1,9 @@ #!/usr/bin/env python -from autosubmit_api.bgtasks.bgtask import VerifyComplete +from autosubmit_api.bgtasks.tasks.job_times_updater import JobTimesUpdater def main(): - VerifyComplete.run() + JobTimesUpdater.run() if __name__ == "__main__": diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 6f9bb2a2aaa0b33bf250e8e0ba4b93858abcc5bd..a829b9ce72f6fb798f35448dfa62f9f98e8d282c 100644 GIT binary patch delta 54 xcmZozz}T>Wae_3X{6raNM){2iPX6r1x`u{UhNhEO`YXfPm;IHwpyF1BMgX1X4j}*l delta 54 xcmZozz}T>Wae_3X%tRSyMwyKXPX6phA% Date: Tue, 13 Feb 2024 11:28:20 +0100 Subject: [PATCH 04/18] removed currently_running view --- autosubmit_api/database/extended_db.py | 3 - .../experiment/common_db_requests.py | 33 ----- .../business/process_graph_drawings.py | 113 +++++++++++------- tests/experiments/as_times.db | Bin 20480 -> 20480 bytes 4 files changed, 71 insertions(+), 78 deletions(-) diff --git a/autosubmit_api/database/extended_db.py b/autosubmit_api/database/extended_db.py index d246901..3cfc703 100644 --- a/autosubmit_api/database/extended_db.py +++ b/autosubmit_api/database/extended_db.py @@ -29,8 +29,5 @@ class ExtendedDB: def prepare_as_times_db(self): prepare_completed_times_db() prepare_status_db() - self.as_times_db_manager.create_view('currently_running', - 'select s.name, s.status, t.total_jobs from experiment_status as s inner join experiment_times as t on s.name = t.name where s.status="RUNNING" ORDER BY t.total_jobs' - ) diff --git a/autosubmit_api/experiment/common_db_requests.py b/autosubmit_api/experiment/common_db_requests.py index 752d5e8..9d9d4a1 100644 --- a/autosubmit_api/experiment/common_db_requests.py +++ b/autosubmit_api/experiment/common_db_requests.py @@ -324,22 +324,6 @@ def get_experiment_status(): return experiment_status -def get_currently_running_experiments(): - """ - Gets the list of currently running experiments ordered by total_jobs - Connects to AS_TIMES - :return: map of expid -> total_jobs - :rtype: OrderedDict() str -> int - """ - experiment_running = OrderedDict() - current_running = _get_exp_only_active() - if current_running: - for item in current_running: - name, status, total_jobs = item - experiment_running[name] = total_jobs - return experiment_running - - def get_specific_experiment_status(expid): """ Gets the current status from database.\n @@ -653,23 +637,6 @@ def _get_exp_status(): return dict() -def _get_exp_only_active(): - """ - Get all registers of experiments ACTIVE - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - conn.text_factory = str - cur = conn.cursor() - cur.execute("select name, status, total_jobs from currently_running") - rows = cur.fetchall() - return rows - except Exception as exp: - print((traceback.format_exc())) - print(exp) - return None - - def _get_specific_exp_status(expid): """ Get all registers from experiment_status.\n diff --git a/autosubmit_api/workers/business/process_graph_drawings.py b/autosubmit_api/workers/business/process_graph_drawings.py index 7a51772..c6fa84c 100644 --- a/autosubmit_api/workers/business/process_graph_drawings.py +++ b/autosubmit_api/workers/business/process_graph_drawings.py @@ -1,49 +1,78 @@ import time import traceback -from ...experiment import common_db_requests as DbRequests -from ...common import utils as common_utils -from ...database.db_jobdata import ExperimentGraphDrawing -from ...builders.configuration_facade_builder import ConfigurationFacadeDirector, AutosubmitConfigurationFacadeBuilder -from ...builders.joblist_loader_builder import JobListLoaderBuilder, JobListLoaderDirector, JobListHelperBuilder +from autosubmit_api.database import tables +from autosubmit_api.database.common import create_as_times_db_engine +from autosubmit_api.common import utils as common_utils +from autosubmit_api.database.db_jobdata import ExperimentGraphDrawing +from autosubmit_api.builders.configuration_facade_builder import ( + ConfigurationFacadeDirector, + AutosubmitConfigurationFacadeBuilder, +) +from autosubmit_api.builders.joblist_loader_builder import ( + JobListLoaderBuilder, + JobListLoaderDirector, +) from typing import List, Any + def process_active_graphs(): - """ - Process the list of active experiments to generate the positioning of their graphs - """ - try: - currently_running = DbRequests.get_currently_running_experiments() - - for expid in currently_running: - - try: - autosubmit_configuration_facade = ConfigurationFacadeDirector(AutosubmitConfigurationFacadeBuilder(expid)).build_autosubmit_configuration_facade() - if common_utils.is_version_historical_ready(autosubmit_configuration_facade.get_autosubmit_version()): - # job_count = currently_running.get(expid, 0) - _process_graph(expid, autosubmit_configuration_facade.chunk_size) - except Exception as exp: - print((traceback.format_exc())) - print(("Error while processing: {}".format(expid))) - - except Exception as exp: - print((traceback.format_exc())) - print(("Error while processing graph drawing: {}".format(exp))) + """ + Process the list of active experiments to generate the positioning of their graphs + """ + try: + with create_as_times_db_engine().connect() as conn: + query_result = conn.execute( + tables.experiment_status_table.select().where() + ).all() + + active_experiments: List[str] = [exp.name for exp in query_result] + + for expid in active_experiments: + try: + autosubmit_configuration_facade = ConfigurationFacadeDirector( + AutosubmitConfigurationFacadeBuilder(expid) + ).build_autosubmit_configuration_facade() + if common_utils.is_version_historical_ready( + autosubmit_configuration_facade.get_autosubmit_version() + ): + _process_graph(expid, autosubmit_configuration_facade.chunk_size) + except Exception as exp: + print((traceback.format_exc())) + print(("Error while processing: {}".format(expid))) + + except Exception as exp: + print((traceback.format_exc())) + print(("Error while processing graph drawing: {}".format(exp))) + def _process_graph(expid, chunk_size): - # type: (str, int) -> List[Any] | None - result = None - experimentGraphDrawing = ExperimentGraphDrawing(expid) - locked = experimentGraphDrawing.locked - # print("Start Processing {} with {} jobs".format(expid, job_count)) - if not locked: - start_time = time.time() - job_list_loader = JobListLoaderDirector(JobListLoaderBuilder(expid)).build_loaded_joblist_loader() - current_data = experimentGraphDrawing.get_validated_data(job_list_loader.jobs) - if not current_data: - print(("Must update {}".format(expid))) - result = experimentGraphDrawing.calculate_drawing(job_list_loader.jobs, independent=False, num_chunks=chunk_size, job_dictionary=job_list_loader.job_dictionary) - print(("Time Spent in {}: {} seconds.".format(expid, int(time.time() - start_time)))) - else: - print(("{} Locked".format(expid))) - - return result \ No newline at end of file + # type: (str, int) -> List[Any] | None + result = None + experimentGraphDrawing = ExperimentGraphDrawing(expid) + locked = experimentGraphDrawing.locked + # print("Start Processing {} with {} jobs".format(expid, job_count)) + if not locked: + start_time = time.time() + job_list_loader = JobListLoaderDirector( + JobListLoaderBuilder(expid) + ).build_loaded_joblist_loader() + current_data = experimentGraphDrawing.get_validated_data(job_list_loader.jobs) + if not current_data: + print(("Must update {}".format(expid))) + result = experimentGraphDrawing.calculate_drawing( + job_list_loader.jobs, + independent=False, + num_chunks=chunk_size, + job_dictionary=job_list_loader.job_dictionary, + ) + print( + ( + "Time Spent in {}: {} seconds.".format( + expid, int(time.time() - start_time) + ) + ) + ) + else: + print(("{} Locked".format(expid))) + + return result diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index a829b9ce72f6fb798f35448dfa62f9f98e8d282c..dd846a25021a24072ee08856906e7775e5fdcf6d 100644 GIT binary patch delta 45 pcmZozz}T>Wae_3X(nJ|&Mx~7j?*6Ps=2oVblh^pGLRr^fEC4T-44nV~ delta 45 pcmZozz}T>Wae_3X{6raNM){2i?*6QXrdEbVlh^pGLRr^fEC4Lk3~c}a -- GitLab From f127898685fb16cb9b759c51bb074899bf089a2f Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Tue, 13 Feb 2024 14:56:40 +0100 Subject: [PATCH 05/18] removed usage of experiment_times and job_times --- .../autosubmit_legacy/job/job_list.py | 2 +- autosubmit_api/bgtasks/scheduler.py | 4 ++-- .../bgtasks/tasks/job_times_updater.py | 2 +- autosubmit_api/database/__init__.py | 7 +++++++ autosubmit_api/database/db_common.py | 8 ++++---- autosubmit_api/database/extended_db.py | 8 ++------ autosubmit_api/database/queries.py | 8 -------- autosubmit_api/database/tables.py | 11 ----------- autosubmit_api/experiment/common_requests.py | 3 ++- .../experiment_history_db_manager.py | 5 +---- autosubmit_api/views/v4.py | 8 ++------ .../workers/business/populate_times.py | 2 +- tests/bgtasks/test_status_updater.py | 3 ++- tests/conftest.py | 6 +++++- tests/experiments/as_times.db | Bin 20480 -> 8192 bytes .../metadata/data/job_data_a007.db | 0 .../metadata/data/job_data_a3tb.db | Bin 0 -> 750592 bytes tests/test_endpoints_v3.py | 6 +----- 18 files changed, 31 insertions(+), 52 deletions(-) create mode 100755 tests/experiments/metadata/data/job_data_a007.db create mode 100644 tests/experiments/metadata/data/job_data_a3tb.db diff --git a/autosubmit_api/autosubmit_legacy/job/job_list.py b/autosubmit_api/autosubmit_legacy/job/job_list.py index 40cff2a..2715556 100644 --- a/autosubmit_api/autosubmit_legacy/job/job_list.py +++ b/autosubmit_api/autosubmit_legacy/job/job_list.py @@ -590,7 +590,7 @@ class JobList: conn = DbRequests.create_connection(db_file) # job_data = None # Job information from worker database - job_times = DbRequests.get_times_detail_by_expid(conn, expid) + job_times = dict() # REMOVED: DbRequests.get_times_detail_by_expid(conn, expid) conn.close() # Job information from job historic data # print("Get current job data structure...") diff --git a/autosubmit_api/bgtasks/scheduler.py b/autosubmit_api/bgtasks/scheduler.py index 7623f8a..26aafc5 100644 --- a/autosubmit_api/bgtasks/scheduler.py +++ b/autosubmit_api/bgtasks/scheduler.py @@ -17,9 +17,9 @@ from autosubmit_api.logger import logger, with_log_run_times REGISTERED_TASKS: List[BackgroundTaskTemplate] = [ PopulateDetailsDB, - PopulateQueueRuntimes, + # PopulateQueueRuntimes, StatusUpdater, - JobTimesUpdater, + # JobTimesUpdater, PopulateGraph, ] diff --git a/autosubmit_api/bgtasks/tasks/job_times_updater.py b/autosubmit_api/bgtasks/tasks/job_times_updater.py index e47ca18..dd8c817 100644 --- a/autosubmit_api/bgtasks/tasks/job_times_updater.py +++ b/autosubmit_api/bgtasks/tasks/job_times_updater.py @@ -57,4 +57,4 @@ class JobTimesUpdater(BackgroundTaskTemplate): @classmethod def procedure(cls): - verify_last_completed(1800) \ No newline at end of file + pass \ No newline at end of file diff --git a/autosubmit_api/database/__init__.py b/autosubmit_api/database/__init__.py index e69de29..0ac9383 100644 --- a/autosubmit_api/database/__init__.py +++ b/autosubmit_api/database/__init__.py @@ -0,0 +1,7 @@ +from autosubmit_api.database.common import create_as_times_db_engine +from autosubmit_api.database.tables import experiment_status_table + + +def prepare_db(): + with create_as_times_db_engine().connect() as conn: + experiment_status_table.create(conn, checkfirst=True) \ No newline at end of file diff --git a/autosubmit_api/database/db_common.py b/autosubmit_api/database/db_common.py index d9f714b..7b370b8 100644 --- a/autosubmit_api/database/db_common.py +++ b/autosubmit_api/database/db_common.py @@ -231,7 +231,7 @@ def search_experiment_by_id(query, exp_type=None, only_active=None, owner=None): experiment_times = dict() if len(table) > 0: experiment_status = DbRequests.get_experiment_status() - experiment_times = DbRequests.get_experiment_times() + # REMOVED: experiment_times = DbRequests.get_experiment_times() for row in table: expid = str(row[1]) @@ -268,7 +268,7 @@ def search_experiment_by_id(query, exp_type=None, only_active=None, owner=None): try: current_run = ExperimentHistoryDirector(ExperimentHistoryBuilder(expid)).build_reader_experiment_history().manager.get_experiment_run_dc_with_max_id() - if current_run and current_run.total > 0 and (current_run.total == total or current_run.modified_timestamp > last_modified_timestamp): + if current_run and current_run.total > 0: completed = current_run.completed total = current_run.total submitted = current_run.submitted @@ -313,7 +313,7 @@ def get_current_running_exp(): experiment_status = dict() experiment_times = dict() experiment_status = DbRequests.get_experiment_status() - experiment_times = DbRequests.get_experiment_times() + # REMOVED: experiment_times = DbRequests.get_experiment_times() for row in table: expid = str(row[1]) status = "NOT RUNNING" @@ -353,7 +353,7 @@ def get_current_running_exp(): # Try to retrieve experiment_run data try: current_run = ExperimentHistoryDirector(ExperimentHistoryBuilder(expid)).build_reader_experiment_history().manager.get_experiment_run_dc_with_max_id() - if current_run and current_run.total > 0 and (current_run.total == total or current_run.modified_timestamp > last_modified_timestamp): + if current_run and current_run.total > 0: completed = current_run.completed total = current_run.total submitted = current_run.submitted diff --git a/autosubmit_api/database/extended_db.py b/autosubmit_api/database/extended_db.py index 3cfc703..518941a 100644 --- a/autosubmit_api/database/extended_db.py +++ b/autosubmit_api/database/extended_db.py @@ -1,6 +1,6 @@ from autosubmit_api.config.basicConfig import APIBasicConfig from autosubmit_api.database.db_manager import DbManager -from autosubmit_api.experiment.common_db_requests import prepare_completed_times_db, prepare_status_db +from autosubmit_api.database import prepare_db from autosubmit_api.workers.populate_details.populate import DetailsProcessor class ExtendedDB: @@ -15,7 +15,7 @@ class ExtendedDB: Create tables and views that are required """ self.prepare_main_db() - self.prepare_as_times_db() + prepare_db() def prepare_main_db(self): @@ -25,9 +25,5 @@ class ExtendedDB: 'listexp', 'select id,name,user,created,model,branch,hpc,description from experiment left join details on experiment.id = details.exp_id' ) - - def prepare_as_times_db(self): - prepare_completed_times_db() - prepare_status_db() diff --git a/autosubmit_api/database/queries.py b/autosubmit_api/database/queries.py index d23d684..ad3e327 100644 --- a/autosubmit_api/database/queries.py +++ b/autosubmit_api/database/queries.py @@ -20,9 +20,6 @@ def generate_query_listexp_extended( select( tables.experiment_table, tables.details_table, - tables.experiment_times_table.c.exp_id, - tables.experiment_times_table.c.total_jobs, - tables.experiment_times_table.c.completed_jobs, tables.experiment_status_table.c.exp_id, tables.experiment_status_table.c.status, ) @@ -31,11 +28,6 @@ def generate_query_listexp_extended( tables.experiment_table.c.id == tables.details_table.c.exp_id, isouter=True, ) - .join( - tables.experiment_times_table, - tables.experiment_table.c.id == tables.experiment_times_table.c.exp_id, - isouter=True, - ) .join( tables.experiment_status_table, tables.experiment_table.c.id == tables.experiment_status_table.c.exp_id, diff --git a/autosubmit_api/database/tables.py b/autosubmit_api/database/tables.py index bc3913d..e4929c6 100644 --- a/autosubmit_api/database/tables.py +++ b/autosubmit_api/database/tables.py @@ -28,17 +28,6 @@ details_table = Table( # AS_TIMES TABLES -experiment_times_table = Table( - "experiment_times", - metadata_obj, - Column("exp_id", Integer, primary_key=True), - Column("name", Text, nullable=False), - Column("created", Integer, nullable=False), - Column("modified", Integer, nullable=False), - Column("total_jobs", Integer, nullable=False), - Column("completed_jobs", Integer, nullable=False), -) - experiment_status_table = Table( "experiment_status", metadata_obj, diff --git a/autosubmit_api/experiment/common_requests.py b/autosubmit_api/experiment/common_requests.py index f963dad..8e3d910 100644 --- a/autosubmit_api/experiment/common_requests.py +++ b/autosubmit_api/experiment/common_requests.py @@ -172,7 +172,8 @@ def get_experiment_data(expid): result["completed_jobs"] = experiment_run.completed result["db_historic_version"] = experiment_history.manager.db_version else: - _, result["total_jobs"], result["completed_jobs"] = DbRequests.get_experiment_times_by_expid(expid) + result["total_jobs"] = 0 + result["completed_jobs"] = 0 result["db_historic_version"] = "NA" except Exception as exp: diff --git a/autosubmit_api/history/database_managers/experiment_history_db_manager.py b/autosubmit_api/history/database_managers/experiment_history_db_manager.py index 6d03428..0a821a3 100644 --- a/autosubmit_api/history/database_managers/experiment_history_db_manager.py +++ b/autosubmit_api/history/database_managers/experiment_history_db_manager.py @@ -176,10 +176,7 @@ class ExperimentHistoryDbManager(DatabaseManager): def get_experiment_run_dc_with_max_id(self): """ Get Current (latest) ExperimentRun data class. """ - if self.db_version >= Models.DatabaseVersion.EXPERIMENT_HEADER_SCHEMA_CHANGES.value: - return ExperimentRun.from_model(self._get_experiment_run_with_max_id()) - else: - return ExperimentRun(run_id=0) + return ExperimentRun.from_model(self._get_experiment_run_with_max_id()) def register_experiment_run_dc(self, experiment_run_dc): self._insert_experiment_run(experiment_run_dc) diff --git a/autosubmit_api/views/v4.py b/autosubmit_api/views/v4.py index 07db10c..f42b77e 100644 --- a/autosubmit_api/views/v4.py +++ b/autosubmit_api/views/v4.py @@ -165,8 +165,8 @@ class ExperimentView(MethodView): # Get current run data from history last_modified_timestamp = exp.created - completed = exp.completed_jobs if exp.completed_jobs else 0 - total = exp.total_jobs if exp.total_jobs else 0 + completed = 0 + total = 0 submitted = 0 queuing = 0 running = 0 @@ -181,10 +181,6 @@ class ExperimentView(MethodView): if ( current_run and current_run.total > 0 - and ( - current_run.total == total - or current_run.modified_timestamp > last_modified_timestamp - ) ): completed = current_run.completed total = current_run.total diff --git a/autosubmit_api/workers/business/populate_times.py b/autosubmit_api/workers/business/populate_times.py index 5c5e306..89bbc79 100644 --- a/autosubmit_api/workers/business/populate_times.py +++ b/autosubmit_api/workers/business/populate_times.py @@ -38,7 +38,7 @@ def process_completed_times(time_condition=60): stdOut, _ = currentDirectories.communicate() if currentDirectories else (None, None) # Building connection to ecearth - current_table = DbRequests.prepare_completed_times_db() + current_table = dict() # REMOVED: DbRequests.prepare_completed_times_db() # Build list of all folder in /esarchive/autosubmit which should be considered as experiments (although some might not be) # Pre process _preprocess_completed_times() diff --git a/tests/bgtasks/test_status_updater.py b/tests/bgtasks/test_status_updater.py index 7e4db33..6d23029 100644 --- a/tests/bgtasks/test_status_updater.py +++ b/tests/bgtasks/test_status_updater.py @@ -1,5 +1,5 @@ from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater -from autosubmit_api.database import tables +from autosubmit_api.database import prepare_db, tables from autosubmit_api.database.common import ( create_autosubmit_db_engine, create_as_times_db_engine, @@ -9,6 +9,7 @@ from autosubmit_api.history.database_managers.database_models import RunningStat class TestStatusUpdater: def test_same_tables(self, fixture_mock_basic_config): + prepare_db() StatusUpdater.run() diff --git a/tests/conftest.py b/tests/conftest.py index 8fa8be4..d609778 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,4 +1,4 @@ -# Conftest file for sharing fixtures +# Conftest file for sharing fixtures # Reference: https://docs.pytest.org/en/latest/reference/fixtures.html#conftest-py-sharing-fixtures-across-multiple-files import os @@ -17,6 +17,7 @@ FAKE_EXP_DIR = "./tests/experiments/" def fixture_disable_protection(monkeypatch: pytest.MonkeyPatch): monkeypatch.setenv("PROTECTION_LEVEL", "NONE") + @pytest.fixture def fixture_mock_basic_config(monkeypatch: pytest.MonkeyPatch): # Patch APIBasicConfig parent BasicConfig @@ -25,6 +26,9 @@ def fixture_mock_basic_config(monkeypatch: pytest.MonkeyPatch): monkeypatch.setattr(BasicConfig, "LOCAL_ROOT_DIR", FAKE_EXP_DIR) monkeypatch.setattr(BasicConfig, "DB_DIR", FAKE_EXP_DIR) monkeypatch.setattr(BasicConfig, "DB_FILE", "autosubmit.db") + monkeypatch.setattr( + BasicConfig, "JOBDATA_DIR", os.path.join(FAKE_EXP_DIR, "metadata", "data") + ) monkeypatch.setattr( BasicConfig, "DB_PATH", os.path.join(FAKE_EXP_DIR, "autosubmit.db") ) diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index dd846a25021a24072ee08856906e7775e5fdcf6d..b724c52b2b5cd4f28182a5f93ddc31c741d5b1b3 100644 GIT binary patch delta 263 zcmZozz}Vn0L0XW7fq{Vuh+%+nqK+{?3xi(KB3_^nBfk&>ztCnufhBxgjoFOs;`;iG z&8(B3aH%sgP3GZNtmjOvD2UHYQSkH&admeMQt;>=6TO;reSjR1-u zi58b6mXsD_5l>Cd&r2zePsvP6!)jb^K2Rz%H3eC#48*2@AWvV%phyL8*GL5oh>JA2 bG&eac`j0;*P07RsicqBM0OC@+w>gB=Ik zr`T=heV!fm4fY9ko93jYO5d2YvBS{cYLqmO?ZiJnuH;LPUeydnNyl+5jghkONDxKg zIU#}|r1=r!$8Cx73;(z+;_by9=d`fyeqQ7iV)NgGC3lG|t}guGmnaZ`00bZa0SG_< z0uZ=of$Jx+cq*S4Z*-=$OiHiLscTr&W~#?D*7e42#C8>_(vV1_vQv}DSeRty2`~J< zYP5-AGkQW@a;Q`fDoT^Ql$vWn+}12g7`bdT8;K|L z`MI0aTZ3NeUDxHwWWH0~u5BCk$=Hp)+3TwGhKvP?<`IvYRA@gLnT3r>JL7I3MCf_Wo9=+&NTc;ymBST3t63hf+B(7c)cs3~u+ctj(Jl=9DE!D#wj_RpuQWNOGgM@J1Hw@WS$YpSEH{c^NGA z;g;dtoDlZ9Ez4lR$R;ExpJ;b#uw&SUcX~%t{^NCTKLq~XoNxM3AOHafKmY;|fB*y_ z009U<00IzrzyjF+Kj6v5&>#Q-2tWV=5P$##AOHafKmY=L0e}B5CcX>&g8~5vKmY;| zfB*y_009U<00Izz!2d3gjKqaxG%AW(nYHMrpDX^c`Pkq8M-taU;%njyKcPSX0uX=z z1Rwwb2tWV=5P$##An;EFGLcy!xiVMw_vQXy4D|nxp;RbsgulUsqUFw z%h;BBt!eMpR9C%vRqxfScU9$%p{d12*OA%z>H1=qt#xR+uHDwvrD+%boTeF{#piKN z)7Ij10X`l0h#wulTq^!h{~vAie6e#4zSPa{QkAvlcj>jK&(E%o3pN%v>DtuH;l_!D z7aj*PYW1bXS@w7BzS%>y!}Y~_%@V)SSUSdx3pU<(qkdqqe&~3^d1;~X!llN{WbjY3 zI9@7LOI_8%?x9jwpze;D`gG$ayt(t059k+e+__VK)ppiqz`zFZ-)3EY{~2n>z5Fsb+U}Zd|MDYdi6?{F-_)k+gaext?UE z$4d5Dc3&btJv*~_%s6K-oauiaS~8Y&Kr7WdLusa#(oLEnsxkKSG?Rsna5?c)}1qJ<~3_7mhE@PgBz&qX8)=64-G+yd94hT!+W{4IqVodNv+^ zvmTF^ufrq#EId*j^tWMtRs+>zuaAFX48#~XXE3ndFgF=Oa@DWBOgDGxeu2^EviWx~ zWc?QNJHh?m{7dtr=7-HcGCyd(&-^WYkNIx%SIoDYZ#Lgx{*3t(<|F1S%vtkZ^QGp4 z=8$=xxoGY-8|K~SKI3oALE~fQE#@8OPV;&*XWC}3`7Cp@d9}I0yu|pP@on=0Q#Zb5 z{G0J*;|s>;jK_?R8^34#j`0!We;I#lyvlg3@$1GrjdvJtF@DbYN#m8q%ZwKrOU9gW zzj4GEH|oYc#+}Bnu}3c&MdKDDYgopO#x`TKah0JPmm3!v>-F#I|EYgN|E&Hm`WN)S z)<3ELnf?*|kMs}dzpej<{!abv`p@gH(|<~TmHrC-l>Q?9h5G$^L$B!v^ol;L-=b%A zOTSUyRYmvg|~-@X)&xoh$Fy~`OqYs)D- zZ(p|YEG{SU+`UY#6qa}4`TXTxJfFARgJ<9JO?c*)Z^W~Ec_*Ho%i!DEUoJlvzhAh# z4bKafx1!_|%UyW>#quVUn9En=_a82A#Pj>h#NEHQ{2V;LyL>sG-&wv4&;MDb!`Z(t z6Wjl<B#q2 z%d|$myi7;GFD;vResS5r^BL)i9)I>A9v^!Ek4KmA z_{ahte=?89hiCElKgaR-!>v(+NUOaxc zhR6F~fXDwnfX939#N&VM!{dE-;qlx1@pxStkKdZW<2_Y8&H(+|TPk?`#uy&&9>(KW z%Xs|S?RdOv0FPfT;_=Qsc>KyB9&g1YYrnJ`k9QRC_=Vf>c>DA5cyk_)H_=r8JXV1A z1}p&WZJ2-U^_Xt$r!cG9Pp9zs3CyPUb6GrIgIU)e!K7=i#;j^TgB@9W2s5s|Y6l)a zi4~yzI3`{Du^aGsn5O)dm~o9JTzlE|c)XY<{lRWLPHe$rX*2L#$8N42z6OuISK)E{ zm3WL@frm}Ae;ZBy2AcINXu6+6Gk+CL_BAxim(!G9MlS>e<3pg%4;Zfo9WEICpt&CX2gVipm-J77emL$xG?z=V~sYDXsVD36q%8}em>zT75# z$q7(;^ZJl4*_&H8cIdmDK5?QQt(Iz)Qgvdi`-%>|$0@HI7%A=<9~~**RoWsI;}B68 z;bzWP zm?VEk9Isvt1q8ob)${4I5)eG5zcpRUA;Fg7$bt9=$<-nz9z zFBzBdhVpqkkroThsuhPv$484L?NO}cudqheH8=7r`0{7FI`mr&{-vGFp$XndEm
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Date: Tue, 13 Feb 2024 15:57:49 +0100 Subject: [PATCH 06/18] quickfix tasks module --- autosubmit_api/app.py | 8 +++----- autosubmit_api/bgtasks/tasks/__init__.py | 0 autosubmit_api/database/__init__.py | 18 +++++++++++++++--- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes 4 files changed, 18 insertions(+), 8 deletions(-) create mode 100644 autosubmit_api/bgtasks/tasks/__init__.py diff --git a/autosubmit_api/app.py b/autosubmit_api/app.py index 5c7acd7..6e63fa4 100644 --- a/autosubmit_api/app.py +++ b/autosubmit_api/app.py @@ -6,6 +6,7 @@ from flask import Flask from autosubmit_api.bgtasks.scheduler import create_bind_scheduler from autosubmit_api.blueprints.v3 import create_v3_blueprint from autosubmit_api.blueprints.v4 import create_v4_blueprint +from autosubmit_api.database import prepare_db from autosubmit_api.database.extended_db import ExtendedDB from autosubmit_api.experiment import common_requests as CommonRequests from autosubmit_api.logger import get_app_logger @@ -66,11 +67,8 @@ def create_app(): ) # Prepare DB - ext_db = ExtendedDB( - APIBasicConfig.DB_DIR, APIBasicConfig.DB_FILE, APIBasicConfig.AS_TIMES_DB - ) - ext_db.prepare_db() - + prepare_db() + # Background Scheduler create_bind_scheduler(app) diff --git a/autosubmit_api/bgtasks/tasks/__init__.py b/autosubmit_api/bgtasks/tasks/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/autosubmit_api/database/__init__.py b/autosubmit_api/database/__init__.py index 0ac9383..e2c02e2 100644 --- a/autosubmit_api/database/__init__.py +++ b/autosubmit_api/database/__init__.py @@ -1,7 +1,19 @@ -from autosubmit_api.database.common import create_as_times_db_engine -from autosubmit_api.database.tables import experiment_status_table +from sqlalchemy import text +from autosubmit_api.database.common import ( + create_as_times_db_engine, + create_autosubmit_db_engine, +) +from autosubmit_api.database.tables import experiment_status_table, details_table def prepare_db(): with create_as_times_db_engine().connect() as conn: - experiment_status_table.create(conn, checkfirst=True) \ No newline at end of file + experiment_status_table.create(conn, checkfirst=True) + + with create_autosubmit_db_engine().connect() as conn: + details_table.create(conn, checkfirst=True) + + view_name = "listexp" + view_from = "select id,name,user,created,model,branch,hpc,description from experiment left join details on experiment.id = details.exp_id" + new_view_stmnt = f"CREATE VIEW IF NOT EXISTS {view_name} as {view_from}" + conn.execute(text(new_view_stmnt)) diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index b724c52b2b5cd4f28182a5f93ddc31c741d5b1b3..668a6fa93ea4ca479c7410c907ebe1dee8db4824 100644 GIT binary patch delta 49 pcmZp0XmFSy&B#7c#+i|QV}h$ZyQ!6_k(Ghj8vs6C3`76` delta 49 pcmZp0XmFSy&B!uQ#+i|2V}h$ZyNQ*lv6ZpO8vs3*3_$<@ -- GitLab From b8c442bc2a40118d5fdfb9a1864a8c050023a200 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Wed, 14 Feb 2024 13:49:16 +0100 Subject: [PATCH 07/18] fix tests fixture --- README.md | 2 +- autosubmit_api/config/confConfigStrategy.py | 2 +- tests/conftest.py | 25 +++++++++--------- tests/experiments/.autosubmitrc | 18 +++++++++++++ tests/experiments/as_times.db | Bin 8192 -> 8192 bytes .../metadata/structures/structure_a003.db | Bin 0 -> 12288 bytes .../metadata/structures/structure_a007.db | Bin 0 -> 12288 bytes .../metadata/structures/structure_a3tb.db | Bin 0 -> 12288 bytes tests/test_config.py | 25 ++++++++++++++++++ 9 files changed, 58 insertions(+), 14 deletions(-) create mode 100644 tests/experiments/.autosubmitrc create mode 100644 tests/experiments/metadata/structures/structure_a003.db create mode 100644 tests/experiments/metadata/structures/structure_a007.db create mode 100755 tests/experiments/metadata/structures/structure_a3tb.db diff --git a/README.md b/README.md index dcc7389..dc078e6 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ pytest tests/* ### Run tests with coverage HTML report: ```bash -pytest --cov=autosubmit_api --cov-config=.coveragerc --cov-report=html tests/* +pytest --cov=autosubmit_api --cov-config=.coveragerc --cov-report=html tests/ ``` You will find the report in `htmlcov/index.html` diff --git a/autosubmit_api/config/confConfigStrategy.py b/autosubmit_api/config/confConfigStrategy.py index 9ccd8ee..2bbadb2 100644 --- a/autosubmit_api/config/confConfigStrategy.py +++ b/autosubmit_api/config/confConfigStrategy.py @@ -647,7 +647,7 @@ class confConfigStrategy(IConfigStrategy): if self._proj_parser_file == '': self._proj_parser = None else: - self._proj_parser = AutosubmitConfig.get_parser( + self._proj_parser = confConfigStrategy.get_parser( self.parser_factory, self._proj_parser_file) return True except Exception as e: diff --git a/tests/conftest.py b/tests/conftest.py index d609778..ee750ce 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -20,19 +20,20 @@ def fixture_disable_protection(monkeypatch: pytest.MonkeyPatch): @pytest.fixture def fixture_mock_basic_config(monkeypatch: pytest.MonkeyPatch): + monkeypatch.setenv("AUTOSUBMIT_CONFIGURATION", os.path.join(FAKE_EXP_DIR, ".autosubmitrc")) # Patch APIBasicConfig parent BasicConfig - monkeypatch.setattr(BasicConfig, "read", custom_return_value(None)) - monkeypatch.setattr(APIBasicConfig, "read", custom_return_value(None)) - monkeypatch.setattr(BasicConfig, "LOCAL_ROOT_DIR", FAKE_EXP_DIR) - monkeypatch.setattr(BasicConfig, "DB_DIR", FAKE_EXP_DIR) - monkeypatch.setattr(BasicConfig, "DB_FILE", "autosubmit.db") - monkeypatch.setattr( - BasicConfig, "JOBDATA_DIR", os.path.join(FAKE_EXP_DIR, "metadata", "data") - ) - monkeypatch.setattr( - BasicConfig, "DB_PATH", os.path.join(FAKE_EXP_DIR, "autosubmit.db") - ) - monkeypatch.setattr(BasicConfig, "AS_TIMES_DB", "as_times.db") + # monkeypatch.setattr(BasicConfig, "read", custom_return_value(None)) + # monkeypatch.setattr(APIBasicConfig, "read", custom_return_value(None)) + # monkeypatch.setattr(BasicConfig, "LOCAL_ROOT_DIR", FAKE_EXP_DIR) + # monkeypatch.setattr(BasicConfig, "DB_DIR", FAKE_EXP_DIR) + # monkeypatch.setattr(BasicConfig, "DB_FILE", "autosubmit.db") + # monkeypatch.setattr( + # BasicConfig, "JOBDATA_DIR", os.path.join(FAKE_EXP_DIR, "metadata", "data") + # ) + # monkeypatch.setattr( + # BasicConfig, "DB_PATH", os.path.join(FAKE_EXP_DIR, "autosubmit.db") + # ) + # monkeypatch.setattr(BasicConfig, "AS_TIMES_DB", "as_times.db") yield APIBasicConfig diff --git a/tests/experiments/.autosubmitrc b/tests/experiments/.autosubmitrc new file mode 100644 index 0000000..d2f3642 --- /dev/null +++ b/tests/experiments/.autosubmitrc @@ -0,0 +1,18 @@ +[database] +path = ./tests/experiments/ +filename = autosubmit.db + +[local] +path = ./tests/experiments/ + +[globallogs] +path = ./tests/experiments/logs + +[historicdb] +path = ./tests/experiments/metadata/data + +[structures] +path = ./tests/experiments/metadata/structures + +[historiclog] +path = ./tests/experiments/metadata/logs \ No newline at end of file diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 668a6fa93ea4ca479c7410c907ebe1dee8db4824..ed8f01eeefc418b04555f6251cf9cb59167b514b 100644 GIT binary patch delta 58 scmZp0XmFSy&FDN)#+lK1V}g@Bmx->Sv6YFrm8s$6HS!9`+-oRY0K?`EcmMzZ delta 58 scmZp0XmFSy&B#7c#+i|QV}g@Bm$9y)sg&M<^gayZc=|CO4@U8c;HP3dITDj`?wZ={cy8pe$bId5EU${~Y_KaM z=KXOpVj`Xj7PKQ4bbWvKuRBDtD&GxShh1-HzR_;XMN(d>FTYg_+wbcN8Jrx))6-AG zw0GydiAZG3^UlaCd8@O&e%9ZU&2$>(4?@rBclwPc^d-HUh8Pfl00bZa0SG_<0uX=z z1Rwx`+b8hQ(DtmJZP&QpZn{1Xy{LO2#Gs{P!q@cxm_TR|(k zSm9x7zp|z|IR!G8Eve2*wsfsnlDUI+7|DyK@43MfO)I&7!fbWaaf9%U*Lk37PBEL7 zo6F_dzGX$T8Zx^2eA%k>(KgbzX_yy;zMyBcK);$7bV$!{-z&z6ApijgKmY;|fB*y_ z009U<;J+4ltnXQhYJuNO=6e_3w+^|D@a=Lz{S cAls-fx_|AF?i6zly4?P&Pj#zt=Vtx?Z|s=+O8@`> literal 0 HcmV?d00001 diff --git a/tests/experiments/metadata/structures/structure_a007.db b/tests/experiments/metadata/structures/structure_a007.db new file mode 100644 index 0000000000000000000000000000000000000000..1db581bacb13626eed16874a91a27b31f468662b GIT binary patch literal 12288 zcmeI$F>ljA6bJBg?8Z>3Iape@Tto#8w6)zR^56v%8HnUMP3%lmI)&m$k(vhFiJP@ow9uP$#FBl_) z9Hw1O`(;zo8|`wCUgzUw?U3vy-`41FQmR~#$_4$oYyt8RfB*y_009U<00Izz00bZa zfqxbF@$MNh#oQ%ftiQuOqnI4I0QWz_>dY&73EOKA^9xGbKwpQ7d z7V}{;88Z>j1PeM53;MplePf20EXwzTcDL_sWe?hpxtP?it*^f>l{elt6*4+`AJ0xd z9;dZCA56tWj(O1@xm6UM*Y)@2o@;5>E58Umqd(|p8qr<4o(|C<009U<00Izz00bZa z0SG_<0(Vcq&{f+Rn5ND5%(Pji#fL{GZwKvs(Bffxf4!_$YchAx2_t#a@;x`$Tv2xn zIrKX%*XN-Z^$+B@=k0eQFALN))v$9>8MyiWr>a_WWkx((c{+#Mm(eAOHafKmY;|fB*y_ z009X6*8-MiJ4(I=zP<9-A8FNEw&Hr}Uw)$P7+GRb?Z5I|Gwf{I)n5XIThQuS&CTX6 css7c5<`kV{QTbom)ST-5{EOwkfxq?tAIJjxbpQYW literal 0 HcmV?d00001 diff --git a/tests/experiments/metadata/structures/structure_a3tb.db b/tests/experiments/metadata/structures/structure_a3tb.db new file mode 100755 index 0000000000000000000000000000000000000000..45dbb0f57b16cd6af2db84180d89348307c2729c GIT binary patch literal 12288 zcmeI#&r8EF6u|MMippR=ZoB5V!4RbM?v$cJsZ86`4y9@ag>}^~g>Pj_-q{ydGwQi^k>gb=bG2ld#7%@4Op{j~Y6km7Xe zw!0s~>8wR(-F@Fxz&-*9Ab_i}d y00IagfB*srAb Date: Wed, 14 Feb 2024 14:50:47 +0100 Subject: [PATCH 08/18] include assert error messages --- autosubmit_api/experiment/common_requests.py | 2 +- tests/docker/Dockerfile | 17 ++++++++++++++ tests/experiments/as_times.db | Bin 8192 -> 8192 bytes tests/test_endpoints_v3.py | 23 +++++++++++++++++++ 4 files changed, 41 insertions(+), 1 deletion(-) create mode 100644 tests/docker/Dockerfile diff --git a/autosubmit_api/experiment/common_requests.py b/autosubmit_api/experiment/common_requests.py index 8e3d910..5d29898 100644 --- a/autosubmit_api/experiment/common_requests.py +++ b/autosubmit_api/experiment/common_requests.py @@ -727,7 +727,7 @@ def get_experiment_tree_rundetail(expid, run_id): print((traceback.format_exc())) return {'tree': [], 'jobs': [], 'total': 0, 'reference': [], 'error': True, 'error_message': str(e), 'pkl_timestamp': 0} base_list['error'] = False - base_list['error_message'] = 'None' + base_list['error_message'] = '' base_list['pkl_timestamp'] = pkl_timestamp return base_list diff --git a/tests/docker/Dockerfile b/tests/docker/Dockerfile new file mode 100644 index 0000000..60b823e --- /dev/null +++ b/tests/docker/Dockerfile @@ -0,0 +1,17 @@ +FROM python:3.8-slim-bullseye + +WORKDIR / + +RUN apt-get update && apt-get install -y git + +RUN git clone https://earth.bsc.es/gitlab/es/autosubmit_api.git + +WORKDIR /autosubmit_api/ + +RUN git checkout v4.0.0b4 + +RUN pip install . + +RUN pip install -U pytest pytest-cov + +RUN pytest --cov=autosubmit_api --cov-config=.coveragerc --cov-report=html tests/ \ No newline at end of file diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index ed8f01eeefc418b04555f6251cf9cb59167b514b..aaf59db395bd3f51b877b4e12c0cd433e5d84f1c 100644 GIT binary patch delta 49 pcmZp0XmFSy&FDE%#+lJ`V}h$ZyNQ*lft8Wb8vs$-47mUR delta 49 pcmZp0XmFSy&FDN)#+lK1V}h$ZyRnstxs|Em8vs!|48i~a diff --git a/tests/test_endpoints_v3.py b/tests/test_endpoints_v3.py index d0f5896..7d0e791 100644 --- a/tests/test_endpoints_v3.py +++ b/tests/test_endpoints_v3.py @@ -89,6 +89,7 @@ class TestExpInfo: expid = "a003" response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["expid"] == expid assert resp_obj["total_jobs"] == 8 @@ -97,6 +98,7 @@ class TestExpInfo: expid = "a3tb" response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["expid"] == expid assert resp_obj["total_jobs"] == 55 @@ -113,12 +115,14 @@ class TestPerformance: expid = "a007" response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["Parallelization"] == 8 expid = "a3tb" response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["Parallelization"] == 768 @@ -129,6 +133,7 @@ class TestPerformance: expid = "a003" response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["Parallelization"] == 16 @@ -145,6 +150,7 @@ class TestTree: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == 8 assert resp_obj["total"] == len(resp_obj["jobs"]) @@ -160,6 +166,7 @@ class TestTree: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == 55 assert resp_obj["total"] == len(resp_obj["jobs"]) @@ -179,6 +186,7 @@ class TestRunsList: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert isinstance(resp_obj["runs"], list) @@ -192,6 +200,7 @@ class TestRunDetail: response = fixture_client.get(self.endpoint.format(expid=expid, runId=2)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == 8 @@ -204,6 +213,7 @@ class TestQuick: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == len(resp_obj["tree_view"]) assert resp_obj["total"] == len(resp_obj["view_data"]) @@ -221,6 +231,7 @@ class TestGraph: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -235,6 +246,7 @@ class TestGraph: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -247,6 +259,7 @@ class TestGraph: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -259,6 +272,7 @@ class TestGraph: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -271,6 +285,7 @@ class TestExpCount: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == sum( [resp_obj["counters"][key] for key in resp_obj["counters"]] @@ -284,6 +299,7 @@ class TestExpCount: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total"] == sum( [resp_obj["counters"][key] for key in resp_obj["counters"]] @@ -308,6 +324,7 @@ class TestSummary: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["n_sim"] > 0 @@ -322,6 +339,7 @@ class TestStatistics: ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["Statistics"]["Period"]["From"] == "None" @@ -334,6 +352,7 @@ class TestCurrentConfig: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert ( resp_obj["configuration_filesystem"]["CONFIG"]["AUTOSUBMIT_VERSION"] @@ -345,6 +364,7 @@ class TestCurrentConfig: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert ( resp_obj["configuration_filesystem"]["conf"]["config"]["AUTOSUBMIT_VERSION"] @@ -360,6 +380,7 @@ class TestPklInfo: response = fixture_client.get(self.endpoint.format(expid=expid, timestamp=0)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert len(resp_obj["pkl_content"]) == 8 @@ -375,6 +396,7 @@ class TestPklTreeInfo: response = fixture_client.get(self.endpoint.format(expid=expid, timestamp=0)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert len(resp_obj["pkl_content"]) == 8 @@ -390,5 +412,6 @@ class TestExpRunLog: response = fixture_client.get(self.endpoint.format(expid=expid)) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["found"] == True -- GitLab From dc06d1554bceb03082d9afdf1b6ba78ac3e046ac Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Wed, 14 Feb 2024 15:04:50 +0100 Subject: [PATCH 09/18] fix protection level fixture --- autosubmit_api/auth/__init__.py | 6 +++--- tests/conftest.py | 2 ++ tests/experiments/as_times.db | Bin 8192 -> 8192 bytes tests/test_auth.py | 6 ++++++ 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/autosubmit_api/auth/__init__.py b/autosubmit_api/auth/__init__.py index b15562c..92ee07a 100644 --- a/autosubmit_api/auth/__init__.py +++ b/autosubmit_api/auth/__init__.py @@ -3,7 +3,7 @@ from http import HTTPStatus from flask import request import jwt from autosubmit_api.logger import logger -from autosubmit_api.config import PROTECTION_LEVEL, JWT_ALGORITHM, JWT_SECRET +from autosubmit_api import config from enum import IntEnum @@ -45,12 +45,12 @@ def with_auth_token( def inner_wrapper(*args, **kwargs): try: current_token = request.headers.get("Authorization") - jwt_token = jwt.decode(current_token, JWT_SECRET, JWT_ALGORITHM) + jwt_token = jwt.decode(current_token, config.JWT_SECRET, config.JWT_ALGORITHM) except Exception as exc: error_msg = "Unauthorized" if isinstance(exc, jwt.ExpiredSignatureError): error_msg = "Expired token" - auth_level = _parse_protection_level_env(PROTECTION_LEVEL) + auth_level = _parse_protection_level_env(config.PROTECTION_LEVEL) if threshold <= auth_level: # If True, will trigger *_on_fail if raise_on_fail: raise AppAuthError(error_msg) diff --git a/tests/conftest.py b/tests/conftest.py index ee750ce..9d3f98e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -7,6 +7,7 @@ import pytest from autosubmitconfigparser.config.basicconfig import BasicConfig from autosubmit_api.app import create_app from autosubmit_api.config.basicConfig import APIBasicConfig +from autosubmit_api import config from tests.custom_utils import custom_return_value FAKE_EXP_DIR = "./tests/experiments/" @@ -15,6 +16,7 @@ FAKE_EXP_DIR = "./tests/experiments/" #### FIXTURES #### @pytest.fixture(autouse=True) def fixture_disable_protection(monkeypatch: pytest.MonkeyPatch): + monkeypatch.setattr(config, "PROTECTION_LEVEL", "NONE") monkeypatch.setenv("PROTECTION_LEVEL", "NONE") diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index aaf59db395bd3f51b877b4e12c0cd433e5d84f1c..922044b6ef2ad0e745b1d769441aa83ed22a7691 100644 GIT binary patch delta 47 scmZp0XmFSy%@{XP#+fm0V}h$Zo2iw7v6ac>)$%GZ=2dwWc8I7E06^XhfB*mh delta 47 scmZp0XmFSy&FDE%#+lJ`V}h$Zn~9aFftAtZ)$%GZ=2dwWc8I7E06LruQvd(} diff --git a/tests/test_auth.py b/tests/test_auth.py index ce59c9d..5fef206 100644 --- a/tests/test_auth.py +++ b/tests/test_auth.py @@ -1,13 +1,19 @@ +import os from uuid import uuid4 import pytest from autosubmit_api.auth import ProtectionLevels, with_auth_token from autosubmit_api import auth from autosubmit_api.auth.utils import validate_client from autosubmit_api.config.basicConfig import APIBasicConfig +from autosubmit_api import config from tests.custom_utils import custom_return_value, dummy_response class TestCommonAuth: + def test_mock_env_protection_level(self): + assert os.environ.get("PROTECTION_LEVEL") == "NONE" + assert config.PROTECTION_LEVEL == "NONE" + def test_levels_enum(self): assert ProtectionLevels.ALL > ProtectionLevels.WRITEONLY assert ProtectionLevels.WRITEONLY > ProtectionLevels.NONE -- GitLab From 40bca2b86b89bd48e32ebb630cfb410dae2a7a13 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Wed, 14 Feb 2024 16:59:35 +0100 Subject: [PATCH 10/18] fix graph path config --- autosubmit_api/config/basicConfig.py | 6 ++- autosubmit_api/database/db_jobdata.py | 3 +- tests/docker/Dockerfile | 2 +- tests/experiments/.autosubmitrc | 5 ++- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes .../graph/graph_data_a003.db | Bin .../metadata/graph/graph_data_a3tb.db | Bin 0 -> 8192 bytes tests/test_config.py | 4 ++ tests/test_endpoints_v3.py | 40 ++++++++++++++++-- 9 files changed, 51 insertions(+), 9 deletions(-) rename tests/experiments/{as_metadata => metadata}/graph/graph_data_a003.db (100%) create mode 100755 tests/experiments/metadata/graph/graph_data_a3tb.db diff --git a/autosubmit_api/config/basicConfig.py b/autosubmit_api/config/basicConfig.py index fdb9e57..95acbff 100644 --- a/autosubmit_api/config/basicConfig.py +++ b/autosubmit_api/config/basicConfig.py @@ -27,8 +27,8 @@ class APIBasicConfig(BasicConfig): Extended class to manage configuration for Autosubmit path, database and default values for new experiments in the Autosubmit API """ - GRAPHDATA_DIR = os.path.join(os.path.expanduser('~'), 'autosubmit', 'as_metadata', 'graph') - FILE_STATUS_DIR = os.path.join(os.path.expanduser('~'), 'autosubmit', 'as_metadata', 'test') + GRAPHDATA_DIR = os.path.join(os.path.expanduser('~'), 'autosubmit', 'metadata', 'graph') + FILE_STATUS_DIR = os.path.join(os.path.expanduser('~'), 'autosubmit', 'metadata', 'test') FILE_STATUS_DB = 'status.db' ALLOWED_CLIENTS = set([]) @@ -45,6 +45,8 @@ class APIBasicConfig(BasicConfig): if parser.has_option('graph', 'path'): APIBasicConfig.GRAPHDATA_DIR = parser.get('graph', 'path') + else: + APIBasicConfig.GRAPHDATA_DIR = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, 'metadata', 'graph') if parser.has_option('statusdb', 'path'): APIBasicConfig.FILE_STATUS_DIR = parser.get('statusdb', 'path') if parser.has_option('statusdb', 'filename'): diff --git a/autosubmit_api/database/db_jobdata.py b/autosubmit_api/database/db_jobdata.py index d9fb4e1..6f0826c 100644 --- a/autosubmit_api/database/db_jobdata.py +++ b/autosubmit_api/database/db_jobdata.py @@ -533,8 +533,7 @@ class ExperimentGraphDrawing(MainDataBase): APIBasicConfig.read() self.expid = expid self.folder_path = APIBasicConfig.LOCAL_ROOT_DIR - self.database_path = os.path.join( - self.folder_path, "as_metadata", "graph" , "graph_data_" + str(expid) + ".db") + self.database_path = os.path.join(APIBasicConfig.GRAPHDATA_DIR, "graph_data_" + str(expid) + ".db") self.create_table_query = textwrap.dedent( '''CREATE TABLE IF NOT EXISTS experiment_graph_draw ( diff --git a/tests/docker/Dockerfile b/tests/docker/Dockerfile index 60b823e..9e2ed0c 100644 --- a/tests/docker/Dockerfile +++ b/tests/docker/Dockerfile @@ -2,7 +2,7 @@ FROM python:3.8-slim-bullseye WORKDIR / -RUN apt-get update && apt-get install -y git +RUN apt-get update && apt-get install -y git graphviz RUN git clone https://earth.bsc.es/gitlab/es/autosubmit_api.git diff --git a/tests/experiments/.autosubmitrc b/tests/experiments/.autosubmitrc index d2f3642..da7bbe7 100644 --- a/tests/experiments/.autosubmitrc +++ b/tests/experiments/.autosubmitrc @@ -15,4 +15,7 @@ path = ./tests/experiments/metadata/data path = ./tests/experiments/metadata/structures [historiclog] -path = ./tests/experiments/metadata/logs \ No newline at end of file +path = ./tests/experiments/metadata/logs + +[graph] +path = ./tests/experiments/metadata/graph \ No newline at end of file diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 922044b6ef2ad0e745b1d769441aa83ed22a7691..3f9a4743b4dd8df93226cb03fa54a25b3ca4572f 100644 GIT binary patch delta 49 ncmZp0XmFSy%~&u|#+k8TV}h$ZyP1`#1rSYMBd-i+Uqi3~VLc5% delta 49 pcmZp0XmFSy%@{XP#+fm0V}h$ZyQ!6dv6YF@8vs~y4CVj; diff --git a/tests/experiments/as_metadata/graph/graph_data_a003.db b/tests/experiments/metadata/graph/graph_data_a003.db similarity index 100% rename from tests/experiments/as_metadata/graph/graph_data_a003.db rename to tests/experiments/metadata/graph/graph_data_a003.db diff --git a/tests/experiments/metadata/graph/graph_data_a3tb.db b/tests/experiments/metadata/graph/graph_data_a3tb.db new file mode 100755 index 0000000000000000000000000000000000000000..ff0fb9fcdbfb86d91e53f51afa5666b2c2a28d6b GIT binary patch literal 8192 zcmeI#!E3@W6bA4_guy`cw(Hw%1KGuc*L5RESy#1Iq-;=9nr)R;B?MNF`j?x+S`QYy zihLgl;pHVc{BD^|z04^3TI*aI8n7PYoIMjU#<-m=JFAp+yDIEj*5|_6)5oA=Px00LbV^82|tP literal 0 HcmV?d00001 diff --git a/tests/test_config.py b/tests/test_config.py index 6c6daf8..64b1245 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -35,6 +35,10 @@ class TestBasicConfig: FAKE_EXP_DIR, "metadata", "logs" ) + assert APIBasicConfig.GRAPHDATA_DIR == os.path.join( + FAKE_EXP_DIR, "metadata", "graph" + ) + class TestConfigResolver: def test_simple_init(self, monkeypatch: pytest.MonkeyPatch): # Conf test decision diff --git a/tests/test_endpoints_v3.py b/tests/test_endpoints_v3.py index 7d0e791..4d5b036 100644 --- a/tests/test_endpoints_v3.py +++ b/tests/test_endpoints_v3.py @@ -230,7 +230,6 @@ class TestGraph: query_string={"loggedUser": random_user}, ) resp_obj: dict = response.get_json() - assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -245,7 +244,6 @@ class TestGraph: query_string={"loggedUser": random_user}, ) resp_obj: dict = response.get_json() - assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -258,7 +256,6 @@ class TestGraph: query_string={"loggedUser": random_user}, ) resp_obj: dict = response.get_json() - assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) @@ -271,7 +268,44 @@ class TestGraph: query_string={"loggedUser": random_user}, ) resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" + assert resp_obj["error"] == False + assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) + def test_graph_standard_none_retro3(self, fixture_client: FlaskClient): + expid = "a3tb" + random_user = str(uuid4()) + response = fixture_client.get( + self.endpoint.format(expid=expid, graph_type="standard", grouped="none"), + query_string={"loggedUser": random_user}, + ) + resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" + assert resp_obj["error"] == False + assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) + + def test_graph_standard_datemember_retro3(self, fixture_client: FlaskClient): + expid = "a3tb" + random_user = str(uuid4()) + response = fixture_client.get( + self.endpoint.format( + expid=expid, graph_type="standard", grouped="date-member" + ), + query_string={"loggedUser": random_user}, + ) + resp_obj: dict = response.get_json() + assert resp_obj["error_message"] == "" + assert resp_obj["error"] == False + assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) + + def test_graph_standard_status_retro3(self, fixture_client: FlaskClient): + expid = "a3tb" + random_user = str(uuid4()) + response = fixture_client.get( + self.endpoint.format(expid=expid, graph_type="standard", grouped="status"), + query_string={"loggedUser": random_user}, + ) + resp_obj: dict = response.get_json() assert resp_obj["error_message"] == "" assert resp_obj["error"] == False assert resp_obj["total_jobs"] == len(resp_obj["nodes"]) -- GitLab From b043d642ca7883f7638c154bd1cb35b4df8a9e26 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Thu, 15 Feb 2024 12:57:11 +0100 Subject: [PATCH 11/18] removed unused workers --- .../autosubmit_legacy/job/job_list.py | 4 +- autosubmit_api/bgtasks/bgtask.py | 13 +- autosubmit_api/bgtasks/scheduler.py | 4 - .../bgtasks/tasks/job_times_updater.py | 60 -- .../experiment/common_db_requests.py | 686 ------------------ .../workers/business/populate_times.py | 365 ---------- .../workers/populate_queue_run_times.py | 10 - autosubmit_api/workers/verify_complete.py | 10 - tests/experiments/as_times.db | Bin 8192 -> 8192 bytes 9 files changed, 4 insertions(+), 1148 deletions(-) delete mode 100644 autosubmit_api/bgtasks/tasks/job_times_updater.py delete mode 100644 autosubmit_api/workers/business/populate_times.py delete mode 100644 autosubmit_api/workers/populate_queue_run_times.py delete mode 100644 autosubmit_api/workers/verify_complete.py diff --git a/autosubmit_api/autosubmit_legacy/job/job_list.py b/autosubmit_api/autosubmit_legacy/job/job_list.py index 2715556..dab3d9a 100644 --- a/autosubmit_api/autosubmit_legacy/job/job_list.py +++ b/autosubmit_api/autosubmit_legacy/job/job_list.py @@ -590,7 +590,7 @@ class JobList: conn = DbRequests.create_connection(db_file) # job_data = None # Job information from worker database - job_times = dict() # REMOVED: DbRequests.get_times_detail_by_expid(conn, expid) + # job_times = dict() # REMOVED: DbRequests.get_times_detail_by_expid(conn, expid) conn.close() # Job information from job historic data # print("Get current job data structure...") @@ -612,7 +612,7 @@ class JobList: # print("Start main loop") for job in allJobs: job_info = JobList.retrieve_times( - job.status, job.name, job._tmp_path, make_exception=False, job_times=job_times, seconds=timeseconds, job_data_collection=job_data) + job.status, job.name, job._tmp_path, make_exception=False, job_times=None, seconds=timeseconds, job_data_collection=job_data) # if job_info: job_name_to_job_info[job.name] = job_info time_total = (job_info.queue_time + diff --git a/autosubmit_api/bgtasks/bgtask.py b/autosubmit_api/bgtasks/bgtask.py index c043c57..a23aa27 100644 --- a/autosubmit_api/bgtasks/bgtask.py +++ b/autosubmit_api/bgtasks/bgtask.py @@ -2,7 +2,7 @@ from abc import ABC, abstractmethod import traceback from autosubmit_api.logger import logger from autosubmit_api.config.basicConfig import APIBasicConfig -from autosubmit_api.workers.business import populate_times, process_graph_drawings +from autosubmit_api.workers.business import process_graph_drawings from autosubmit_api.workers.populate_details.populate import DetailsProcessor @@ -11,6 +11,7 @@ class BackgroundTaskTemplate(ABC): Interface to define Background Tasks. Do not override the run method. """ + logger = logger @classmethod @@ -50,16 +51,6 @@ class PopulateDetailsDB(BackgroundTaskTemplate): return DetailsProcessor(APIBasicConfig).process() -class PopulateQueueRuntimes(BackgroundTaskTemplate): - id = "TASK_POPQUE" - trigger_options = {"trigger": "interval", "minutes": 3} - - @classmethod - def procedure(cls): - """Process and updates queuing and running times.""" - populate_times.process_completed_times() - - class PopulateGraph(BackgroundTaskTemplate): id = "TASK_POPGRPH" trigger_options = {"trigger": "interval", "hours": 24} diff --git a/autosubmit_api/bgtasks/scheduler.py b/autosubmit_api/bgtasks/scheduler.py index 26aafc5..6e890a6 100644 --- a/autosubmit_api/bgtasks/scheduler.py +++ b/autosubmit_api/bgtasks/scheduler.py @@ -3,10 +3,8 @@ from flask_apscheduler import APScheduler from autosubmit_api.bgtasks.bgtask import ( BackgroundTaskTemplate, PopulateDetailsDB, - PopulateQueueRuntimes, PopulateGraph, ) -from autosubmit_api.bgtasks.tasks.job_times_updater import JobTimesUpdater from autosubmit_api.bgtasks.tasks.status_updater import StatusUpdater from autosubmit_api.config import ( DISABLE_BACKGROUND_TASKS, @@ -17,9 +15,7 @@ from autosubmit_api.logger import logger, with_log_run_times REGISTERED_TASKS: List[BackgroundTaskTemplate] = [ PopulateDetailsDB, - # PopulateQueueRuntimes, StatusUpdater, - # JobTimesUpdater, PopulateGraph, ] diff --git a/autosubmit_api/bgtasks/tasks/job_times_updater.py b/autosubmit_api/bgtasks/tasks/job_times_updater.py deleted file mode 100644 index dd8c817..0000000 --- a/autosubmit_api/bgtasks/tasks/job_times_updater.py +++ /dev/null @@ -1,60 +0,0 @@ -import os -import time -from autosubmit_api.bgtasks.bgtask import BackgroundTaskTemplate -from autosubmit_api.common import utils as common_utils -from autosubmit_api.components.jobs import utils as JUtils -from autosubmit_api.config.basicConfig import APIBasicConfig -from autosubmit_api.experiment import common_db_requests as DbRequests -from autosubmit_api.experiment.common_requests import SAFE_TIME_LIMIT - - -def verify_last_completed(seconds=300): - """ - Verifying last 300 seconds by default - """ - # Basic info - t0 = time.time() - APIBasicConfig.read() - # Current timestamp - current_st = time.time() - # Current latest detail - td0 = time.time() - latest_detail = DbRequests.get_latest_completed_jobs(seconds) - t_data = time.time() - td0 - # Main Loop - for job_name, detail in list(latest_detail.items()): - tmp_path = os.path.join( - APIBasicConfig.LOCAL_ROOT_DIR, job_name[:4], APIBasicConfig.LOCAL_TMP_DIR) - detail_id, submit, start, finish, status = detail - submit_time, start_time, finish_time, status_text_res = JUtils.get_job_total_stats( - common_utils.Status.COMPLETED, job_name, tmp_path) - submit_ts = int(time.mktime(submit_time.timetuple())) if len( - str(submit_time)) > 0 else 0 - start_ts = int(time.mktime(start_time.timetuple())) if len( - str(start_time)) > 0 else 0 - finish_ts = int(time.mktime(finish_time.timetuple())) if len( - str(finish_time)) > 0 else 0 - if (finish_ts != finish): - #print("\tMust Update") - DbRequests.update_job_times(detail_id, - int(current_st), - submit_ts, - start_ts, - finish_ts, - status, - debug=False, - no_modify_time=True) - t1 = time.time() - # Timer safeguard - if (t1 - t0) > SAFE_TIME_LIMIT: - raise Exception( - "Time limit reached {0:06.2f} seconds on verify_last_completed while reading {1}. Time spent on reading data {2:06.2f} seconds.".format((t1 - t0), job_name, t_data)) - - -class JobTimesUpdater(BackgroundTaskTemplate): - id = "TASK_JBTMUPDTR" - trigger_options = {"trigger": "interval", "minutes": 10} - - @classmethod - def procedure(cls): - pass \ No newline at end of file diff --git a/autosubmit_api/experiment/common_db_requests.py b/autosubmit_api/experiment/common_db_requests.py index 9d9d4a1..801e7e4 100644 --- a/autosubmit_api/experiment/common_db_requests.py +++ b/autosubmit_api/experiment/common_db_requests.py @@ -1,11 +1,7 @@ import os -import time -import textwrap import traceback import sqlite3 from datetime import datetime -from collections import OrderedDict -from typing import List, Tuple, Dict from autosubmit_api.config.basicConfig import APIBasicConfig APIBasicConfig.read() @@ -15,98 +11,8 @@ DB_FILES_STATUS = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, "as_metadata", "te # PATH_DB_DATA = "/esarchive/autosubmit/as_metadata/data/" -def prepare_status_db(): - """ - Creates table of experiment status if it does not exist. - :return: Map from experiment name to (Id of experiment, Status, Seconds) - :rtype: Dictionary Key: String, Value: Integer, String, Integer - """ - conn = create_connection(DB_FILE_AS_TIMES) - create_table_query = textwrap.dedent( - '''CREATE TABLE - IF NOT EXISTS experiment_status ( - exp_id integer PRIMARY KEY, - name text NOT NULL, - status text NOT NULL, - seconds_diff integer NOT NULL, - modified text NOT NULL, - FOREIGN KEY (exp_id) REFERENCES experiment (id) - );''') - # drop_table_query = ''' DROP TABLE experiment_status ''' - # create_table(conn, drop_table_query) - create_table(conn, create_table_query) - current_table = _get_exp_status() - current_table_expid = dict() - # print(current_table) - # print(type(current_table)) - for item in current_table: - exp_id, expid, status, seconds = item - current_table_expid[expid] = (exp_id, status, seconds) - return current_table_expid - - -def prepare_completed_times_db(): - """ - Creates two tables: - "experiment_times" that stores general information about experiments' jobs completed updates - "job_times" that stores information about completed time for jobs in the database as_times.db - Then retrieves all the experiments data from "experiment_times". - :return: Dictionary that maps experiment name to experiment data. - :rtype: Dictionary: Key String, Value 6-tuple (exp_id, name, created, modified, total_jobs, completed_jobs) - """ - conn = create_connection(DB_FILE_AS_TIMES) - create_table_header_query = textwrap.dedent( - '''CREATE TABLE - IF NOT EXISTS experiment_times ( - exp_id integer PRIMARY KEY, - name text NOT NULL, - created int NOT NULL, - modified int NOT NULL, - total_jobs int NOT NULL, - completed_jobs int NOT NULL, - FOREIGN KEY (exp_id) REFERENCES experiment (id) - );''') - - create_table_detail_query = textwrap.dedent( - '''CREATE TABLE - IF NOT EXISTS job_times ( - detail_id integer PRIMARY KEY AUTOINCREMENT, - exp_id integer NOT NULL, - job_name text NOT NULL, - created integer NOT NULL, - modified integer NOT NULL, - submit_time int NOT NULL, - start_time int NOT NULL, - finish_time int NOT NULL, - status text NOT NULL, - FOREIGN KEY (exp_id) REFERENCES experiment (id) - );''') - - drop_table_header_query = ''' DROP TABLE experiment_times ''' - drop_table_details_query = ''' DROP TABLE job_times ''' - # create_table(conn, drop_table_details_query) - # create_table(conn, drop_table_header_query) - # return - create_table(conn, create_table_header_query) - create_table(conn, create_table_detail_query) - current_table = _get_exp_times() - current_table_expid = dict() - - for item in current_table: - try: - exp_id, name, created, modified, total_jobs, completed_jobs = item - current_table_expid[name] = (exp_id, int(created), int( - modified), int(total_jobs), int(completed_jobs)) - except Exception as ex: - print((traceback.format_exc())) - print(item) - print((str(name) + " ~ " + str(created) + "\t" + str(modified))) - - return current_table_expid - # STATUS ARCHIVE - def insert_archive_status(status, alatency, abandwidth, clatency, cbandwidth, rtime): try: @@ -146,99 +52,6 @@ def get_last_read_archive_status(): # INSERTIONS - -def insert_experiment_times_header(expid, timest, total_jobs, completed_jobs, debug=False, log=None): - """ - Inserts into experiment times header. Requires ecearth.db connection. - :param expid: Experiment name - :type expid: String - :param timest: timestamp of the pkl last modified date - :type timest: Integer - :param total_jobs: Total number of jobs - :type total_jobs: Integer - :param completed_jobs: Number of completed jobs - :type completed_jobs: Integer - :param debug: Flag (testing purposes) - :type debug: Boolean - :param conn_ecearth: ecearth.db connection - :type conn: sqlite3 connection - :return: exp_id of the experiment (not the experiment name) - :rtype: Integer - """ - try: - current_id = _get_id_db(create_connection(APIBasicConfig.DB_PATH), expid) - if (current_id): - if (debug == True): - print(("INSERTING INTO EXPERIMENT_TIMES " + str(current_id) + "\t" + str(expid) + - "\t" + str(timest) + "\t" + str(total_jobs) + "\t" + str(completed_jobs))) - return current_id - row_content = (current_id, expid, int(timest), int(timest), total_jobs, completed_jobs) - result = _create_exp_times(row_content) - return current_id - else: - return -1 - except sqlite3.Error as e: - print(("Error on Insert : " + str(type(e).__name__))) - print(current_id) - - -def _create_exp_times(row_content): - """ - Create experiment times - :param conn: - :param details: - :return: - """ - try: - conn = create_connection(DB_FILE_AS_TIMES) - sql = ''' INSERT OR REPLACE INTO experiment_times(exp_id, name, created, modified, total_jobs, completed_jobs) VALUES(?,?,?,?,?,?) ''' - # print(row_content) - cur = conn.cursor() - cur.execute(sql, row_content) - # print(cur) - conn.commit() - return cur.lastrowid - except sqlite3.Error as e: - print(("Error on Insert : " + str(type(e).__name__))) - print(row_content) - - -def create_many_job_times(list_job): - try: - conn = create_connection(DB_FILE_AS_TIMES) - sql = ''' INSERT INTO job_times(exp_id, job_name, created, modified, submit_time, start_time, finish_time, status) VALUES(?,?,?,?,?,?,?,?) ''' - # print(row_content) - cur = conn.cursor() - cur.executemany(sql, list_job) - # print(cur) - # Commit outside the loop - conn.commit() - except sqlite3.Error as e: - print((traceback.format_exc())) - print(("Error on Insert : " + str(type(e).__name__))) - # print((exp_id, job_name, timest, timest, - # submit_time, start_time, finish_time, status)) - - -def _insert_into_ecearth_details(exp_id, user, created, model, branch, hpc): - """ - Inserts into the details table of ecearth.db - :return: Id - :rtype: int - """ - conn = create_connection(APIBasicConfig.DB_PATH) - if conn: - try: - sql = ''' INSERT INTO details(exp_id, user, created, model, branch, hpc) VALUES(?,?,?,?,?,?) ''' - cur = conn.cursor() - cur.execute(sql, (exp_id, user, created, model, branch, hpc)) - conn.commit() - return cur.lastrowid - except Exception as exp: - print(exp) - return False - - def create_connection(db_file): # type: (str) -> sqlite3.Connection """ @@ -253,63 +66,8 @@ def create_connection(db_file): print(exp) -def create_table(conn, create_table_sql): - """ create a table from the create_table_sql statement - :param conn: Connection object - :param create_table_sql: a CREATE TABLE statement - :return: - """ - try: - c = conn.cursor() - c.execute(create_table_sql) - except Exception as e: - print(e) - - # SELECTS -def get_times_detail(exp_id): - """ - Gets the current detail of the experiment from job_times - :param exp_id: Id of the experiment - :type exp_id: Integer - :return: Dictionary Key: Job Name, Values: 5-tuple (submit time, start time, finish time, status, detail id) - :rtype: dict - """ - # conn = create_connection(DB_FILE_AS_TIMES) - try: - current_table_detail = dict() - current_table = _get_job_times(exp_id) - if current_table is None: - return None - for item in current_table: - detail_id, exp_id, job_name, created, modified, submit_time, start_time, finish_time, status = item - current_table_detail[job_name] = ( - submit_time, start_time, finish_time, status, detail_id) - return current_table_detail - except Exception as exp: - print((traceback.format_exc())) - return None - - -def get_times_detail_by_expid(conn, expid): - """ - Gets the detail of times of the experiment by expid (name of experiment).\n - :param conn: ecearth.db connection - :rtype conn: sqlite3 connection - :param expid: Experiment name - :type expid: str - :return: Dictionary Key: Job Name, Values: 5-tuple (submit time, start time, finish time, status, detail id) - :rtype: dict - """ - # conn = create_connection(DB_FILE_AS_TIMES) - exp_id = _get_id_db(conn, expid) - if (exp_id): - return get_times_detail(exp_id) - else: - return None - - def get_experiment_status(): """ Gets table experiment_status as dictionary @@ -337,287 +95,6 @@ def get_specific_experiment_status(expid): return (name, status) -def get_experiment_times(): - # type: () -> Dict[str, Tuple[int, int, int]] - """ - Gets table experiment_times as dictionary - conn is expected to reference as_times.db - """ - # conn = create_connection(DB_FILE_AS_TIMES) - experiment_times = dict() - current_table = _get_exp_times() - for item in current_table: - exp_id, name, created, modified, total_jobs, completed_jobs = item - experiment_times[name] = (total_jobs, completed_jobs, modified) - # if extended == True: - # experiment_times[name] = (total_jobs, completed_jobs, created, modified) - return experiment_times - - -def get_experiment_times_by_expid(expid): - """[summary] - :return: exp_id, total number of jobs, number of completed jobs - :rtype 3-tuple: (int, int, int) - """ - current_row = _get_exp_times_by_expid(expid) - if current_row: - exp_id, name, created, modified, total_jobs, completed_jobs = current_row - return (exp_id, total_jobs, completed_jobs) - return None - - -def get_experiment_times_group(): - """ - Gets table experiment_times as dictionary id -> name - conn is expected to reference as_times.db - """ - experiment_times = dict() - current_table = _get_exp_times() - for item in current_table: - exp_id, name, created, modified, total_jobs, completed_jobs = item - if name not in list(experiment_times.keys()): - experiment_times[name] = list() - experiment_times[name].append(exp_id) - # if extended == True: - # experiment_times[name] = (total_jobs, completed_jobs, created, modified) - return experiment_times - - -def get_exps_base(): - """ - Get exp name and id from experiment table in ecearth.db - :param conn: ecearth.db connection - :param expid: - :return: - """ - conn = create_connection(APIBasicConfig.DB_PATH) - result = dict() - conn.text_factory = str - cur = conn.cursor() - cur.execute( - "SELECT name, id FROM experiment WHERE autosubmit_version IS NOT NULL") - rows = cur.fetchall() - cur.close() - conn.close() - if (rows): - for row in rows: - _name, _id = row - result[_name] = _id - else: - return None - return result - - -def get_exps_detailed_complete(): - """ - Get information from details table - :param conn: ecearth.db connection - :param expid: - :return: Dictionary exp_id -> (user, created, model, branch, hpc) - """ - all_details = _get_exps_detailed_complete(create_connection(APIBasicConfig.DB_PATH)) - result = dict() - if (all_details): - for item in all_details: - exp_id, user, created, model, branch, hpc = item - result[exp_id] = (user, created, model, branch, hpc) - return result - - -def get_latest_completed_jobs(seconds=300): - """ - Get latest completed jobs - """ - result = dict() - latest_completed_detail = _get_latest_completed_jobs(seconds) - if (latest_completed_detail): - for item in latest_completed_detail: - detail_id, exp_id, job_name, created, modified, submit_time, start_time, finish_time, status = item - result[job_name] = (detail_id, submit_time, - start_time, finish_time, status) - return result - - -def _get_exps_detailed_complete(conn): - """ - Get information from details table - :param conn: ecearth.db connection - :param expid: - :return: - """ - conn.text_factory = str - cur = conn.cursor() - cur.execute( - "SELECT * FROM details") - rows = cur.fetchall() - cur.close() - conn.close() - return rows - - -def _get_exp_times(): - # type: () -> List[Tuple[int, str, int, int, int, int]] - """ - Get all experiments from table experiment_times.\n - :return: Row content (exp_id, name, created, modified, total_jobs, completed_jobs) - :rtype: 6-tuple (int, str, int, int, int, int) - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - conn.text_factory = str - cur = conn.cursor() - cur.execute( - "SELECT exp_id, name, created, modified, total_jobs, completed_jobs FROM experiment_times") - rows = cur.fetchall() - conn.close() - return rows - except Exception as exp: - print((traceback.format_exc())) - return list() - - -def _get_exp_times_by_expid(expid): - """ - Returns data from experiment_time table by expid. - - :param expid: expid/name - :type expid: str - :return: Row content (exp_id, name, created, modified, total_jobs, completed_jobs) - :rtype: 6-tuple (int, str, str, str, int, int) - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - conn.text_factory = str - cur = conn.cursor() - cur.execute( - "SELECT exp_id, name, created, modified, total_jobs, completed_jobs FROM experiment_times WHERE name=?", (expid,)) - rows = cur.fetchall() - conn.close() - return rows[0] if len(rows) > 0 else None - except Exception as exp: - print((traceback.format_exc())) - return None - - -def _get_job_times(exp_id): - """ - Get exp job times detail for a given expid from job_times. - :param exp_id: Experiment id (not name) - :type exp_id: Integer - :return: Detail content - :rtype: list of 9-tuple: (detail_id, exp_id, job_name, created, modified, submit_time, start_time, finish_time, status) - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - cur = conn.cursor() - cur.execute("SELECT detail_id, exp_id, job_name, created, modified, submit_time, start_time, finish_time, status FROM job_times WHERE exp_id=?", (exp_id,)) - rows = cur.fetchall() - conn.close() - return rows - except Exception as ex: - print((traceback.format_exc())) - print((str(exp_id))) - print((str(ex))) - return None - - -def _get_latest_completed_jobs(seconds=300): - """ - get latest completed jobs, defaults at 300 seconds, 5 minutes - """ - current_ts = time.time() - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - cur = conn.cursor() - cur.execute("SELECT detail_id, exp_id, job_name, created, modified, submit_time, start_time, finish_time, status FROM job_times WHERE (? - modified)<=? AND status='COMPLETED'", (current_ts, seconds)) - rows = cur.fetchall() - conn.close() - return rows - except Exception as ex: - print((traceback.format_exc())) - print((str(seconds))) - print((str(ex))) - return None - - -def _delete_many_from_job_times_detail(detail_list): - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - cur = conn.cursor() - #print("Cursor defined") - cur.executemany( - "DELETE FROM job_times WHERE detail_id=?", detail_list) - # print(cur.rowcount) - cur.close() - conn.commit() - conn.close() - # No reliable way to get any feedback from cursor at this point, so let's just return 1 - return True - except Exception as exp: - # print("Error while trying to delete " + - # str(detail_id) + " from job_times.") - print((traceback.format_exc())) - return None - - -def delete_experiment_data(exp_id): - # type: (int) -> bool - """ - Deletes experiment data from experiment_times and job_times in as_times.db - - :param exp_id: Id of experiment - :type exp_id: int - """ - deleted_e = _delete_from_experiment_times(exp_id) - deleted_j = _delete_from_job_times(exp_id) - print(("Main exp " + str(deleted_e) + "\t" + str(deleted_j))) - if deleted_e and deleted_j: - return True - return False - - -def _delete_from_experiment_times(exp_id): - """ - Deletes an experiment from experiment_times in as_times.db - - :param exp_id: Id of experiment - :type exp_id: int - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - cur = conn.cursor() - cur.execute("DELETE FROM experiment_times WHERE exp_id=?", (exp_id,)) - conn.commit() - conn.close() - return True - except Exception as exp: - print(("Error while trying to delete " + - str(exp_id) + " from experiment_times.")) - print((traceback.format_exc())) - return None - - -def _delete_from_job_times(exp_id): - """ - Deletes an experiment from job_times in as_times.db - - :param exp_id: Id of experiment - :type exp_id: int - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - cur = conn.cursor() - cur.execute("DELETE FROM job_times WHERE exp_id=?", (exp_id,)) - conn.commit() - conn.close() - return True - except Exception as exp: - print(("Error while trying to delete " + - str(exp_id) + " from job_times.")) - print((traceback.format_exc())) - return None - - def _get_exp_status(): """ Get all registers from experiment_status.\n @@ -659,167 +136,4 @@ def _get_specific_exp_status(expid): return (0, expid, "NOT RUNNING", 0) -def _get_id_db(conn, expid): - """ - Get exp_id of the experiment (different than the experiment name). - :param conn: ecearth.db connection - :type conn: sqlite3 connection - :param expid: Experiment name - :type expid: String - :return: Id of the experiment - :rtype: Integer or None - """ - try: - cur = conn.cursor() - cur.execute("SELECT id FROM experiment WHERE name=?", (expid,)) - row = cur.fetchone() - return row[0] - except Exception as exp: - print(("Couldn't get exp_id for {0}".format(expid))) - print(traceback.format_exc()) - return None - - # UPDATES - - -def update_exp_status(expid, status, seconds_diff): - """ - Update existing experiment_status. - :param expid: Experiment name - :type expid: String - :param status: Experiment status - :type status: String - :param seconds_diff: Indicator of how long it has been active since the last time it was checked - :type seconds_diff: Integer - :return: Id of register - :rtype: Integer - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - sql = ''' UPDATE experiment_status SET status = ?, seconds_diff = ?, modified = ? WHERE name = ? ''' - cur = conn.cursor() - cur.execute(sql, (status, seconds_diff, - datetime.today().strftime('%Y-%m-%d-%H:%M:%S'), expid)) - conn.commit() - return cur.lastrowid - except sqlite3.Error as e: - print(("Error while trying to update " + - str(expid) + " in experiment_status.")) - print((traceback.format_exc())) - print(("Error on Update: " + str(type(e).__name__))) - - -def _update_ecearth_details(exp_id, user, created, model, branch, hpc): - """ - Updates ecearth.db table details. - """ - conn = create_connection(APIBasicConfig.DB_PATH) - if conn: - try: - sql = ''' UPDATE details SET user=?, created=?, model=?, branch=?, hpc=? where exp_id=? ''' - cur = conn.cursor() - cur.execute(sql, (user, created, model, branch, hpc, exp_id)) - conn.commit() - return True - except Exception as exp: - print(exp) - return False - return False - - -def update_experiment_times(exp_id, modified, completed_jobs, total_jobs, debug=False): - """ - Update existing experiment times header - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - if (debug == True): - print(("UPDATE experiment_times " + str(exp_id) + "\t" + - str(completed_jobs) + "\t" + str(total_jobs))) - return - sql = ''' UPDATE experiment_times SET modified = ?, completed_jobs = ?, total_jobs = ? WHERE exp_id = ? ''' - cur = conn.cursor() - cur.execute(sql, (int(modified), completed_jobs, total_jobs, exp_id)) - conn.commit() - # print("Updated header") - return exp_id - except sqlite3.Error as e: - print(("Error while trying to update " + - str(exp_id) + " in experiment_times.")) - print((traceback.format_exc())) - print(("Error on Update: " + str(type(e).__name__))) - - -def update_experiment_times_only_modified(exp_id, modified): - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - sql = ''' UPDATE experiment_times SET modified = ? WHERE exp_id = ? ''' - cur = conn.cursor() - cur.execute(sql, (int(modified), exp_id)) - conn.commit() - # print("Updated header") - return exp_id - except sqlite3.Error as e: - print(("Error while trying to update " + - str(exp_id) + " in experiment_times.")) - print((traceback.format_exc())) - print(("Error on Update: " + str(type(e).__name__))) - - -def update_job_times(detail_id, modified, submit_time, start_time, finish_time, status, debug=False, no_modify_time=False): - """ - Update single experiment job detail \n - :param conn: Connection to as_times.db. \n - :type conn: sqlite3 connection. \n - :param detail_id: detail_id in as_times.job_times. \n - :type detail_id: Integer. \n - :param modified: Timestamp of current date of pkl \n - :type modified: Integer. \n - """ - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - if (debug == True): - print(("UPDATING JOB TIMES " + str(detail_id) + " ~ " + str(modified) + "\t" + - str(submit_time) + "\t" + str(start_time) + "\t" + str(finish_time) + "\t" + str(status))) - return - if no_modify_time == False: - sql = ''' UPDATE job_times SET modified = ?, submit_time = ?, start_time = ?, finish_time = ?, status = ? WHERE detail_id = ? ''' - cur = conn.cursor() - cur.execute(sql, (modified, submit_time, start_time, - finish_time, status, detail_id)) - # Commit outside the loop - conn.commit() - cur.close() - conn.close() - else: - sql = ''' UPDATE job_times SET submit_time = ?, start_time = ?, finish_time = ?, status = ? WHERE detail_id = ? ''' - cur = conn.cursor() - cur.execute(sql, (submit_time, start_time, - finish_time, status, detail_id)) - # Commit outside the loop - conn.commit() - cur.close() - conn.close() - - except sqlite3.Error as e: - print(("Error while trying to update " + - str(detail_id) + " in job_times.")) - print((traceback.format_exc())) - print(("Error on Update: " + str(type(e).__name__))) - - -def update_many_job_times(list_jobs): - try: - conn = create_connection(os.path.join(APIBasicConfig.DB_DIR, APIBasicConfig.AS_TIMES_DB)) - sql = ''' UPDATE job_times SET modified = ?, submit_time = ?, start_time = ?, finish_time = ?, status = ? WHERE detail_id = ? ''' - cur = conn.cursor() - cur.executemany(sql, list_jobs) - # Commit outside the loop - conn.commit() - cur.close() - conn.close() - except sqlite3.Error as e: - print("Error while trying to update many in update_many_job_times.") - print((traceback.format_exc())) - print(("Error on Update: " + str(type(e).__name__))) diff --git a/autosubmit_api/workers/business/populate_times.py b/autosubmit_api/workers/business/populate_times.py deleted file mode 100644 index 89bbc79..0000000 --- a/autosubmit_api/workers/business/populate_times.py +++ /dev/null @@ -1,365 +0,0 @@ -import datetime -import os -import pwd -import time -import subprocess -import traceback -import socket -import pickle -from autosubmit_api.builders.configuration_facade_builder import AutosubmitConfigurationFacadeBuilder, ConfigurationFacadeDirector -from autosubmit_api.components.experiment.pkl_organizer import PklOrganizer -from autosubmit_api.components.jobs.utils import get_job_total_stats -from autosubmit_api.config.config_common import AutosubmitConfigResolver -from autosubmit_api.experiment import common_db_requests as DbRequests -from autosubmit_api.config.basicConfig import APIBasicConfig -from autosubmit_api.common.utils import Status -from bscearth.utils.config_parser import ConfigParserFactory - - -SAFE_TIME_LIMIT = 300 - - -def process_completed_times(time_condition=60): - """ - Tests for completed jobs of all autosubmit experiments and updates their completion times data in job_times and experiment_times. - :param time_condition: Time difference in seconds that qualifies a experiment as out of date. - :type time_condition: Integer - """ - try: - t0 = time.time() - DEBUG = False - APIBasicConfig.read() - path = APIBasicConfig.LOCAL_ROOT_DIR - # Time test for data retrieval - # All experiment from file system - currentDirectories = subprocess.Popen(['ls', '-t', path], - stdout=subprocess.PIPE, - stderr=subprocess.STDOUT) if (os.path.exists(path)) else None - stdOut, _ = currentDirectories.communicate() if currentDirectories else (None, None) - # Building connection to ecearth - - current_table = dict() # REMOVED: DbRequests.prepare_completed_times_db() - # Build list of all folder in /esarchive/autosubmit which should be considered as experiments (although some might not be) - # Pre process - _preprocess_completed_times() - experiments = stdOut.split() if stdOut else [] - counter = 0 - - # Get current `details` from ecearth.db and convert to set for effcient contain test - details_table_ids_set = set(DbRequests.get_exps_detailed_complete().keys()) - # Get current `experiments` from ecearth.db - experiments_table = DbRequests.get_exps_base() - - for expid in experiments: - # Experiment names should be 4 char long - if (len(expid) != 4): - counter += 1 - continue - # Experiment names must correspond to an experiment that contains a .pkl file - exp_str = expid.decode("UTF-8") - full_path = os.path.join(path, exp_str, "pkl", "job_list_" + exp_str + ".pkl") - timest = 0 - if os.path.exists(full_path): - # get time of last modification - timest = int(os.stat(full_path).st_mtime) - else: - counter += 1 - continue - counter += 1 - experiments_table_exp_id = experiments_table.get(exp_str, None) - if current_table.get(exp_str, None) is None: - # Pkl exists but is not registered in the table - # INSERT - # print("Pkl of " + exp_str + " exists but not in the table: INSERT") - current_id = _process_pkl_insert_times(exp_str, full_path, timest, APIBasicConfig, DEBUG) - _process_details_insert_or_update(exp_str, experiments_table_exp_id, experiments_table_exp_id in details_table_ids_set) - else: - exp_id, created, modified, total_jobs, completed_jobs = current_table[exp_str] - time_diff = int(timest - modified) - # print("Pkl of " + exp_str + " exists") - current_id = _process_pkl_insert_times(exp_str, full_path, timest, APIBasicConfig, DEBUG) - if time_diff > time_condition: - # Update table - _process_pkl_update_times(exp_str, full_path, timest, APIBasicConfig, exp_id, DEBUG) - _process_details_insert_or_update(exp_str, experiments_table_exp_id, experiments_table_exp_id in details_table_ids_set) - DbRequests.update_experiment_times_only_modified(exp_id, timest) - t1 = time.time() - # Timer safeguard - if (t1 - t0) > SAFE_TIME_LIMIT: - raise Exception( - "Time limit reached {0:06.2f} seconds on process_completed_times while processing {1}. Time spent on reading data {2:06.2f} seconds.".format((t1 - t0), exp_str, (t1 - t0))) - except Exception as ex: - print((traceback.format_exc())) - print(str(ex)) - - -def _describe_experiment(experiment_id): - user = "" - created = "" - model = "" - branch = "" - hpc = "" - APIBasicConfig.read() - exp_path = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, experiment_id) - if not os.path.exists(exp_path): - return user, created, model, branch, hpc - - user = os.stat(exp_path).st_uid - try: - user = pwd.getpwuid(user).pw_name - except: - pass - - created = datetime.datetime.fromtimestamp( - os.path.getmtime(exp_path)) - - try: - as_conf = AutosubmitConfigResolver( - experiment_id, APIBasicConfig, ConfigParserFactory()) - as_conf.reload() - - project_type = as_conf.get_project_type() - if project_type != "none": - if not as_conf.check_proj(): - return False - if (as_conf.get_svn_project_url()): - model = as_conf.get_svn_project_url() - branch = as_conf.get_svn_project_url() - else: - model = as_conf.get_git_project_origin() - branch = as_conf.get_git_project_branch() - if model is "": - model = "Not Found" - if branch is "": - branch = "Not Found" - hpc = as_conf.get_platform() - except: - pass - return user, created, model, branch, hpc - - -def _process_details_insert_or_update(expid, exp_id, current_details): - """ - Decides whether the experiment should be inserted or updated in the details table. - :param expid: name of experiment e.g: a001 - :type expid: str - :param exp_id: id of experiment e.g: 1 - :type exp_id: int - :param current_details: True if it exp_id exists in details table, False otherwise - :rtype: bool - :result: True if successful, False otherwise - :rtype: bool - """ - result = False - if exp_id: - try: - user, created, model, branch, hpc = _describe_experiment(expid) - if current_details: - # Update - result = DbRequests._update_ecearth_details(exp_id, user, created, model, branch, hpc) - else: - # Insert - _Id = DbRequests._insert_into_ecearth_details(exp_id, user, created, model, branch, hpc) - result = True if _Id else False - except Exception as exp: - print(exp) - return result - - -def _preprocess_completed_times(): - """ - Preprocess table to get rid of possible conflicts - :param current_table: table experiment_times from as_times.db - """ - current_table = DbRequests.get_experiment_times_group() - for name, _ids in list(current_table.items()): - if len(_ids) > 1: - print((str(name) + " has more than 1 register.")) - for i in range(0, len(_ids) - 1): - _id = _ids[i] - deleted_outdated = DbRequests.delete_experiment_data(_id) - -def _process_pkl_update_times(expid, path_pkl, timest_pkl, BasicConfig, exp_id, debug=False): - """ - Updates register in job_times and experiment_times for the given experiment. - :param expid: Experiment name - :type expid: String - :param path_pkl: path to the pkl file (DEPRECATED) - :type path_pkl: String - :param timest_pkl: Timestamp of the last modified date of the pkl file - :type timest_pkl: Integer - :param BasicConfig: Configuration of AS - :type BasicConfig: Object - :param exp_id: Id of experiment - :type exp_id: Integer - :param debug: Flag (testing purposes) - :type debug: Boolean - :return: Nothing - """ - # debug = True - try: - found_in_pkl = list() - BasicConfig.read() - - tmp_path = os.path.join(BasicConfig.LOCAL_ROOT_DIR, expid, BasicConfig.LOCAL_TMP_DIR) - job_times_db = dict() - total_jobs = 0 - completed_jobs = 0 - fd = None - # t_start = time.time() - # Get current detail from database - experiment_times_detail = DbRequests.get_times_detail(exp_id) - # t_seconds = time.time() - t_start - must_update_header = False - - to_update = [] - to_create = [] - - # Read PKL - autosubmit_config_facade = ConfigurationFacadeDirector( - AutosubmitConfigurationFacadeBuilder(expid)).build_autosubmit_configuration_facade() - pkl_organizer = PklOrganizer(autosubmit_config_facade) - for job_item in pkl_organizer.current_content: - total_jobs += 1 - status_code = job_item.status - job_name = job_item.name - found_in_pkl.append(job_name) - status_text = str(Status.VALUE_TO_KEY[status_code]) - if (status_code == Status.COMPLETED): - completed_jobs += 1 - if (experiment_times_detail) and job_name in list(experiment_times_detail.keys()): - # If job in pkl exists in database, retrieve data from database - submit_time, start_time, finish_time, status_text_in_table, detail_id = experiment_times_detail[job_name] - if (status_text_in_table != status_text): - # If status has changed - submit_time, start_time, finish_time, _ = get_job_total_stats(status_code, job_name, tmp_path) - submit_ts = int(time.mktime(submit_time.timetuple())) if len(str(submit_time)) > 0 else 0 - start_ts = int(time.mktime(start_time.timetuple())) if len(str(start_time)) > 0 else 0 - finish_ts = int(time.mktime(finish_time.timetuple())) if len(str(finish_time)) > 0 else 0 - # UPDATE - must_update_header = True - to_update.append((int(timest_pkl), - submit_ts, - start_ts, - finish_ts, - status_text, - detail_id)) - - else: - # Insert only if it is not WAITING nor READY - if (status_code not in [Status.WAITING, Status.READY]): - submit_time, start_time, finish_time, status_text = get_job_total_stats(status_code, job_name, tmp_path) - must_update_header = True - to_create.append((exp_id, - job_name, - int(timest_pkl), - int(timest_pkl), - int(time.mktime(submit_time.timetuple())) if len(str(submit_time)) > 0 else 0, - int(time.mktime(start_time.timetuple())) if len(str(start_time)) > 0 else 0, - int(time.mktime(finish_time.timetuple())) if len(str(finish_time)) > 0 else 0, - status_text)) - - - # Update Many - if len(to_update) > 0: - DbRequests.update_many_job_times(to_update) - # Create Many - if len(to_create) > 0: - DbRequests.create_many_job_times(to_create) - - if must_update_header == True: - exp_id = DbRequests.update_experiment_times(exp_id, int(timest_pkl), completed_jobs, total_jobs, debug) - - # Reviewing for deletes: - if len(found_in_pkl) > 0 and (experiment_times_detail): - detail_list = [] - for key in experiment_times_detail: - if key not in found_in_pkl: - # Delete Row - submit_time, start_time, finish_time, status_text_in_table, detail_id = experiment_times_detail[key] - detail_list.append((detail_id,)) - if len(detail_list) > 0: - DbRequests._delete_many_from_job_times_detail(detail_list) - - except (socket.error, EOFError): - # print(str(expid) + "\t EOF Error") - pass - except Exception as ex: - print(expid) - print((traceback.format_exc())) - - -def _process_pkl_insert_times(expid, path_pkl, timest_pkl, BasicConfig, debug=False): - """ - Process Pkl contents and insert information into database if status of jobs is not WAITING (to save space). - :param conn: Connection to database - :type conn: Sqlite3 connection object - :param expid: Experiment name - :type expid: String - :param path_pkl: Path to the pkl file - :type path_pkl: String - :param timest_pkl: Timestamp of the pkl modified date - :type timest_pkl: Integer - :param BasicConfig: Configuration data of AS - :type BasicConfig: Object - :param debug: Flag (proper name should be test) - :type debug: Boolean - """ - # BasicConfig.read() - # path = BasicConfig.LOCAL_ROOT_DIR - # db_file = os.path.join(path, DbRequests.DB_FILE_AS_TIMES) - # Build tmp path to search for TOTAL_STATS files - tmp_path = os.path.join(BasicConfig.LOCAL_ROOT_DIR, expid, BasicConfig.LOCAL_TMP_DIR) - job_times = dict() # Key: job_name - total_jobs = 0 - completed_jobs = 0 - status_code = Status.UNKNOWN - status_text = str(Status.VALUE_TO_KEY[status_code]) - try: - # Read PKL - autosubmit_config_facade = ConfigurationFacadeDirector( - AutosubmitConfigurationFacadeBuilder(expid)).build_autosubmit_configuration_facade() - pkl_organizer = PklOrganizer(autosubmit_config_facade) - for job_item in pkl_organizer.current_content: - total_jobs += 1 - status_code = job_item.status - job_name = job_item.name - status_text = str(Status.VALUE_TO_KEY[status_code]) - if (status_code == Status.COMPLETED): - completed_jobs += 1 - job_times[job_name] = status_code - except: - pass - - try: - # Insert header - current_id = DbRequests.insert_experiment_times_header(expid, int(timest_pkl), total_jobs, completed_jobs, debug) - if(current_id > 0): - # Insert detail - to_insert_many = [] - for job_name in job_times: - # Inserting detail. Do not insert WAITING or READY jobs. - status_code = job_times[job_name] - if (status_code not in [Status.WAITING, Status.READY]): - submit_time, start_time, finish_time, status_text = get_job_total_stats(status_code, job_name, tmp_path) - to_insert_many.append((current_id, - job_name, - int(timest_pkl), - int(timest_pkl), - int(time.mktime(submit_time.timetuple())) if len( - str(submit_time)) > 0 else 0, - int(time.mktime(start_time.timetuple())) if len( - str(start_time)) > 0 else 0, - int(time.mktime(finish_time.timetuple())) if len( - str(finish_time)) > 0 else 0, - status_text)) - if len(to_insert_many) > 0: - DbRequests.create_many_job_times(to_insert_many) - else: - pass - - return current_id - except Exception as ex: - print(expid) - print((traceback.format_exc())) - return 0 diff --git a/autosubmit_api/workers/populate_queue_run_times.py b/autosubmit_api/workers/populate_queue_run_times.py deleted file mode 100644 index 0236886..0000000 --- a/autosubmit_api/workers/populate_queue_run_times.py +++ /dev/null @@ -1,10 +0,0 @@ -from autosubmit_api.bgtasks.bgtask import PopulateQueueRuntimes - - -def main(): - """ Process and updates queuing and running times. """ - PopulateQueueRuntimes.run() - - -if __name__ == "__main__": - main() diff --git a/autosubmit_api/workers/verify_complete.py b/autosubmit_api/workers/verify_complete.py deleted file mode 100644 index 490b9d4..0000000 --- a/autosubmit_api/workers/verify_complete.py +++ /dev/null @@ -1,10 +0,0 @@ -#!/usr/bin/env python -from autosubmit_api.bgtasks.tasks.job_times_updater import JobTimesUpdater - - -def main(): - JobTimesUpdater.run() - - -if __name__ == "__main__": - main() diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 3f9a4743b4dd8df93226cb03fa54a25b3ca4572f..c70732eb783e06bcef253b4f0e7ac92c0a225396 100644 GIT binary patch delta 58 scmZp0XmFSy%~&>3#+k8fV}g@Bm#MCyk(H^5m8s$6HS!9`+-oRY0M^qE*Z=?k delta 58 rcmZp0XmFSy%~&u|#+k8TV}g@Bmx->SnU$#p5KUequYk Date: Thu, 15 Feb 2024 15:53:31 +0100 Subject: [PATCH 12/18] remove history module dead code --- autosubmit_api/components/jobs/test.py | 36 -- autosubmit_api/config/files/autosubmit.conf | 42 -- autosubmit_api/config/files/expdef.conf | 77 ---- autosubmit_api/config/files/jobs.conf | 96 ----- autosubmit_api/config/files/platforms.conf | 55 --- autosubmit_api/database/data/autosubmit.sql | 8 - .../experiment/experiment_db_manager.py | 38 -- autosubmit_api/history/experiment_history.py | 305 +-------------- .../history/platform_monitor/__init__.py | 0 .../output_examples/pending.txt | 1 - .../output_examples/wrapper1.txt | 3 - .../output_examples/wrapper2.txt | 3 - .../output_examples/wrapper_big.txt | 33 -- .../platform_monitor/platform_monitor.py | 30 -- .../platform_monitor/platform_utils.py | 70 ---- .../history/platform_monitor/slurm_monitor.py | 65 ---- .../platform_monitor/slurm_monitor_item.py | 98 ----- .../history/platform_monitor/test.py | 94 ----- autosubmit_api/history/test.py | 367 ------------------ autosubmit_api/history/test_job_history.py | 71 ---- autosubmit_api/history/test_strategies.py | 94 ----- autosubmit_api/history/test_utils.py | 32 -- .../workers/populate_details/test.py | 53 --- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes 24 files changed, 7 insertions(+), 1664 deletions(-) delete mode 100644 autosubmit_api/components/jobs/test.py delete mode 100644 autosubmit_api/config/files/autosubmit.conf delete mode 100644 autosubmit_api/config/files/expdef.conf delete mode 100644 autosubmit_api/config/files/jobs.conf delete mode 100644 autosubmit_api/config/files/platforms.conf delete mode 100644 autosubmit_api/database/data/autosubmit.sql delete mode 100644 autosubmit_api/experiment/experiment_db_manager.py delete mode 100644 autosubmit_api/history/platform_monitor/__init__.py delete mode 100644 autosubmit_api/history/platform_monitor/output_examples/pending.txt delete mode 100644 autosubmit_api/history/platform_monitor/output_examples/wrapper1.txt delete mode 100644 autosubmit_api/history/platform_monitor/output_examples/wrapper2.txt delete mode 100644 autosubmit_api/history/platform_monitor/output_examples/wrapper_big.txt delete mode 100644 autosubmit_api/history/platform_monitor/platform_monitor.py delete mode 100644 autosubmit_api/history/platform_monitor/platform_utils.py delete mode 100644 autosubmit_api/history/platform_monitor/slurm_monitor.py delete mode 100644 autosubmit_api/history/platform_monitor/slurm_monitor_item.py delete mode 100644 autosubmit_api/history/platform_monitor/test.py delete mode 100644 autosubmit_api/history/test.py delete mode 100644 autosubmit_api/history/test_job_history.py delete mode 100644 autosubmit_api/history/test_strategies.py delete mode 100644 autosubmit_api/history/test_utils.py delete mode 100644 autosubmit_api/workers/populate_details/test.py diff --git a/autosubmit_api/components/jobs/test.py b/autosubmit_api/components/jobs/test.py deleted file mode 100644 index dc64a75..0000000 --- a/autosubmit_api/components/jobs/test.py +++ /dev/null @@ -1,36 +0,0 @@ -#!/usr/bin/env python - -import unittest -from components.jobs.joblist_loader import JobListLoader - - -class TestJobListHelper(unittest.TestCase): - def setUp(self): - pass - - def get_joblist_helper(self): - pass - -class TestJobListLoader(unittest.TestCase): - def setUp(self): - pass - - def tearDown(self): - pass - - def test_load(self): - pass - # loader = JobListLoader("a29z") - # loader.load_jobs() - # self.assertTrue(len(loader.jobs) > 0) - # for job in loader.jobs: - # job.do_print() - - # def test_loader(self): - # tree = - - # def test_load_out_err_files(self): - - -if __name__ == '__main__': - unittest.main() diff --git a/autosubmit_api/config/files/autosubmit.conf b/autosubmit_api/config/files/autosubmit.conf deleted file mode 100644 index 90770b8..0000000 --- a/autosubmit_api/config/files/autosubmit.conf +++ /dev/null @@ -1,42 +0,0 @@ -[config] -# Experiment identifier -# No need to change -EXPID = -# No need to change. -# Autosubmit version identifier -AUTOSUBMIT_VERSION = -# Default maximum number of jobs to be waiting in any platform -# Default = 3 -MAXWAITINGJOBS = 3 -# Default maximum number of jobs to be running at the same time at any platform -# Default = 6 -TOTALJOBS = 6 -# Time (seconds) between connections to the HPC queue scheduler to poll already submitted jobs status -# Default = 10 -SAFETYSLEEPTIME = 10 -# Number of retrials if a job fails. Can ve override at job level -# Default = 0 -RETRIALS = 0 - -[mail] -# Enable mail notifications -# Default = False -NOTIFICATIONS = False -# Mail address where notifications will be received -TO = - -[communications] -# Communications library used to connect with platforms: paramiko or saga. -# Default = paramiko -API = paramiko - -[storage] -# Defines the way of storing the progress of the experiment. The available options are: -# A PICKLE file (pkl) or an SQLite database (db). Default = pkl -TYPE = pkl -# Defines if the remote logs will be copied to the local platform. Default = True. -COPY_REMOTE_LOGS = True - -[migrate] -# Changes experiment files owner. -TO_USER = diff --git a/autosubmit_api/config/files/expdef.conf b/autosubmit_api/config/files/expdef.conf deleted file mode 100644 index 96e2b6f..0000000 --- a/autosubmit_api/config/files/expdef.conf +++ /dev/null @@ -1,77 +0,0 @@ -[DEFAULT] -# Experiment identifier -# No need to change -EXPID = -# HPC name. -# No need to change -HPCARCH = - -[experiment] -# Supply the list of start dates. Available formats: YYYYMMDD YYYYMMDDhh YYYYMMDDhhmm -# You can also use an abbreviated syntax for multiple dates with common parts: 200001[01 15] <=> 20000101 20000115 -# 200001[01-04] <=> 20000101 20000102 20000103 20000104 -# DATELIST = 19600101 19650101 19700101 -# DATELIST = 1960[0101 0201 0301] -# DATELIST = 19[60-65] -DATELIST = -# Supply the list of members. Format fcX -# You can also use an abreviated syntax for multiple members: fc[0 1 2] <=> fc0 fc1 fc2 -# fc[0-2] <=> fc0 fc1 fc2 -# MEMBERS = fc0 fc1 fc2 fc3 fc4 -# MEMBERS = fc[0-4] -MEMBERS = -# Chunk size unit. STRING = hour, day, month, year -CHUNKSIZEUNIT = month -# Chunk size. NUMERIC = 4, 6, 12 -CHUNKSIZE = -# Total number of chunks in experiment. NUMERIC = 30, 15, 10 -NUMCHUNKS = -# Initial chunk of the experiment. Optional. DEFAULT = 1 -CHUNKINI = -# Calendar used. LIST: standard, noleap -CALENDAR = standard - -[project] -# Select project type. STRING = git, svn, local, none -# If PROJECT_TYPE is set to none, Autosubmit self-contained dummy templates will be used -PROJECT_TYPE = -# Destination folder name for project. type = STRING, default = leave empty, -PROJECT_DESTINATION = - -# If PROJECT_TYPE is not git, no need to change -[git] -# Repository URL STRING = 'https://github.com/torvalds/linux.git' -PROJECT_ORIGIN = -# Select branch or tag, STRING, default = 'master', help = {'master' (default), 'develop', 'v3.1b', ...} -PROJECT_BRANCH = -# type = STRING, default = leave empty, help = if model branch is a TAG leave empty -PROJECT_COMMIT = -# type = STRING, default = leave empty and will load all submodules, help = loadThisSubmodule alsoloadthis anotherLoad ... -PROJECT_SUBMODULES = -# If PROJECT_TYPE is not svn, no need to change -[svn] -# type = STRING, help = 'https://svn.ec-earth.org/ecearth3' -PROJECT_URL = -# Select revision number. NUMERIC = 1778 -PROJECT_REVISION = - -# If PROJECT_TYPE is not local, no need to change -[local] -# type = STRING, help = /foo/bar/ecearth -PROJECT_PATH = - -# If PROJECT_TYPE is none, no need to change -[project_files] -# Where is PROJECT CONFIGURATION file location relative to project root path -FILE_PROJECT_CONF = -# Where is JOBS CONFIGURATION file location relative to project root path -FILE_JOBS_CONF = -# Default job scripts type in the project. type = STRING, default = bash, supported = 'bash', 'python' or 'r' -JOB_SCRIPTS_TYPE = - -[rerun] -# Is a rerun or not? [Default: Do set FALSE]. BOOLEAN = TRUE, FALSE -RERUN = FALSE -# If RERUN = TRUE then supply the list of chunks to rerun -# LIST = [ 19601101 [ fc0 [1 2 3 4] fc1 [1] ] 19651101 [ fc0 [16-30] ] ] -CHUNKLIST = \ No newline at end of file diff --git a/autosubmit_api/config/files/jobs.conf b/autosubmit_api/config/files/jobs.conf deleted file mode 100644 index eaf192c..0000000 --- a/autosubmit_api/config/files/jobs.conf +++ /dev/null @@ -1,96 +0,0 @@ -# Example job with all options specified - -## Job name -# [JOBNAME] -## Script to execute. If not specified, job will be omitted from workflow. -## Path relative to the project directory -# FILE = -## Platform to execute the job. If not specified, defaults to HPCARCH in expdef file. -## LOCAL is always defined and represents the current machine -# PLATFORM = -## Queue to add the job to. If not specified, uses PLATFORM default. -# QUEUE = -## Defines dependencies from job as a list of parents jobs separated by spaces. -## Dependencies to jobs in previous chunk, member o startdate, use -(DISTANCE) -# DEPENDENCIES = INI SIM-1 CLEAN-2 -## Define if jobs runs once, once per stardate, once per member or once per chunk. Options: once, date, member, chunk. -## If not specified, defaults to once -# RUNNING = once -## Specifies that job has only to be run after X dates, members or chunk. A job will always be created for the last -## If not specified, defaults to 1 -# FREQUENCY = 3 -## Specifies if a job with FREQUENCY > 1 has only to wait for all the jobs in the previous chunks on its period or just -## for the ones in the chunk it is going to execute -## If not specified, defaults to True -# WAIT = False -## Defines if job is only to be executed in reruns. If not specified, defaults to false. -# RERUN_ONLY = False -## Defines jobs needed to be rerun if this job is going to be rerunned -# RERUN_DEPENDENCIES = RERUN INI LOCAL_SETUP REMOTE_SETUP TRANSFER -## Wallclock to be submitted to the HPC queue in format HH:MM. If not specified, defaults to empty. -# WALLCLOCK = 00:05 -## Processors number to be submitted to the HPC. If not specified, defaults to 1. -# PROCESSORS = 1 -## Threads number to be submitted to the HPC. If not specified, defaults to 1. -# THREADS = 1 -## Tasks number (number of processes per node) to be submitted to the HPC. If not specified, defaults to empty. -# TASKS = 16 -## Memory requirements for the job in MB. Optional. If not specified, then not defined for the scheduler. -# MEMORY = 4096 -## Memory per task requirements for the job in MB. Optional. If not specified, then not defined for the scheduler. -# MEMORY_PER_TASK = 1024 -## Scratch free space requirements for the job in percentage (%). If not specified, it won't be defined on the template. -# SCRATCH_FREE_SPACE = 10 -## Number of retrials if a job fails. If not specified, defaults to the value given on experiment's autosubmit.conf -# RETRIALS = 4 -## Some jobs can not be checked before running previous jobs. Set this option to false if that is the case -# CHECK = False -## Select the interpreter that will run the job. Options: bash, python, r Default: bash -# TYPE = bash -## Synchronize a chunk job with its dependency chunks at a 'date' or 'member' level -# SYNCHRONIZE = date | member -## Optional. Custom directives for the resource manager of the platform used for that job. -## Put as many as you wish in json formatted array. -# CUSTOM_DIRECTIVE = ["#PBS -v myvar=value, "#PBS -v othervar=value"] - -[LOCAL_SETUP] -FILE = LOCAL_SETUP.sh -PLATFORM = LOCAL - -[REMOTE_SETUP] -FILE = REMOTE_SETUP.sh -DEPENDENCIES = LOCAL_SETUP -WALLCLOCK = 00:05 - -[INI] -FILE = INI.sh -DEPENDENCIES = REMOTE_SETUP -RUNNING = member -WALLCLOCK = 00:05 - -[SIM] -FILE = SIM.sh -DEPENDENCIES = INI SIM-1 CLEAN-2 -RUNNING = chunk -WALLCLOCK = 00:05 -PROCESSORS = 2 -THREADS = 1 -TASKS = 1 - -[POST] -FILE = POST.sh -DEPENDENCIES = SIM -RUNNING = chunk -WALLCLOCK = 00:05 - -[CLEAN] -FILE = CLEAN.sh -DEPENDENCIES = POST -RUNNING = chunk -WALLCLOCK = 00:05 - -[TRANSFER] -FILE = TRANSFER.sh -PLATFORM = LOCAL -DEPENDENCIES = CLEAN -RUNNING = member diff --git a/autosubmit_api/config/files/platforms.conf b/autosubmit_api/config/files/platforms.conf deleted file mode 100644 index a06f59d..0000000 --- a/autosubmit_api/config/files/platforms.conf +++ /dev/null @@ -1,55 +0,0 @@ -# Example platform with all options specified - -## Platform name -# [PLATFORM] -## Queue type. Options: PBS, SGE, PS, LSF, ecaccess, SLURM. Required -# TYPE = -## Version of queue manager to use. Needed only in PBS (options: 10, 11, 12) and ecaccess (options: pbs, loadleveler) -# VERSION = -## Hostname of the HPC. Required -# HOST = -## Project for the machine scheduler. Required -# PROJECT = -## Budget account for the machine scheduler. If omitted, takes the value defined in PROJECT -# BUDGET = -## Option to add project name to host. This is required for some HPCs. -# ADD_PROJECT_TO_HOST = False -## User for the machine scheduler. Required -# USER = -## Optional. If given, Autosubmit will change owner of files in given platform when using migrate_exp. -# USER_TO = -## Path to the scratch directory for the machine. Required. -# SCRATCH_DIR = /scratch -## Path to the machine's temporary directory for migrate purposes. -# TEMP_DIR = /tmp -## If true, Autosubmit test command can use this queue as a main queue. Defaults to False -# TEST_SUITE = False -## If given, Autosubmit will add jobs to the given queue. Required for some platforms. -# QUEUE = -## Optional. If given, Autosubmit will submit the serial jobs with the exclusivity directive. -# EXCLUSIVITY = -## Optional. If specified, autosubmit will run jobs with only one processor in the specified platform. -# SERIAL_PLATFORM = SERIAL_PLATFORM_NAME -## Optional. If specified, autosubmit will run jobs with only one processor in the specified queue. -## Autosubmit will ignore this configuration if SERIAL_PLATFORM is provided -# SERIAL_QUEUE = SERIAL_QUEUE_NAME -## Optional. Default number of processors per node to be used in jobs -# PROCESSORS_PER_NODE = -## Optional. Integer. Scratch free space requirements for the platform in percentage (%). -## If not specified, it won't be defined on the template. -# SCRATCH_FREE_SPACE = -## Optional. Integer. Default Maximum number of jobs to be waiting in any platform queue -## Default = 3 -# MAX_WAITING_JOBS = -## Optional. Integer. Default maximum number of jobs to be running at the same time at any platform -## Default = 6 -# TOTAL_JOBS = -## Max wallclock per job submitted to the HPC queue in format HH:MM. If not specified, defaults to empty. -## Optional. Required for wrappers. -# MAX_WALLCLOCK = 72:00 -## Max processors number per job submitted to the HPC. If not specified, defaults to empty. -## Optional. Required for wrappers. -# MAX_PROCESSORS = 1 -## Optional. Custom directives for the resource manager of the platform used. -## Put as many as you wish in a json formatted array. -# CUSTOM_DIRECTIVE = ["#PBS -v myvar=value, "#PBS -v othervar=value"] diff --git a/autosubmit_api/database/data/autosubmit.sql b/autosubmit_api/database/data/autosubmit.sql deleted file mode 100644 index f1a1332..0000000 --- a/autosubmit_api/database/data/autosubmit.sql +++ /dev/null @@ -1,8 +0,0 @@ -CREATE TABLE experiment( - id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT, - name VARCHAR NOT NULL, - description VARCHAR NOT NULL, - autosubmit_version VARCHAR); -CREATE TABLE db_version( - version INTEGER NOT NULL); -INSERT INTO db_version (version) VALUES (1); \ No newline at end of file diff --git a/autosubmit_api/experiment/experiment_db_manager.py b/autosubmit_api/experiment/experiment_db_manager.py deleted file mode 100644 index f07f39d..0000000 --- a/autosubmit_api/experiment/experiment_db_manager.py +++ /dev/null @@ -1,38 +0,0 @@ -# References BasicConfig.DB_PATH - -import history.database_managers.database_models as Models -from history.database_managers.database_manager import DatabaseManager -from config.basicConfig import APIBasicConfig -from typing import List - -class ExperimentDbManager(DatabaseManager): - # The current implementation only handles the experiment table. The details table is ignored because it is handled by a different worker. - def __init__(self, basic_config, expid): - # type: (APIBasicConfig, str) -> None - super(ExperimentDbManager, self).__init__(expid, basic_config) - self.basic_config = basic_config - self._ecearth_file_path = self.basic_config.DB_PATH - - def get_experiment_row_by_expid(self, expid): - # type: (str) -> Models.ExperimentRow | None - """ - Get the experiment from ecearth.db by expid as Models.ExperimentRow. - """ - statement = self.get_built_select_statement("experiment", "name=?") - current_rows = self.get_from_statement_with_arguments(self._ecearth_file_path, statement, (expid,)) - if len(current_rows) <= 0: - return None - # raise ValueError("Experiment {0} not found in {1}".format(expid, self._ecearth_file_path)) - return Models.ExperimentRow(*current_rows[0]) - - def get_experiments_with_valid_version(self): - # type: () -> List[Models.ExperimentRow] - statement = self.get_built_select_statement("experiment", "autosubmit_version IS NOT NULL") - rows = self.get_from_statement(self._ecearth_file_path, statement) - return [Models.ExperimentRow(*row) for row in rows] - - # def insert_experiment_details(self, exp_id, user, created, model, branch, hpc): - - # statement = ''' INSERT INTO details(exp_id, user, created, model, branch, hpc) VALUES(?,?,?,?,?,?) ''' - # arguments = (exp_id, user, status, 0, HUtils.get_current_datetime()) - # return self.insert_statement_with_arguments(self._as_times_file_path, statement, arguments) \ No newline at end of file diff --git a/autosubmit_api/history/experiment_history.py b/autosubmit_api/history/experiment_history.py index f36521d..f9ae423 100644 --- a/autosubmit_api/history/experiment_history.py +++ b/autosubmit_api/history/experiment_history.py @@ -15,20 +15,14 @@ # You should have received a copy of the GNU General Public License # along with Autosubmit. If not, see . -import os import traceback -from .database_managers import database_models as Models -from ..history import utils as HUtils -from ..performance import utils as PUtils -from time import time, sleep -from ..history.database_managers.experiment_history_db_manager import ExperimentHistoryDbManager -from ..history.database_managers.database_manager import DEFAULT_JOBDATA_DIR, DEFAULT_HISTORICAL_LOGS_DIR -from ..history.strategies import PlatformInformationHandler, SingleAssociationStrategy, StraightWrapperAssociationStrategy, TwoDimWrapperDistributionStrategy, GeneralizedWrapperDistributionStrategy -from ..history.data_classes.job_data import JobData -from ..history.data_classes.experiment_run import ExperimentRun -from ..history.platform_monitor.slurm_monitor import SlurmMonitor -from ..history.internal_logging import Logging -from ..config.basicConfig import APIBasicConfig +from autosubmit_api.history.database_managers import database_models as Models +from autosubmit_api.performance import utils as PUtils +from autosubmit_api.history.database_managers.experiment_history_db_manager import ExperimentHistoryDbManager +from autosubmit_api.history.data_classes.job_data import JobData +from autosubmit_api.history.data_classes.experiment_run import ExperimentRun +from autosubmit_api.history.internal_logging import Logging +from autosubmit_api.config.basicConfig import APIBasicConfig from typing import List, Dict, Tuple, Any SECONDS_WAIT_PLATFORM = 60 @@ -47,133 +41,11 @@ class ExperimentHistory(): self._log.log(str(exp), traceback.format_exc()) self.manager = None - def initialize_database(self): - try: - self.manager.initialize() - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - self.manager = None - def is_header_ready(self): if self.manager: return self.manager.is_header_ready_db_version() return False - - def write_submit_time(self, job_name, submit=0, status="UNKNOWN", ncpus=0, wallclock="00:00", qos="debug", date="", - member="", section="", chunk=0, platform="NA", job_id=0, wrapper_queue=None, wrapper_code=None, children=""): - try: - next_counter = self._get_next_counter_by_job_name(job_name) - current_experiment_run = self.manager.get_experiment_run_dc_with_max_id() - job_data_dc = JobData(_id=0, - counter=next_counter, - job_name=job_name, - submit=submit, - status=status, - rowtype=self._get_defined_rowtype(wrapper_code), - ncpus=ncpus, - wallclock=wallclock, - qos=self._get_defined_queue_name(wrapper_queue, wrapper_code, qos), - date=date, - member=member, - section=section, - chunk=chunk, - platform=platform, - job_id=job_id, - children=children, - run_id=current_experiment_run.run_id) - return self.manager.register_submitted_job_data_dc(job_data_dc) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - return None - - def write_start_time(self, job_name, start=0, status="UNKWOWN", ncpus=0, wallclock="00:00", qos="debug", date="", - member="", section="", chunk=0, platform="NA", job_id=0, wrapper_queue=None, wrapper_code=None, children=""): - try: - job_data_dc_last = self.manager.get_job_data_dc_unique_latest_by_job_name(job_name) - if not job_data_dc_last: - job_data_dc_last = self.write_submit_time(job_name=job_name, - status=status, - ncpus=ncpus, - wallclock=wallclock, - qos=qos, - date=date, - member=member, - section=section, - chunk=chunk, - platform=platform, - job_id=job_id, - wrapper_queue=wrapper_queue, - wrapper_code=wrapper_code) - self._log.log("write_start_time {0} start not found.".format(job_name)) - job_data_dc_last.start = start - job_data_dc_last.qos = self._get_defined_queue_name(wrapper_queue, wrapper_code, qos) - job_data_dc_last.status = status - job_data_dc_last.rowtype = self._get_defined_rowtype(wrapper_code) - job_data_dc_last.job_id = job_id - job_data_dc_last.children = children - return self.manager.update_job_data_dc_by_id(job_data_dc_last) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def write_finish_time(self, job_name, finish=0, status="UNKNOWN", ncpus=0, wallclock="00:00", qos="debug", date="", - member="", section="", chunk=0, platform="NA", job_id=0, out_file=None, err_file=None, - wrapper_queue=None, wrapper_code=None, children=""): - try: - job_data_dc_last = self.manager.get_job_data_dc_unique_latest_by_job_name(job_name) - if not job_data_dc_last: - job_data_dc_last = self.write_submit_time(job_name=job_name, - status=status, - ncpus=ncpus, - wallclock=wallclock, - qos=qos, - date=date, - member=member, - section=section, - chunk=chunk, - platform=platform, - job_id=job_id, - wrapper_queue=wrapper_queue, - wrapper_code=wrapper_code, - children=children) - self._log.log("write_finish_time {0} submit not found.".format(job_name)) - job_data_dc_last.finish = finish if finish > 0 else int(time()) - job_data_dc_last.status = status - job_data_dc_last.job_id = job_id - job_data_dc_last.rowstatus = Models.RowStatus.PENDING_PROCESS - job_data_dc_last.out = out_file if out_file else "" - job_data_dc_last.err = err_file if err_file else "" - return self.manager.update_job_data_dc_by_id(job_data_dc_last) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def write_platform_data_after_finish(self, job_data_dc, platform_obj): - """ - Call it in a thread. - """ - try: - sleep(SECONDS_WAIT_PLATFORM) - ssh_output = platform_obj.check_job_energy(job_data_dc.job_id) - slurm_monitor = SlurmMonitor(ssh_output) - self._verify_slurm_monitor(slurm_monitor, job_data_dc) - job_data_dcs_in_wrapper = self.manager.get_job_data_dcs_last_by_wrapper_code(job_data_dc.wrapper_code) - job_data_dcs_to_update = [] - if len(job_data_dcs_in_wrapper) > 0: - info_handler = PlatformInformationHandler(StraightWrapperAssociationStrategy(self._historiclog_dir_path)) - job_data_dcs_to_update = info_handler.execute_distribution(job_data_dc, job_data_dcs_in_wrapper, slurm_monitor) - if len(job_data_dcs_to_update) == 0: - info_handler.strategy = TwoDimWrapperDistributionStrategy(self._historiclog_dir_path) - job_data_dcs_to_update = info_handler.execute_distribution(job_data_dc, job_data_dcs_in_wrapper, slurm_monitor) - if len(job_data_dcs_to_update) == 0: - info_handler.strategy = GeneralizedWrapperDistributionStrategy(self._historiclog_dir_path) - job_data_dcs_to_update = info_handler.execute_distribution(job_data_dc, job_data_dcs_in_wrapper, slurm_monitor) - else: - info_handler = PlatformInformationHandler(SingleAssociationStrategy(self._historiclog_dir_path)) - job_data_dcs_to_update = info_handler.execute_distribution(job_data_dc, job_data_dcs_in_wrapper, slurm_monitor) - return self.manager.update_list_job_data_dc_by_each_id(job_data_dcs_to_update) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - def get_historic_job_data(self, job_name): # type: (str) -> List[Dict[str, Any]] result = [] @@ -231,166 +103,3 @@ class ExperimentHistory(): "err": job_data_dc.err }) return result - - - def update_job_finish_time_if_zero(self, job_name, finish_ts): - # type: (str, int) -> JobData - try: - job_data_dc = self.manager.get_job_data_dc_unique_latest_by_job_name(job_name) - if job_data_dc and job_data_dc.finish == 0: - job_data_dc.finish = finish_ts - return self.manager.update_job_data_dc_by_id(job_data_dc) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def _verify_slurm_monitor(self, slurm_monitor, job_data_dc): - try: - if slurm_monitor.header.status not in ["COMPLETED", "FAILED"]: - self._log.log("Assertion Error on job {0} with ssh_output {1}".format(job_data_dc.job_name, slurm_monitor.original_input), - "Slurm status {0} is not COMPLETED nor FAILED for ID {1}.\n".format(slurm_monitor.header.status, slurm_monitor.header.name)) - if not slurm_monitor.steps_plus_extern_approximate_header_energy(): - self._log.log("Assertion Error on job {0} with ssh_output {1}".format(job_data_dc.job_name, slurm_monitor.original_input), - "Steps + extern != total energy for ID {0}. Number of steps {1}.\n".format(slurm_monitor.header.name, slurm_monitor.step_count)) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def process_status_changes(self, job_list=None, chunk_unit="NA", chunk_size=0, current_config=""): - """ Detect status differences between job_list and current job_data rows, and update. Creates a new run if necessary. """ - try: - current_experiment_run_dc = self.manager.get_experiment_run_dc_with_max_id() - update_these_changes = self._get_built_list_of_changes(job_list) - should_create_new_run = self.should_we_create_a_new_run(job_list, len(update_these_changes), current_experiment_run_dc, chunk_unit, chunk_size) - if len(update_these_changes) > 0 and should_create_new_run == False: - self.manager.update_many_job_data_change_status(update_these_changes) - if should_create_new_run: - return self.create_new_experiment_run(chunk_unit, chunk_size, current_config, job_list) - return self.update_counts_on_experiment_run_dc(current_experiment_run_dc, job_list) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def _get_built_list_of_changes(self, job_list): - """ Return: List of (current timestamp, current datetime str, status, rowstatus, id in job_data). One tuple per change. """ - job_data_dcs = self.detect_changes_in_job_list(job_list) - return [(HUtils.get_current_datetime(), job.status, Models.RowStatus.CHANGED, job._id) for job in job_data_dcs] - - def process_job_list_changes_to_experiment_totals(self, job_list=None): - """ Updates current experiment_run row with totals calculated from job_list. """ - try: - current_experiment_run_dc = self.manager.get_experiment_run_dc_with_max_id() - return self.update_counts_on_experiment_run_dc(current_experiment_run_dc, job_list) - except Exception as exp: - self._log.log(str(exp), traceback.format_exc()) - - def should_we_create_a_new_run(self, job_list, changes_count, current_experiment_run_dc, new_chunk_unit, new_chunk_size): - if len(job_list) != current_experiment_run_dc.total: - return True - if changes_count > int(self._get_date_member_completed_count(job_list)): - return True - return self._chunk_config_has_changed(current_experiment_run_dc, new_chunk_unit, new_chunk_size) - - def _chunk_config_has_changed(self, current_exp_run_dc, new_chunk_unit, new_chunk_size): - if not current_exp_run_dc: - return True - if current_exp_run_dc.chunk_unit != new_chunk_unit or current_exp_run_dc.chunk_size != new_chunk_size: - return True - return False - - def update_counts_on_experiment_run_dc(self, experiment_run_dc, job_list=None): - """ Return updated row as Models.ExperimentRun. """ - status_counts = self.get_status_counts_from_job_list(job_list) - experiment_run_dc.completed = status_counts[HUtils.SupportedStatus.COMPLETED] - experiment_run_dc.failed = status_counts[HUtils.SupportedStatus.FAILED] - experiment_run_dc.queuing = status_counts[HUtils.SupportedStatus.QUEUING] - experiment_run_dc.submitted = status_counts[HUtils.SupportedStatus.SUBMITTED] - experiment_run_dc.running = status_counts[HUtils.SupportedStatus.RUNNING] - experiment_run_dc.suspended = status_counts[HUtils.SupportedStatus.SUSPENDED] - experiment_run_dc.total = status_counts["TOTAL"] - return self.manager.update_experiment_run_dc_by_id(experiment_run_dc) - - def finish_current_experiment_run(self): - if self.manager.is_there_a_last_experiment_run(): - current_experiment_run_dc = self.manager.get_experiment_run_dc_with_max_id() - current_experiment_run_dc.finish = int(time()) - return self.manager.update_experiment_run_dc_by_id(current_experiment_run_dc) - return None - - def create_new_experiment_run(self, chunk_unit="NA", chunk_size=0, current_config="", job_list=None): - """ Also writes the finish timestamp of the previous run. """ - self.finish_current_experiment_run() - return self._create_new_experiment_run_dc_with_counts(chunk_unit=chunk_unit, chunk_size=chunk_size, current_config=current_config, job_list=job_list) - - def _create_new_experiment_run_dc_with_counts(self, chunk_unit, chunk_size, current_config="", job_list=None): - """ Create new experiment_run row and return the new Models.ExperimentRun data class from database. """ - status_counts = self.get_status_counts_from_job_list(job_list) - experiment_run_dc = ExperimentRun(0, - chunk_unit=chunk_unit, - chunk_size=chunk_size, - metadata=current_config, - start=int(time()), - completed=status_counts[HUtils.SupportedStatus.COMPLETED], - total=status_counts["TOTAL"], - failed=status_counts[HUtils.SupportedStatus.FAILED], - queuing=status_counts[HUtils.SupportedStatus.QUEUING], - running=status_counts[HUtils.SupportedStatus.RUNNING], - submitted=status_counts[HUtils.SupportedStatus.SUBMITTED], - suspended=status_counts[HUtils.SupportedStatus.SUSPENDED]) - return self.manager.register_experiment_run_dc(experiment_run_dc) - - def detect_changes_in_job_list(self, job_list): - """ Detect changes in job_list compared to the current contents of job_data table. Returns a list of JobData data classes where the status of each item is the new status.""" - job_name_to_job = {job.name: job for job in job_list} - current_job_data_dcs = self.manager.get_all_last_job_data_dcs() - differences = [] - for job_dc in current_job_data_dcs: - if job_dc.job_name in job_name_to_job and job_dc.status != job_name_to_job[job_dc.job_name].status_str: - job_dc.status = job_name_to_job[job_dc.job_name].status_str - differences.append(job_dc) - return differences - - def _get_defined_rowtype(self, code): - if code: - return code - else: - return Models.RowType.NORMAL - - def _get_defined_queue_name(self, wrapper_queue, wrapper_code, qos): - if wrapper_code and wrapper_code > 2 and wrapper_queue is not None: - return wrapper_queue - return qos - - def _get_next_counter_by_job_name(self, job_name): - """ Return the counter attribute from the latest job data row by job_name. """ - job_data_dc = self.manager.get_job_data_dc_unique_latest_by_job_name(job_name) - max_counter = self.manager.get_job_data_max_counter() - if job_data_dc: - return max(max_counter, job_data_dc.counter + 1) - else: - return max_counter - - def _get_date_member_completed_count(self, job_list): - """ Each item in the job_list must have attributes: date, member, status_str. """ - job_list = job_list if job_list else [] - return sum(1 for job in job_list if job.date is not None and job.member is not None and job.status_str == HUtils.SupportedStatus.COMPLETED) - - def get_status_counts_from_job_list(self, job_list): - """ - Return dict with keys COMPLETED, FAILED, QUEUING, SUBMITTED, RUNNING, SUSPENDED, TOTAL. - """ - result = { - HUtils.SupportedStatus.COMPLETED: 0, - HUtils.SupportedStatus.FAILED: 0, - HUtils.SupportedStatus.QUEUING: 0, - HUtils.SupportedStatus.SUBMITTED: 0, - HUtils.SupportedStatus.RUNNING: 0, - HUtils.SupportedStatus.SUSPENDED: 0, - "TOTAL": 0 - } - - if not job_list: - job_list = [] - - for job in job_list: - if job.status_str in result: - result[job.status_str] += 1 - result["TOTAL"] = len(job_list) - return result diff --git a/autosubmit_api/history/platform_monitor/__init__.py b/autosubmit_api/history/platform_monitor/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/autosubmit_api/history/platform_monitor/output_examples/pending.txt b/autosubmit_api/history/platform_monitor/output_examples/pending.txt deleted file mode 100644 index 007e88d..0000000 --- a/autosubmit_api/history/platform_monitor/output_examples/pending.txt +++ /dev/null @@ -1 +0,0 @@ - 17838842 PENDING 4 1 2021-10-11T10:55:53 Unknown Unknown diff --git a/autosubmit_api/history/platform_monitor/output_examples/wrapper1.txt b/autosubmit_api/history/platform_monitor/output_examples/wrapper1.txt deleted file mode 100644 index 61b855c..0000000 --- a/autosubmit_api/history/platform_monitor/output_examples/wrapper1.txt +++ /dev/null @@ -1,3 +0,0 @@ - 12535498 COMPLETED 2 1 2020-11-18T13:54:24 2020-11-18T13:55:55 2020-11-18T13:56:10 2.77K - 12535498.batch COMPLETED 2 1 2020-11-18T13:55:55 2020-11-18T13:55:55 2020-11-18T13:56:10 2.69K 659K 659K - 12535498.extern COMPLETED 2 1 2020-11-18T13:55:55 2020-11-18T13:55:55 2020-11-18T13:56:10 2.77K 24K 24K \ No newline at end of file diff --git a/autosubmit_api/history/platform_monitor/output_examples/wrapper2.txt b/autosubmit_api/history/platform_monitor/output_examples/wrapper2.txt deleted file mode 100644 index 082eb01..0000000 --- a/autosubmit_api/history/platform_monitor/output_examples/wrapper2.txt +++ /dev/null @@ -1,3 +0,0 @@ - 12535498 COMPLETED 2 1 2020-11-18T13:54:24 2020-11-18T13:55:55 2020-11-18T13:56:10 2.77K - 12535498.batch COMPLETED 2 1 2020-11-18T13:55:55 2020-11-18T13:55:55 2020-11-18T13:56:10 2.69K 659K 659K - 12535498.0 COMPLETED 2 1 2020-11-18T13:55:55 2020-11-18T13:55:55 2020-11-18T13:56:10 2.77K 24K 24K \ No newline at end of file diff --git a/autosubmit_api/history/platform_monitor/output_examples/wrapper_big.txt b/autosubmit_api/history/platform_monitor/output_examples/wrapper_big.txt deleted file mode 100644 index 65c6c11..0000000 --- a/autosubmit_api/history/platform_monitor/output_examples/wrapper_big.txt +++ /dev/null @@ -1,33 +0,0 @@ - 17857525 COMPLETED 10 1 2021-10-13T15:51:16 2021-10-13T15:51:17 2021-10-13T15:52:47 19.05K - 17857525.batch COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 13.38K 6264K 6264K - 17857525.extern COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 13.66K 473K 68K - 17857525.0 COMPLETED 10 1 2021-10-13T15:51:21 2021-10-13T15:51:21 2021-10-13T15:51:22 186 352K 312.30K - 17857525.1 COMPLETED 10 1 2021-10-13T15:51:23 2021-10-13T15:51:23 2021-10-13T15:51:24 186 420K 306.70K - 17857525.2 COMPLETED 10 1 2021-10-13T15:51:24 2021-10-13T15:51:24 2021-10-13T15:51:27 188 352K 325.80K - 17857525.3 COMPLETED 10 1 2021-10-13T15:51:28 2021-10-13T15:51:28 2021-10-13T15:51:29 192 352K 341.90K - 17857525.4 COMPLETED 10 1 2021-10-13T15:51:29 2021-10-13T15:51:29 2021-10-13T15:51:31 186 352K 335.20K - 17857525.5 COMPLETED 10 1 2021-10-13T15:51:31 2021-10-13T15:51:31 2021-10-13T15:51:32 186 352K 329.80K - 17857525.6 COMPLETED 10 1 2021-10-13T15:51:32 2021-10-13T15:51:32 2021-10-13T15:51:33 184 428K 311.10K - 17857525.7 COMPLETED 10 1 2021-10-13T15:51:34 2021-10-13T15:51:34 2021-10-13T15:51:35 185 416K 341.40K - 17857525.8 COMPLETED 10 1 2021-10-13T15:51:35 2021-10-13T15:51:35 2021-10-13T15:51:37 180 428K 317.40K - 17857525.9 COMPLETED 10 1 2021-10-13T15:51:39 2021-10-13T15:51:39 2021-10-13T15:51:42 17 424K 272.70K - 17857525.10 COMPLETED 10 1 2021-10-13T15:51:42 2021-10-13T15:51:42 2021-10-13T15:51:44 185 356K 304.20K - 17857525.11 COMPLETED 10 1 2021-10-13T15:51:44 2021-10-13T15:51:44 2021-10-13T15:51:45 189 352K 322.20K - 17857525.12 COMPLETED 10 1 2021-10-13T15:51:45 2021-10-13T15:51:45 2021-10-13T15:51:47 184 388K 310.70K - 17857525.13 COMPLETED 10 1 2021-10-13T15:51:48 2021-10-13T15:51:48 2021-10-13T15:51:49 183 352K 336.90K - 17857525.14 COMPLETED 10 1 2021-10-13T15:51:49 2021-10-13T15:51:49 2021-10-13T15:51:51 183 428K 346.60K - 17857525.15 COMPLETED 10 1 2021-10-13T15:51:51 2021-10-13T15:51:51 2021-10-13T15:51:53 187 352K 335.90K - 17857525.16 COMPLETED 10 1 2021-10-13T15:51:54 2021-10-13T15:51:54 2021-10-13T15:51:55 184 424K 270K - 17857525.17 COMPLETED 10 1 2021-10-13T15:51:55 2021-10-13T15:51:55 2021-10-13T15:51:57 186 352K 304.80K - 17857525.18 COMPLETED 10 1 2021-10-13T15:51:57 2021-10-13T15:51:57 2021-10-13T15:51:59 182 428K 357K - 17857525.19 COMPLETED 10 1 2021-10-13T15:51:59 2021-10-13T15:51:59 2021-10-13T15:52:01 185 420K 280.60K - 17857525.20 COMPLETED 10 1 2021-10-13T15:52:01 2021-10-13T15:52:01 2021-10-13T15:52:03 185 352K 339.90K - 17857525.21 COMPLETED 10 1 2021-10-13T15:52:04 2021-10-13T15:52:04 2021-10-13T15:52:05 188 356K 340.20K - 17857525.22 COMPLETED 10 1 2021-10-13T15:52:06 2021-10-13T15:52:06 2021-10-13T15:52:08 185 352K 287.50K - 17857525.23 COMPLETED 10 1 2021-10-13T15:52:08 2021-10-13T15:52:08 2021-10-13T15:52:11 187 420K 349.40K - 17857525.24 COMPLETED 10 1 2021-10-13T15:52:14 2021-10-13T15:52:14 2021-10-13T15:52:16 185 420K 353.70K - 17857525.25 COMPLETED 10 1 2021-10-13T15:52:20 2021-10-13T15:52:20 2021-10-13T15:52:22 187 352K 340.30K - 17857525.26 COMPLETED 10 1 2021-10-13T15:52:24 2021-10-13T15:52:24 2021-10-13T15:52:32 186 420K 345.80K - 17857525.27 COMPLETED 10 1 2021-10-13T15:52:37 2021-10-13T15:52:37 2021-10-13T15:52:39 184 352K 341K - 17857525.28 COMPLETED 10 1 2021-10-13T15:52:41 2021-10-13T15:52:41 2021-10-13T15:52:43 184 352K 326.20K - 17857525.29 COMPLETED 10 1 2021-10-13T15:52:44 2021-10-13T15:52:44 2021-10-13T15:52:47 183 352K 319.30K diff --git a/autosubmit_api/history/platform_monitor/platform_monitor.py b/autosubmit_api/history/platform_monitor/platform_monitor.py deleted file mode 100644 index 4624978..0000000 --- a/autosubmit_api/history/platform_monitor/platform_monitor.py +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -from abc import ABCMeta, abstractmethod - -class PlatformMonitor(metaclass=ABCMeta): - def __init__(self, platform_output): - self.original_input = platform_output - self.input = str(platform_output).strip() - - - @abstractmethod - def _identify_input_rows(self): - """ """ - diff --git a/autosubmit_api/history/platform_monitor/platform_utils.py b/autosubmit_api/history/platform_monitor/platform_utils.py deleted file mode 100644 index dc50816..0000000 --- a/autosubmit_api/history/platform_monitor/platform_utils.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import os -from time import mktime -from datetime import datetime - -SLURM_DATETIME_FORMAT = "%Y-%m-%dT%H:%M:%S" - -def parse_output_number(string_number): - """ - Parses number in format 1.0K 1.0M 1.0G - - :param string_number: String representation of number - :type string_number: str - :return: number in float format - :rtype: float - """ - number = 0.0 - if (string_number): - last_letter = string_number.strip()[-1] - multiplier = 1.0 - if last_letter == "G": - multiplier = 1000000000.0 # Billion - number = float(string_number[:-1]) - elif last_letter == "M": - multiplier = 1000000.0 # Million - number = float(string_number[:-1]) - elif last_letter == "K": - multiplier = 1000.0 # Thousand - number = float(string_number[:-1]) - else: - number = float(string_number) - try: - number = float(number) * multiplier - except Exception as exp: - number = 0.0 - pass - return number - -def try_parse_time_to_timestamp(input): - """ - Receives a string in format "%Y-%m-%dT%H:%M:%S" and tries to parse it to timestamp. - """ - try: - return int(mktime(datetime.strptime(input, SLURM_DATETIME_FORMAT).timetuple())) - except: - return 0 - -def read_example(example_name): - source_path = "autosubmit_api/history/platform_monitor/output_examples/" - file_path = os.path.join(source_path, example_name) - with open(file_path, "r") as fp: - output_ssh = fp.read() - return output_ssh \ No newline at end of file diff --git a/autosubmit_api/history/platform_monitor/slurm_monitor.py b/autosubmit_api/history/platform_monitor/slurm_monitor.py deleted file mode 100644 index 30d7e4b..0000000 --- a/autosubmit_api/history/platform_monitor/slurm_monitor.py +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -from .platform_monitor import PlatformMonitor -from .slurm_monitor_item import SlurmMonitorItem - -class SlurmMonitor(PlatformMonitor): - """ Manages Slurm commands interpretation. """ - def __init__(self, platform_output): - super(SlurmMonitor, self).__init__(platform_output) - self._identify_input_rows() - - @property - def steps_energy(self): - return sum([step.energy for step in self.input_items if step.is_step]) - - @property - def total_energy(self): - return max(self.header.energy, self.steps_energy + self.extern.energy) - - @property - def step_count(self): - return len([step for step in self.input_items if step.is_step]) - - def _identify_input_rows(self): - lines = self.input.split("\n") - self.input_items = [SlurmMonitorItem.from_line(line) for line in lines] - - @property - def steps(self): - return [item for item in self.input_items if item.is_step] - - @property - def header(self): - return next((header for header in self.input_items if header.is_header), None) - - @property - def batch(self): - return next((batch for batch in self.input_items if batch.is_batch), None) - - @property - def extern(self): - return next((extern for extern in self.input_items if extern.is_extern), None) - - def steps_plus_extern_approximate_header_energy(self): - return abs(self.steps_energy + self.extern.energy - self.header.energy) <= 10 - - def print_items(self): - for item in self.input_items: - print(item) diff --git a/autosubmit_api/history/platform_monitor/slurm_monitor_item.py b/autosubmit_api/history/platform_monitor/slurm_monitor_item.py deleted file mode 100644 index 65ed787..0000000 --- a/autosubmit_api/history/platform_monitor/slurm_monitor_item.py +++ /dev/null @@ -1,98 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -from . import platform_utils as utils - -class SlurmMonitorItem(): - def __init__(self, name, status, ncpus, nnodes, submit, start, finish, energy="0", MaxRSS=0.0, AveRSS=0.0): - self.name = str(name) - self.status = str(status) - self.ncpus = int(ncpus) - self.nnodes = int(nnodes) - self.submit = utils.try_parse_time_to_timestamp(submit) - self.start = utils.try_parse_time_to_timestamp(start) - self.finish = utils.try_parse_time_to_timestamp(finish) - self.energy_str = energy - self.energy = utils.parse_output_number(energy) - self.MaxRSS = utils.parse_output_number(MaxRSS) - self.AveRSS = utils.parse_output_number(AveRSS) - - @property - def is_header(self): - return not self.is_detail - - @property - def is_detail(self): - if self.name.find(".") >= 0: - return True - return False - - @property - def is_extern(self): - if self.name.find(".ext") >= 0: - return True - return False - - @property - def is_batch(self): - if self.name.find(".bat") >= 0: - return True - return False - - @property - def step_number(self): - if self.is_step == True: - point_loc = self.name.find(".") - return int(self.name[point_loc+1:]) - return -1 - - @property - def is_step(self): - if self.name.find(".") >= 0 and self.is_batch == False and self.is_extern == False: - return True - return False - - @classmethod - def from_line(cls, line): - line = line.strip().split() - if len(line) < 2: - raise Exception("Slurm parser found a line too short {0}".format(line)) - new_item = cls(line[0], - line[1], - str(line[2]) if len(line) > 2 else 0, - str(line[3]) if len(line) > 3 else 0, - str(line[4]) if len(line) > 4 else 0, - str(line[5]) if len(line) > 5 else 0, - str(line[6]) if len(line) > 6 else 0, - str(line[7]) if len(line) > 7 else 0, - str(line[8]) if len(line) > 8 else 0, - str(line[9]) if len(line) > 9 else 0) - return new_item - - def get_as_dict(self): - return {"ncpus": self.ncpus, - "nnodes": self.nnodes, - "submit": self.submit, - "start": self.start, - "finish": self.finish, - "energy": self.energy, - "MaxRSS": self.MaxRSS, - "AveRSS": self.AveRSS} - - def __str__(self): - return "Name {0}, Status {1}, NCpus {2}, NNodes {3}, Submit {4}, Start {5}, Finish {6}, Energy {7}, MaxRSS {8}, AveRSS {9} [Energy Str {10}]".format(self.name, self.status, self.ncpus, self.nnodes, self.submit, self.start, self.finish, self.energy, self.MaxRSS, self.AveRSS, self.energy_str, self.is_batch) \ No newline at end of file diff --git a/autosubmit_api/history/platform_monitor/test.py b/autosubmit_api/history/platform_monitor/test.py deleted file mode 100644 index 9ae8997..0000000 --- a/autosubmit_api/history/platform_monitor/test.py +++ /dev/null @@ -1,94 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import unittest -from autosubmit_api.history.platform_monitor import platform_utils as utils -from autosubmit_api.history.platform_monitor.slurm_monitor import SlurmMonitor - -class TestSlurmMonitor(unittest.TestCase): - def test_reader_on_simple_wrapper_example_1(self): - ssh_output = utils.read_example("wrapper1.txt") - slurm_monitor = SlurmMonitor(ssh_output) - # Header - self.assertTrue(slurm_monitor.input_items[0].is_batch == False) - self.assertTrue(slurm_monitor.input_items[0].is_detail == False) - self.assertTrue(slurm_monitor.input_items[0].is_extern == False) - self.assertTrue(slurm_monitor.input_items[0].is_header == True) - self.assertTrue(slurm_monitor.input_items[0].is_detail == False) - # Batch - self.assertTrue(slurm_monitor.input_items[1].is_batch == True) - self.assertTrue(slurm_monitor.input_items[1].is_detail == True) - self.assertTrue(slurm_monitor.input_items[1].is_extern == False) - self.assertTrue(slurm_monitor.input_items[1].is_header == False) - self.assertTrue(slurm_monitor.input_items[1].is_detail == True) - # Extern - self.assertTrue(slurm_monitor.input_items[2].is_batch == False) - self.assertTrue(slurm_monitor.input_items[2].is_detail == True) - self.assertTrue(slurm_monitor.input_items[2].is_extern == True) - self.assertTrue(slurm_monitor.input_items[2].is_header == False) - self.assertTrue(slurm_monitor.input_items[2].is_detail == True) - header = slurm_monitor.header - batch = slurm_monitor.batch - extern = slurm_monitor.extern - self.assertIsNotNone(header) - self.assertIsNotNone(batch) - self.assertIsNotNone(extern) - # print("{0} {1} <- {2}".format(batch.name, batch.energy, batch.energy_str)) - # print("{0} {1} <- {2}".format(extern.name, extern.energy, extern.energy_str)) - # print("{0} {1} <- {2}".format(header.name, header.energy, header.energy_str)) - self.assertTrue(slurm_monitor.steps_plus_extern_approximate_header_energy()) - - - def test_reader_on_simple_wrapper_example_2(self): - ssh_output = utils.read_example("wrapper2.txt") # not real - slurm_monitor = SlurmMonitor(ssh_output) - # Header - self.assertTrue(slurm_monitor.input_items[0].is_batch == False) - self.assertTrue(slurm_monitor.input_items[0].is_detail == False) - self.assertTrue(slurm_monitor.input_items[0].is_step == False) - self.assertTrue(slurm_monitor.input_items[0].is_extern == False) - self.assertTrue(slurm_monitor.input_items[0].is_header == True) - # Batch - self.assertTrue(slurm_monitor.input_items[1].is_batch == True) - self.assertTrue(slurm_monitor.input_items[1].is_detail == True) - self.assertTrue(slurm_monitor.input_items[1].is_step == False) - self.assertTrue(slurm_monitor.input_items[1].is_extern == False) - self.assertTrue(slurm_monitor.input_items[1].is_header == False) - # Step 0 - self.assertTrue(slurm_monitor.input_items[2].is_batch == False) - self.assertTrue(slurm_monitor.input_items[2].is_detail == True) - self.assertTrue(slurm_monitor.input_items[2].is_step == True) - self.assertTrue(slurm_monitor.input_items[2].is_extern == False) - self.assertTrue(slurm_monitor.input_items[2].is_header == False) - self.assertTrue(slurm_monitor.input_items[2].step_number >= 0) - - def test_reader_on_big_wrapper(self): - ssh_output = utils.read_example("wrapper_big.txt") - slurm_monitor = SlurmMonitor(ssh_output) - self.assertTrue(slurm_monitor.step_count == 30) - header = slurm_monitor.header - batch = slurm_monitor.batch - extern = slurm_monitor.extern - self.assertIsNotNone(header) - self.assertIsNotNone(batch) - self.assertIsNotNone(extern) - self.assertTrue(slurm_monitor.steps_plus_extern_approximate_header_energy()) - - -if __name__ == '__main__': - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/history/test.py b/autosubmit_api/history/test.py deleted file mode 100644 index 9d0bbfd..0000000 --- a/autosubmit_api/history/test.py +++ /dev/null @@ -1,367 +0,0 @@ -#!/usr/bin/python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import unittest -import traceback -import os -import time -import autosubmit_api.common.utils_for_testing as UtilsForTesting -import autosubmit_api.performance.utils as PUtils -from shutil import copy2 -from collections import namedtuple -from autosubmit_api.history.internal_logging import Logging -from autosubmit_api.history.strategies import StraightWrapperAssociationStrategy, GeneralizedWrapperDistributionStrategy, PlatformInformationHandler -from autosubmit_api.config.basicConfig import APIBasicConfig -from autosubmit_api.history.platform_monitor.slurm_monitor import SlurmMonitor -from autosubmit_api.builders.experiment_history_builder import ExperimentHistoryDirector, ExperimentHistoryBuilder -EXPID_TT00_SOURCE = "test_database.db~" -EXPID_TT01_SOURCE = "test_database_no_run.db~" -EXPID = "tt00" -EXPID_NONE = "tt01" -# BasicConfig.read() -JOBDATA_DIR = APIBasicConfig.JOBDATA_DIR -LOCAL_ROOT_DIR = APIBasicConfig.LOCAL_ROOT_DIR -job = namedtuple("Job", ["name", "date", "member", "status_str", "children"]) - -class TestExperimentHistory(unittest.TestCase): - # @classmethod - # def setUpClass(cls): - # cls.exp = ExperimentHistory("tt00") # example database - def setUp(self): - APIBasicConfig.read() - source_path_tt00 = os.path.join(JOBDATA_DIR, EXPID_TT00_SOURCE) - self.target_path_tt00 = os.path.join(JOBDATA_DIR, "job_data_{0}.db".format(EXPID)) - copy2(source_path_tt00, self.target_path_tt00) - source_path_tt01 = os.path.join(JOBDATA_DIR, EXPID_TT01_SOURCE) - self.target_path_tt01 = os.path.join(JOBDATA_DIR, "job_data_{0}.db".format(EXPID_NONE)) - copy2(source_path_tt01, self.target_path_tt01) - self.job_list = [ - job("a29z_20000101_fc2_1_POST", "2000-01-01 00:00:00", "POST", "COMPLETED", ""), - job("a29z_20000101_fc1_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "COMPLETED", ""), - job("a29z_20000101_fc3_1_POST", "2000-01-01 00:00:00", "POST", "RUNNING", ""), - job("a29z_20000101_fc2_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "COMPLETED", ""), - job("a29z_20000101_fc0_3_SIM", "2000-01-01 00:00:00", "SIM", "COMPLETED", ""), - job("a29z_20000101_fc1_2_POST", "2000-01-01 00:00:00", "POST", "QUEUING", ""), - ] # 2 differences, all COMPLETED - self.job_list_large = [ - job("a29z_20000101_fc2_1_POST", "2000-01-01 00:00:00", "POST", "COMPLETED", ""), - job("a29z_20000101_fc1_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "COMPLETED", ""), - job("a29z_20000101_fc3_1_POST", "2000-01-01 00:00:00", "POST", "RUNNING", ""), - job("a29z_20000101_fc2_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "COMPLETED", ""), - job("a29z_20000101_fc0_3_SIM", "2000-01-01 00:00:00", "SIM", "COMPLETED", ""), - job("a29z_20000101_fc1_2_POST", "2000-01-01 00:00:00", "POST", "QUEUING", ""), - job("a29z_20000101_fc1_5_POST", "2000-01-01 00:00:00", "POST", "SUSPENDED", ""), - job("a29z_20000101_fc1_4_POST", "2000-01-01 00:00:00", "POST", "FAILED", ""), - job("a29z_20000101_fc2_5_CLEAN", "2000-01-01 00:00:00", "CLEAN", "SUBMITTED", ""), - job("a29z_20000101_fc0_1_POST", "2000-01-01 00:00:00", "POST", "RUNNING", ""), - ] - # self.logging_tt00 = Logging("tt00", BasicConfig) - # self.exp_db_manager_tt00 = ExperimentHistoryDbManager("tt00", BasicConfig) - # self.exp_db_manager_tt00.initialize() - - def tearDown(self): - os.remove(self.target_path_tt00) - os.remove(self.target_path_tt01) - - def test_get_POST_jobs(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("a28v")).build_reader_experiment_history(UtilsForTesting.get_mock_basic_config()) - completed_post_jobs = exp_history.manager.get_job_data_dcs_COMPLETED_by_section("POST") - completed_sim_jobs = exp_history.manager.get_job_data_dcs_COMPLETED_by_section("SIM") - self.assertTrue(len(completed_post_jobs) == 0) - self.assertTrue(len(completed_sim_jobs) == 42) - - def test_get_job_data_dc_COMPLETED_by_wrapper_run_id(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("a28v")).build_reader_experiment_history(UtilsForTesting.get_mock_basic_config()) - completed_jobs_by_wrapper_and_run_id = exp_history.manager.get_job_data_dc_COMPLETED_by_wrapper_run_id(1644619612435, 6) - self.assertTrue(len(completed_jobs_by_wrapper_and_run_id) == 5) - - def test_queue_time_considering_wrapper_info(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("a28v")).build_reader_experiment_history(UtilsForTesting.get_mock_basic_config()) - sim_job = exp_history.manager.get_job_data_dc_unique_latest_by_job_name("a28v_19500101_fc0_580_SIM") - package_jobs = exp_history.manager.get_job_data_dc_COMPLETED_by_wrapper_run_id(sim_job.rowtype, sim_job.run_id) - self.assertTrue(sim_job.queuing_time == 79244) - # print("Adjusted queue time: {}".format(sim_job.queuing_time_considering_package(package_jobs))) - self.assertTrue(sim_job.queuing_time_considering_package(package_jobs) == (79244 - (63179 + 16065))) - - def test_performance_metrics_historic(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("a28v")).build_reader_experiment_history(UtilsForTesting.get_mock_basic_config()) - sim_job = exp_history.manager.get_job_data_dc_unique_latest_by_job_name("a28v_19500101_fc0_580_SIM") - experiment_run = exp_history.manager.get_experiment_run_by_id(sim_job.run_id) - package_jobs = exp_history.manager.get_job_data_dc_COMPLETED_by_wrapper_run_id(sim_job.rowtype, sim_job.run_id) - calculated_ASYPD = PUtils.calculate_ASYPD_perjob(experiment_run.chunk_unit, experiment_run.chunk_size, sim_job.chunk, sim_job.queuing_time_considering_package(package_jobs) + sim_job.running_time, 0.0, sim_job.status_code) - calculated_SYPD = PUtils.calculate_SYPD_perjob(experiment_run.chunk_unit, experiment_run.chunk_size, sim_job.chunk, sim_job.running_time, sim_job.status_code) - # print("calculated ASYPD: {}".format(calculated_ASYPD)) - # print("calculated SYPD: {}".format(calculated_SYPD)) - self.assertTrue(calculated_ASYPD == round(((1.0/12.0) * 86400) / 15552, 2)) - self.assertTrue(calculated_SYPD == round(((1.0/12.0) * 86400) / 15552, 2)) - - def test_get_historic(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("a28v")).build_reader_experiment_history(UtilsForTesting.get_mock_basic_config()) - result = exp_history.get_historic_job_data("a28v_19500101_fc0_580_SIM") - self.assertTrue(result[0]["ASYPD"] == 0.46) - self.assertTrue(result[0]["SYPD"] == 0.46) - - def test_db_exists(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # # exp_history.initialize_database() - self.assertTrue(exp_history.manager.my_database_exists() == True) - - def test_db_not_exists(self): - # exp_history_db_manager = ExperimentHistoryDbManager("tt99", BasicConfig) - # exp_history_logging = Logging("tt99", BasicConfig) - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder("tt99")).build_reader_experiment_history() # ExperimentHistory("tt99", BasicConfig, exp_history_db_manager, exp_history_logging) - self.assertTrue(exp_history.manager.my_database_exists() == False) - - def test_is_header_ready(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - self.assertTrue(exp_history.is_header_ready() == True) - - def test_detect_differences_job_list(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - differences = exp_history.detect_changes_in_job_list(self.job_list) - expected_differences = ["a29z_20000101_fc3_1_POST", "a29z_20000101_fc1_2_POST"] - for job_dc in differences: - self.assertTrue(job_dc.job_name in expected_differences) - self.assertTrue(len(differences) == 2) - - def test_built_list_of_changes(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - built_differences = exp_history._get_built_list_of_changes(self.job_list) - expected_ids_differences = [90, 101] - for item in built_differences: - self.assertTrue(item[3] in expected_ids_differences) - - def test_get_date_member_count(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - dm_count = exp_history._get_date_member_completed_count(self.job_list) - self.assertTrue(dm_count > 0) - - def test_should_we_create_new_run(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - CHANGES_COUNT = 1 - TOTAL_COUNT = 6 - current_experiment_run_dc = exp_history.manager.get_experiment_run_dc_with_max_id() - current_experiment_run_dc.total = TOTAL_COUNT - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, current_experiment_run_dc.chunk_unit, current_experiment_run_dc.chunk_size) - self.assertTrue(should_we == False) - TOTAL_COUNT_DIFF = 5 - current_experiment_run_dc.total = TOTAL_COUNT_DIFF - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, current_experiment_run_dc.chunk_unit, current_experiment_run_dc.chunk_size) - self.assertTrue(should_we == True) - CHANGES_COUNT = 5 - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, current_experiment_run_dc.chunk_unit, current_experiment_run_dc.chunk_size) - self.assertTrue(should_we == True) - CHANGES_COUNT = 1 - current_experiment_run_dc.total = TOTAL_COUNT - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, current_experiment_run_dc.chunk_unit, current_experiment_run_dc.chunk_size*20) - self.assertTrue(should_we == True) - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, current_experiment_run_dc.chunk_unit, current_experiment_run_dc.chunk_size) - self.assertTrue(should_we == False) - should_we = exp_history.should_we_create_a_new_run(self.job_list, CHANGES_COUNT, current_experiment_run_dc, "day", current_experiment_run_dc.chunk_size) - self.assertTrue(should_we == True) - - def test_status_counts(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - result = exp_history.get_status_counts_from_job_list(self.job_list_large) - self.assertTrue(result["COMPLETED"] == 4) - self.assertTrue(result["QUEUING"] == 1) - self.assertTrue(result["RUNNING"] == 2) - self.assertTrue(result["FAILED"] == 1) - self.assertTrue(result["SUSPENDED"] == 1) - self.assertTrue(result["TOTAL"] == len(self.job_list_large)) - - def test_create_new_experiment_run_with_counts(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - exp_run = exp_history.create_new_experiment_run(job_list=self.job_list) - self.assertTrue(exp_run.chunk_size == 0) - self.assertTrue(exp_run.chunk_unit == "NA") - self.assertTrue(exp_run.total == len(self.job_list)) - self.assertTrue(exp_run.completed == 4) - - def test_finish_current_run(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - exp_run = exp_history.finish_current_experiment_run() - self.assertTrue(len(exp_run.modified) > 0) - self.assertTrue(exp_run.finish > 0) - - def test_process_job_list_changes(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - exp_run = exp_history.process_job_list_changes_to_experiment_totals(self.job_list) - self.assertTrue(exp_run.total == len(self.job_list)) - self.assertTrue(exp_run.completed == 4) - self.assertTrue(exp_run.running == 1) - self.assertTrue(exp_run.queuing == 1) - - def test_calculated_weights(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - job_data_dcs = exp_history.manager.get_all_last_job_data_dcs() - calculated_weights = GeneralizedWrapperDistributionStrategy().get_calculated_weights_of_jobs_in_wrapper(job_data_dcs) - sum_comp_weight = 0 - for job_name in calculated_weights: - sum_comp_weight += calculated_weights[job_name] - self.assertTrue(abs(sum_comp_weight - 1) <= 0.01) - - def test_distribute_energy_in_wrapper_1_to_1(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - ssh_output = ''' 17857525 COMPLETED 10 1 2021-10-13T15:51:16 2021-10-13T15:51:17 2021-10-13T15:52:47 2.41K - 17857525.batch COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.88K 6264K 6264K - 17857525.extern COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.66K 473K 68K - 17857525.0 COMPLETED 10 1 2021-10-13T15:51:21 2021-10-13T15:51:21 2021-10-13T15:51:22 186 352K 312.30K - 17857525.1 COMPLETED 10 1 2021-10-13T15:51:23 2021-10-13T15:51:23 2021-10-13T15:51:24 186 420K 306.70K - 17857525.2 COMPLETED 10 1 2021-10-13T15:51:24 2021-10-13T15:51:24 2021-10-13T15:51:27 188 352K 325.80K - 17857525.3 COMPLETED 10 1 2021-10-13T15:51:28 2021-10-13T15:51:28 2021-10-13T15:51:29 192 352K 341.90K - ''' - slurm_monitor = SlurmMonitor(ssh_output) - job_data_dcs = exp_history.manager.get_all_last_job_data_dcs()[:4] # Get me 4 jobs - weights = StraightWrapperAssociationStrategy().get_calculated_weights_of_jobs_in_wrapper(job_data_dcs) - info_handler = PlatformInformationHandler(StraightWrapperAssociationStrategy()) - job_data_dcs_with_data = info_handler.execute_distribution(job_data_dcs[0], job_data_dcs, slurm_monitor) - self.assertTrue(job_data_dcs_with_data[0].energy == round(slurm_monitor.steps[0].energy + weights[job_data_dcs_with_data[0].job_name]*slurm_monitor.extern.energy, 2)) - self.assertTrue(job_data_dcs_with_data[0].MaxRSS == slurm_monitor.steps[0].MaxRSS) - self.assertTrue(job_data_dcs_with_data[2].energy == round(slurm_monitor.steps[2].energy + weights[job_data_dcs_with_data[2].job_name]*slurm_monitor.extern.energy, 2)) - self.assertTrue(job_data_dcs_with_data[2].AveRSS == slurm_monitor.steps[2].AveRSS) - - def test_distribute_energy_in_wrapper_general_case(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - ssh_output = ''' 17857525 COMPLETED 10 1 2021-10-13T15:51:16 2021-10-13T15:51:17 2021-10-13T15:52:47 2.41K - 17857525.batch COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.88K 6264K 6264K - 17857525.extern COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.66K 473K 68K - 17857525.0 COMPLETED 10 1 2021-10-13T15:51:21 2021-10-13T15:51:21 2021-10-13T15:51:22 186 352K 312.30K - 17857525.1 COMPLETED 10 1 2021-10-13T15:51:23 2021-10-13T15:51:23 2021-10-13T15:51:24 186 420K 306.70K - 17857525.2 COMPLETED 10 1 2021-10-13T15:51:24 2021-10-13T15:51:24 2021-10-13T15:51:27 188 352K 325.80K - 17857525.3 COMPLETED 10 1 2021-10-13T15:51:28 2021-10-13T15:51:28 2021-10-13T15:51:29 192 352K 341.90K - ''' - slurm_monitor = SlurmMonitor(ssh_output) - job_data_dcs = exp_history.manager.get_all_last_job_data_dcs()[:5] # Get me 5 jobs - weights = GeneralizedWrapperDistributionStrategy().get_calculated_weights_of_jobs_in_wrapper(job_data_dcs) - # print(sum(weights[k] for k in weights)) - info_handler = PlatformInformationHandler(GeneralizedWrapperDistributionStrategy()) - job_data_dcs_with_data = info_handler.execute_distribution(job_data_dcs[0], job_data_dcs, slurm_monitor) - self.assertTrue(job_data_dcs_with_data[0].energy == round(slurm_monitor.total_energy * weights[job_data_dcs_with_data[0].job_name], 2)) - self.assertTrue(job_data_dcs_with_data[1].energy == round(slurm_monitor.total_energy * weights[job_data_dcs_with_data[1].job_name], 2)) - self.assertTrue(job_data_dcs_with_data[2].energy == round(slurm_monitor.total_energy * weights[job_data_dcs_with_data[2].job_name], 2)) - self.assertTrue(job_data_dcs_with_data[3].energy == round(slurm_monitor.total_energy * weights[job_data_dcs_with_data[3].job_name], 2)) - self.assertTrue(job_data_dcs_with_data[4].energy == round(slurm_monitor.total_energy * weights[job_data_dcs_with_data[4].job_name], 2)) - sum_energy = sum(job.energy for job in job_data_dcs_with_data[:5]) # Last 1 is original job_data_dc - self.assertTrue(abs(sum_energy - slurm_monitor.total_energy) <= 10) - - def test_process_status_changes(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - CHUNK_UNIT = "month" - CHUNK_SIZE = 20 - CURRENT_CONFIG = "CURRENT CONFIG" - current_experiment_run_dc = exp_history.manager.get_experiment_run_dc_with_max_id() - exp_run = exp_history.process_status_changes(job_list=self.job_list, chunk_unit=CHUNK_UNIT, chunk_size=CHUNK_SIZE, current_config=CURRENT_CONFIG) # Generates new run - self.assertTrue(current_experiment_run_dc.run_id != exp_run.run_id) - self.assertTrue(exp_run.chunk_unit == CHUNK_UNIT) - self.assertTrue(exp_run.metadata == CURRENT_CONFIG) - self.assertTrue(exp_run.total == len(self.job_list)) - current_experiment_run_dc = exp_history.manager.get_experiment_run_dc_with_max_id() - exp_run = exp_history.process_status_changes(job_list=self.job_list, chunk_unit=CHUNK_UNIT, chunk_size=CHUNK_SIZE, current_config=CURRENT_CONFIG) # Same run - self.assertTrue(current_experiment_run_dc.run_id == exp_run.run_id) - new_job_list = [ - job("a29z_20000101_fc2_1_POST", "2000-01-01 00:00:00", "POST", "FAILED", ""), - job("a29z_20000101_fc1_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "FAILED", ""), - job("a29z_20000101_fc3_1_POST", "2000-01-01 00:00:00", "POST", "RUNNING", ""), - job("a29z_20000101_fc2_1_CLEAN", "2000-01-01 00:00:00", "CLEAN", "FAILED", ""), - job("a29z_20000101_fc0_3_SIM", "2000-01-01 00:00:00", "SIM", "FAILED", ""), - job("a29z_20000101_fc1_2_POST", "2000-01-01 00:00:00", "POST", "QUEUING", ""), - ] - current_experiment_run_dc = exp_history.manager.get_experiment_run_dc_with_max_id() - exp_run = exp_history.process_status_changes(job_list=new_job_list, chunk_unit=CHUNK_UNIT, chunk_size=CHUNK_SIZE, current_config=CURRENT_CONFIG) # Generates new run - self.assertTrue(current_experiment_run_dc.run_id != exp_run.run_id) - self.assertTrue(exp_run.total == len(new_job_list)) - self.assertTrue(exp_run.failed == 4) - - def test_write_submit_time(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # exp_history.initialize_database() - JOB_NAME = "a29z_20000101_fc2_1_SIM" - NCPUS = 128 - PLATFORM_NAME = "marenostrum4" - JOB_ID = 101 - inserted_job_data_dc = exp_history.write_submit_time(JOB_NAME, time.time(), "SUBMITTED", NCPUS, "00:30", "debug", "20000101", "fc2", "SIM", 1, PLATFORM_NAME, JOB_ID, "bsc_es", 1, "") - self.assertTrue(inserted_job_data_dc.job_name == JOB_NAME) - self.assertTrue(inserted_job_data_dc.ncpus == NCPUS) - self.assertTrue(inserted_job_data_dc.children == "") - self.assertTrue(inserted_job_data_dc.energy == 0) - self.assertTrue(inserted_job_data_dc.platform == PLATFORM_NAME) - self.assertTrue(inserted_job_data_dc.job_id == JOB_ID) - self.assertTrue(inserted_job_data_dc.qos == "debug") - - - def test_write_start_time(self): - exp_history = ExperimentHistoryDirector(ExperimentHistoryBuilder(EXPID)).build_current_experiment_history() # ExperimentHistory("tt00", BasicConfig, self.exp_db_manager_tt00, self.logging_tt00) - # # exp_history.initialize_database() - JOB_NAME = "a29z_20000101_fc2_1_SIM" - NCPUS = 128 - PLATFORM_NAME = "marenostrum4" - JOB_ID = 101 - inserted_job_data_dc_submit = exp_history.write_submit_time(JOB_NAME, time.time(), "SUBMITTED", NCPUS, "00:30", "debug", "20000101", "fc2", "SIM", 1, PLATFORM_NAME, JOB_ID, "bsc_es", 1, "") - inserted_job_data_dc = exp_history.write_start_time(JOB_NAME, time.time(), "RUNNING", NCPUS, "00:30", "debug", "20000101", "fc2", "SIM", 1, PLATFORM_NAME, JOB_ID, "bsc_es", 1, "") - self.assertTrue(inserted_job_data_dc.job_name == JOB_NAME) - self.assertTrue(inserted_job_data_dc.ncpus == NCPUS) - self.assertTrue(inserted_job_data_dc.children == "") - self.assertTrue(inserted_job_data_dc.energy == 0) - self.assertTrue(inserted_job_data_dc.platform == PLATFORM_NAME) - self.assertTrue(inserted_job_data_dc.job_id == JOB_ID) - self.assertTrue(inserted_job_data_dc.status == "RUNNING") - self.assertTrue(inserted_job_data_dc.qos == "debug") - - - -class TestLogging(unittest.TestCase): - - def setUp(self): - APIBasicConfig.read() - message = "No Message" - try: - raise Exception("Setup test exception") - except: - message = traceback.format_exc() - self.log = Logging("tt00", APIBasicConfig) - self.exp_message = "Exception message" - self.trace_message = message - - def test_build_message(self): - message = self.log.build_message(self.exp_message, self.trace_message) - # print(message) - self.assertIsNotNone(message) - self.assertTrue(len(message) > 0) - - def test_log(self): - self.log.log(self.exp_message, self.trace_message) - - - - - -if __name__ == '__main__': - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/history/test_job_history.py b/autosubmit_api/history/test_job_history.py deleted file mode 100644 index 7e70bb3..0000000 --- a/autosubmit_api/history/test_job_history.py +++ /dev/null @@ -1,71 +0,0 @@ -import unittest -import autosubmit_api.common.utils_for_testing as TestUtils -from autosubmit_api.builders.experiment_history_builder import ExperimentHistoryDirector, ExperimentHistoryBuilder - -class TestJobHistory(unittest.TestCase): - - def setUp(self): - self.basic_config = TestUtils.get_mock_basic_config() - - def test_get_job_history_gets_correct_number_of_cases(self): - # Arrange - sut = ExperimentHistoryDirector(ExperimentHistoryBuilder("a3tb")).build_reader_experiment_history(self.basic_config) - # Act - job_history = sut.get_historic_job_data("a3tb_19930501_fc01_3_SIM") - # Assert - self.assertEqual(len(job_history), 5) # 5 rows in database - - def test_get_job_history_gets_correct_queuing_times(self): - # Arrange - sut = ExperimentHistoryDirector(ExperimentHistoryBuilder("a3tb")).build_reader_experiment_history(self.basic_config) - # Act - job_history = sut.get_historic_job_data("a3tb_19930501_fc01_3_SIM") - counter_to_queue_timedelta_str = {int(job["counter"]): job["queue_time"] for job in job_history} - # Assert - self.assertEqual(counter_to_queue_timedelta_str[18], "0:03:28") - self.assertEqual(counter_to_queue_timedelta_str[19], "0:00:04") - self.assertEqual(counter_to_queue_timedelta_str[20], "0:00:05") - self.assertEqual(counter_to_queue_timedelta_str[24], "0:01:18") - self.assertEqual(counter_to_queue_timedelta_str[25], "0:02:35") - - def test_get_job_history_gets_correct_running_times(self): - # Arrange - sut = ExperimentHistoryDirector(ExperimentHistoryBuilder("a3tb")).build_reader_experiment_history(self.basic_config) - # Act - job_history = sut.get_historic_job_data("a3tb_19930501_fc01_3_SIM") - counter_to_run_timedelta_str = {int(job["counter"]): job["run_time"] for job in job_history} - # Assert - self.assertEqual(counter_to_run_timedelta_str[18], "0:00:54") - self.assertEqual(counter_to_run_timedelta_str[19], "0:00:53") - self.assertEqual(counter_to_run_timedelta_str[20], "0:00:52") - self.assertEqual(counter_to_run_timedelta_str[24], "0:23:16") - self.assertEqual(counter_to_run_timedelta_str[25], "0:07:58") - - def test_get_job_history_gets_correct_SYPD(self): - # Arrange - sut = ExperimentHistoryDirector(ExperimentHistoryBuilder("a3tb")).build_reader_experiment_history(self.basic_config) - # Act - job_history = sut.get_historic_job_data("a3tb_19930501_fc01_3_SIM") - counter_to_SYPD = {int(job["counter"]): job["SYPD"] for job in job_history} - # Assert - self.assertEqual(counter_to_SYPD[18], None) - self.assertEqual(counter_to_SYPD[19], None) - self.assertEqual(counter_to_SYPD[20], None) - self.assertEqual(counter_to_SYPD[24], round(86400*(1.0/12.0)/1396, 2)) - self.assertEqual(counter_to_SYPD[25], round(86400*(1.0/12.0)/478, 2)) - - def test_get_job_history_gets_correct_ASYPD(self): - # Arrange - sut = ExperimentHistoryDirector(ExperimentHistoryBuilder("a3tb")).build_reader_experiment_history(self.basic_config) - # Act - job_history = sut.get_historic_job_data("a3tb_19930501_fc01_3_SIM") - counter_to_ASYPD = {int(job["counter"]): job["ASYPD"] for job in job_history} - # Assert - self.assertEqual(counter_to_ASYPD[18], None) - self.assertEqual(counter_to_ASYPD[19], None) - self.assertEqual(counter_to_ASYPD[20], None) - self.assertEqual(counter_to_ASYPD[24], round(86400*(1.0/12.0)/(1396 + 78), 2)) - self.assertEqual(counter_to_ASYPD[25], round(86400*(1.0/12.0)/(478 + 155), 2)) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/history/test_strategies.py b/autosubmit_api/history/test_strategies.py deleted file mode 100644 index 04d7fa8..0000000 --- a/autosubmit_api/history/test_strategies.py +++ /dev/null @@ -1,94 +0,0 @@ -#!/usr/bin/python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -import unittest -from collections import namedtuple -from autosubmit_api.history.data_classes.job_data import JobData -from autosubmit_api.history.strategies import StraightWrapperAssociationStrategy, GeneralizedWrapperDistributionStrategy, PlatformInformationHandler, TwoDimWrapperDistributionStrategy -from autosubmit_api.history.platform_monitor.slurm_monitor import SlurmMonitor -job_dc = namedtuple("Job", ["job_name", "date", "member", "status_str", "children", "children_list"]) - -class Test2DWrapperDistributionStrategy(unittest.TestCase): - def setUp(self): - self.strategy = TwoDimWrapperDistributionStrategy() - self.job_data_dcs_in_wrapper = [ - JobData(0, job_name="a29z_20000101_fc2_1_POSTR", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc1_1_CLEAN, a29z_20000101_fc3_1_POST"), - JobData(0, job_name="a29z_20000101_fc1_1_CLEAN", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc2_1_CLEAN"), - JobData(0, job_name="a29z_20000101_fc3_1_POST", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc0_3_SIM"), - JobData(0, job_name="a29z_20000101_fc2_1_CLEAN", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children=""), - JobData(0, job_name="a29z_20000101_fc0_3_SIM", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children=""), - JobData(0, job_name="a29z_20000101_fc1_2_POSTR1", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc1_5_POST2"), - JobData(0, job_name="a29z_20000101_fc1_5_POST2", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc1_4_POST3"), - JobData(0, job_name="a29z_20000101_fc1_4_POST3", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc2_5_CLEAN4"), - JobData(0, job_name="a29z_20000101_fc2_5_CLEAN4", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children="a29z_20000101_fc0_1_POST5"), - JobData(0, job_name="a29z_20000101_fc0_1_POST5", status="COMPLETED", submit=10, start=100, finish=200, ncpus=100, energy=0, children=""), - ] - - def test_get_all_children(self): - children = self.strategy._get_all_children(self.job_data_dcs_in_wrapper) - self.assertTrue(len(children) == 8) - - def test_get_roots(self): - roots = self.strategy._get_roots(self.job_data_dcs_in_wrapper) - self.assertTrue(len(roots) == 2) - - def test_get_level(self): - roots = self.strategy._get_roots(self.job_data_dcs_in_wrapper) - job_name_to_children_names = {job.job_name: job.children_list for job in self.job_data_dcs_in_wrapper} - next_level = self.strategy.get_level(roots, job_name_to_children_names) - self.assertTrue(len(next_level) == 3) - - def test_get_jobs_per_level(self): - levels = self.strategy.get_jobs_per_level(self.job_data_dcs_in_wrapper) - for level in levels: - print([job.job_name for job in level]) - self.assertTrue(len(levels) == 5) - self.assertTrue("a29z_20000101_fc0_1_POST5" in [job.job_name for job in levels[4]]) - - def test_energy_distribution(self): - ssh_output = ''' 17857525 COMPLETED 10 1 2021-10-13T15:51:16 2021-10-13T15:51:17 2021-10-13T15:52:47 2.62K - 17857525.batch COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.88K 6264K 6264K - 17857525.extern COMPLETED 10 1 2021-10-13T15:51:17 2021-10-13T15:51:17 2021-10-13T15:52:47 1.66K 473K 68K - 17857525.0 COMPLETED 10 1 2021-10-13T15:51:21 2021-10-13T15:51:21 2021-10-13T15:51:22 186 352K 312.30K - 17857525.1 COMPLETED 10 1 2021-10-13T15:51:23 2021-10-13T15:51:23 2021-10-13T15:51:24 186 420K 306.70K - 17857525.2 COMPLETED 10 1 2021-10-13T15:51:24 2021-10-13T15:51:24 2021-10-13T15:51:27 188 352K 325.80K - 17857525.3 COMPLETED 10 1 2021-10-13T15:51:28 2021-10-13T15:51:28 2021-10-13T15:51:29 192 352K 341.90K - 17857525.4 COMPLETED 10 1 2021-10-13T15:51:28 2021-10-13T15:51:28 2021-10-13T15:51:29 210 352K 341.90K - ''' - slurm_monitor = SlurmMonitor(ssh_output) - info_handler = PlatformInformationHandler(TwoDimWrapperDistributionStrategy()) - job_dcs = info_handler.execute_distribution(self.job_data_dcs_in_wrapper[0], self.job_data_dcs_in_wrapper, slurm_monitor) - for job in job_dcs: - print(("{0} -> {1} and {2} : ncpus {3} running {4}".format(job.job_name, job.energy, job.rowstatus, job.ncpus, job.running_time))) - for level in info_handler.strategy.jobs_per_level: - print([job.job_name for job in level]) - total_in_jobs = sum(job.energy for job in job_dcs[:-1]) # ignore last - self.assertTrue(abs(total_in_jobs - slurm_monitor.total_energy) <= 10) - self.assertTrue(abs(job_dcs[0].energy - 259) < 1) - self.assertTrue(abs(job_dcs[1].energy - 259) < 1) - self.assertTrue(abs(job_dcs[2].energy - 228) < 1) - self.assertTrue(abs(job_dcs[3].energy - 228) < 1) - self.assertTrue(abs(job_dcs[4].energy - 228) < 1) - self.assertTrue(abs(job_dcs[5].energy - 228.67) < 1) - self.assertTrue(abs(job_dcs[6].energy - 228.67) < 1) - self.assertTrue(abs(job_dcs[7].energy - 228.67) < 1) - self.assertTrue(abs(job_dcs[8].energy - 358) < 1) - self.assertTrue(abs(job_dcs[9].energy - 376) < 1) - -if __name__ == '__main__': - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/history/test_utils.py b/autosubmit_api/history/test_utils.py deleted file mode 100644 index 7abcc51..0000000 --- a/autosubmit_api/history/test_utils.py +++ /dev/null @@ -1,32 +0,0 @@ - -import unittest -import history.utils as HUtils - -class TestUtils(unittest.TestCase): - def setUp(self): - pass - - def test_generate_arguments(self): - arguments = {"status": 4, "last": 1, "rowtype": 2} - statement, arg_values = HUtils.get_built_statement_from_kwargs("id", status=4, last=1, rowtype=2) - print(statement) - print(arg_values) - self.assertTrue(statement.find("status") >= 0) - self.assertTrue(statement.find("last") >= 0) - self.assertTrue(statement.find("rowtype") >= 0) - self.assertTrue(statement.find(" ORDER BY id") >= 0) - - def test_generate_arguments_kwargs(self): - def inner_call(expid, **kwargs): - return HUtils.get_built_statement_from_kwargs("created", **kwargs) - arguments = {"status": 4, "last": 1, "rowtype": 2} - answer, arg_values = inner_call("a28v", **arguments) - print(answer) - print(arg_values) - self.assertTrue(answer.find("status") >= 0) - self.assertTrue(answer.find("last") >= 0) - self.assertTrue(answer.find("rowtype") >= 0) - self.assertTrue(answer.find(" ORDER BY created") >= 0) - -if __name__ == "__main__": - unittest.main() \ No newline at end of file diff --git a/autosubmit_api/workers/populate_details/test.py b/autosubmit_api/workers/populate_details/test.py deleted file mode 100644 index 24fc30a..0000000 --- a/autosubmit_api/workers/populate_details/test.py +++ /dev/null @@ -1,53 +0,0 @@ -import unittest -from autosubmit_api.workers.populate_details.populate import DetailsProcessor -import autosubmit_api.common.utils_for_testing as TestUtils - -class TestPopulate(unittest.TestCase): - def setUp(self): - pass - - def test_retrieve_correct_experiments(self): - # Arrange - sut = DetailsProcessor(TestUtils.get_mock_basic_config()) - # Act - experiments = sut._get_experiments() - names = [experiment.name for experiment in experiments] - # Assert - self.assertIn("a28v", names) - self.assertIn("a3tb", names) - - - def test_get_details_from_experiment(self): - # Arrange - sut = DetailsProcessor(TestUtils.get_mock_basic_config()) - # Act - details = sut._get_details_data_from_experiment("a28v") - # Assert - self.assertIsNotNone(details) - self.assertEqual("wuruchi", details.owner) - self.assertIsInstance(details.created, str) - self.assertIsInstance(details.model, str) - self.assertIsInstance(details.branch, str) - self.assertEqual("marenostrum4", details.hpc) - - - def test_get_all_experiment_details_equals_number_of_test_cases(self): - # Arrange - sut = DetailsProcessor(TestUtils.get_mock_basic_config()) - # Act - processed_data = sut._get_all_details() - # Assert - self.assertEqual(len(processed_data), 2) # There are 2 cases in the test_cases folder - - - def test_process_inserts_the_details(self): - # Arrange - sut = DetailsProcessor(TestUtils.get_mock_basic_config()) - # Act - number_rows = sut.process() - # Assert - self.assertEqual(number_rows, 2) - - -if __name__ == '__main__': - unittest.main() \ No newline at end of file diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index c70732eb783e06bcef253b4f0e7ac92c0a225396..43bd6b66db7a106c2f556c68a50b9272caf871ae 100644 GIT binary patch delta 49 pcmZp0XmFSy&Db8vtfF4O;*J delta 49 pcmZp0XmFSy%~&>3#+k8fV}h$ZyOEWtiIu708vtNp4Icmi -- GitLab From 6108b6223506e978bf68b53b1b39a11e94ea1a15 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Fri, 16 Feb 2024 13:29:56 +0100 Subject: [PATCH 13/18] fix outlier calculation #65 --- autosubmit_api/common/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/autosubmit_api/common/utils.py b/autosubmit_api/common/utils.py index 7056076..e0ce68f 100644 --- a/autosubmit_api/common/utils.py +++ b/autosubmit_api/common/utils.py @@ -71,12 +71,12 @@ def parse_number_processors(processors_str): except: return 1 -def get_jobs_with_no_outliers(jobs): +def get_jobs_with_no_outliers(jobs: List): """ Detects outliers and removes them from the returned list """ new_list = [] data_run_times = [job.run_time for job in jobs] # print(data_run_times) - if len(data_run_times) == 0: + if len(data_run_times) <= 1: return jobs mean = statistics.mean(data_run_times) -- GitLab From 5818dfc763e5de13ef6a26dd598e6d18565cf473 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Fri, 16 Feb 2024 17:44:35 +0100 Subject: [PATCH 14/18] applied experiment path builder --- .../autosubmit_legacy/job/job_list.py | 19 +- autosubmit_api/database/db_jobdata.py | 11 +- autosubmit_api/database/db_structure.py | 68 +----- autosubmit_api/experiment/common_requests.py | 20 +- .../experiment_history_db_manager.py | 5 +- autosubmit_api/history/strategies.py | 220 ------------------ autosubmit_api/persistance/experiment.py | 29 ++- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes 8 files changed, 65 insertions(+), 307 deletions(-) delete mode 100644 autosubmit_api/history/strategies.py diff --git a/autosubmit_api/autosubmit_legacy/job/job_list.py b/autosubmit_api/autosubmit_legacy/job/job_list.py index dab3d9a..c9ad0cb 100644 --- a/autosubmit_api/autosubmit_legacy/job/job_list.py +++ b/autosubmit_api/autosubmit_legacy/job/job_list.py @@ -31,6 +31,7 @@ from dateutil.relativedelta import * from bscearth.utils.log import Log from autosubmit_api.autosubmit_legacy.job.job_utils import SubJob from autosubmit_api.autosubmit_legacy.job.job_utils import SubJobManager, job_times_to_text +from autosubmit_api.config.basicConfig import APIBasicConfig from autosubmit_api.performance.utils import calculate_ASYPD_perjob, calculate_SYPD_perjob from autosubmit_api.components.jobs import utils as JUtils from autosubmit_api.monitor.monitor import Monitor @@ -46,6 +47,8 @@ from autosubmit_api.history.data_classes.job_data import JobData from typing import List, Dict, Tuple +from autosubmit_api.persistance.experiment import ExperimentPaths + class JobList: """ @@ -153,8 +156,8 @@ class JobList: date_member_repetition = {} job_name_to_job_title = {} job_name_to_job = {job.job_name: job for job in job_list} - path_to_logs = os.path.join( - BasicConfig.LOCAL_ROOT_DIR, expid, "tmp", "LOG_" + expid) + exp_paths = ExperimentPaths(expid) + path_to_logs = exp_paths.tmp_log_dir packages = {job.rowtype for job in job_list if job.rowtype > 2} package_to_jobs = {package: [ @@ -577,7 +580,7 @@ class JobList: return "" @staticmethod - def get_job_times_collection(basic_config, allJobs, expid, job_to_package=None, package_to_jobs=None, timeseconds=True): + def get_job_times_collection(basic_config: APIBasicConfig, allJobs, expid, job_to_package=None, package_to_jobs=None, timeseconds=True): """ Gets queuing and running time for the collection of jobs @@ -860,23 +863,21 @@ class JobList: """ monitor = Monitor() packages = None + exp_paths = ExperimentPaths(expid) try: - packages = JobPackagePersistence(os.path.join(basic_config.LOCAL_ROOT_DIR, expid, "pkl"), - "job_packages_" + expid).load(wrapper=False) + packages = JobPackagePersistence(exp_paths.job_packages_db).load(wrapper=False) # if the main table exist but is empty, we try the other one if not (any(packages.keys()) or any(packages.values())): Log.info("Wrapper table empty, trying packages.") - packages = JobPackagePersistence(os.path.join(basic_config.LOCAL_ROOT_DIR, expid, "pkl"), - "job_packages_" + expid).load(wrapper=True) + packages = JobPackagePersistence(exp_paths.job_packages_db).load(wrapper=True) except Exception as ex: print("Wrapper table not found, trying packages.") packages = None try: - packages = JobPackagePersistence(os.path.join(basic_config.LOCAL_ROOT_DIR, expid, "pkl"), - "job_packages_" + expid).load(wrapper=True) + packages = JobPackagePersistence(exp_paths.job_packages_db).load(wrapper=True) except Exception as exp2: packages = None pass diff --git a/autosubmit_api/database/db_jobdata.py b/autosubmit_api/database/db_jobdata.py index 6f0826c..44db432 100644 --- a/autosubmit_api/database/db_jobdata.py +++ b/autosubmit_api/database/db_jobdata.py @@ -38,6 +38,8 @@ from autosubmit_api.common.utils import get_jobs_with_no_outliers, Status, datec # import autosubmitAPIwu.experiment.common_db_requests as DbRequests from bscearth.utils.date import Log +from autosubmit_api.persistance.experiment import ExperimentPaths + # Version 15 includes out err MaxRSS AveRSS and rowstatus CURRENT_DB_VERSION = 15 # Used to be 10 or 0 @@ -532,8 +534,9 @@ class ExperimentGraphDrawing(MainDataBase): MainDataBase.__init__(self, expid) APIBasicConfig.read() self.expid = expid + exp_paths = ExperimentPaths(expid) self.folder_path = APIBasicConfig.LOCAL_ROOT_DIR - self.database_path = os.path.join(APIBasicConfig.GRAPHDATA_DIR, "graph_data_" + str(expid) + ".db") + self.database_path = exp_paths.graph_data_db self.create_table_query = textwrap.dedent( '''CREATE TABLE IF NOT EXISTS experiment_graph_draw ( @@ -733,7 +736,7 @@ class ExperimentGraphDrawing(MainDataBase): class JobDataStructure(MainDataBase): - def __init__(self, expid, basic_config): + def __init__(self, expid: str, basic_config: APIBasicConfig): """Initializes the object based on the unique identifier of the experiment. Args: @@ -743,8 +746,8 @@ class JobDataStructure(MainDataBase): # BasicConfig.read() # self.expid = expid self.folder_path = basic_config.JOBDATA_DIR - self.database_path = os.path.join( - self.folder_path, "job_data_" + str(expid) + ".db") + exp_paths = ExperimentPaths(expid) + self.database_path = exp_paths.job_data_db # self.conn = None self.db_version = None # self.jobdata_list = JobDataList(self.expid) diff --git a/autosubmit_api/database/db_structure.py b/autosubmit_api/database/db_structure.py index 87fa177..ea379e9 100644 --- a/autosubmit_api/database/db_structure.py +++ b/autosubmit_api/database/db_structure.py @@ -3,6 +3,8 @@ import textwrap import traceback import pysqlite3 as sqlite3 +from autosubmit_api.persistance.experiment import ExperimentPaths + def get_structure(expid, structures_path): """ Creates file of database and table of experiment structure if it does not exist. @@ -12,10 +14,10 @@ def get_structure(expid, structures_path): :rtype: Dictionary Key: String, Value: List(of String) """ try: + exp_paths = ExperimentPaths(expid) + db_structure_path = exp_paths.structure_db #pkl_path = os.path.join(exp_path, expid, "pkl") - if os.path.exists(structures_path): - db_structure_path = os.path.join( - structures_path, "structure_" + expid + ".db") + if os.path.exists(db_structure_path): # Create file os.umask(0) if not os.path.exists(db_structure_path): @@ -51,8 +53,8 @@ def get_structure(expid, structures_path): return dict() else: # pkl folder not found - raise Exception("structures folder not found " + - str(structures_path)) + raise Exception("structures db not found " + + str(db_structure_path)) except Exception as exp: print((traceback.format_exc())) @@ -100,59 +102,3 @@ def _get_exp_structure(path): except Exception as exp: print((traceback.format_exc())) return dict() - - -def save_structure(graph, exp_id, structures_path): - """ - Saves structure if path is valid - """ - #pkl_path = os.path.join(exp_path, exp_id, "pkl") - if os.path.exists(structures_path): - db_structure_path = os.path.join( - structures_path, "structure_" + exp_id + ".db") - # with open(db_structure_path, "w"): - conn = create_connection(db_structure_path) - deleted = _delete_table_content(conn) - if deleted == True: - nodes_edges = {u for u, v in graph.edges()} - nodes_edges.update({v for u, v in graph.edges()}) - independent_nodes = { - u for u in graph.nodes() if u not in nodes_edges} - data = {(u, v) for u, v in graph.edges()} - data.update({(u, u) for u in independent_nodes}) - # save - _create_edge(conn, data) - #print("Created edge " + str(u) + str(v)) - conn.commit() - else: - # pkl folder not found - raise Exception("pkl folder not found " + str(structures_path)) - - -def _create_edge(conn, data): - """ - Create edge - """ - try: - sql = ''' INSERT INTO experiment_structure(e_from, e_to) VALUES(?,?) ''' - cur = conn.cursor() - cur.executemany(sql, data) - # return cur.lastrowid - except sqlite3.Error as e: - print(("Error on Insert : " + str(type(e).__name__))) - - -def _delete_table_content(conn): - """ - Deletes table content - """ - try: - sql = ''' DELETE FROM experiment_structure ''' - cur = conn.cursor() - cur.execute(sql) - conn.commit() - return True - except Exception as exp: - # print(traceback.format_exc()) - print(("Error on Delete _delete_table_content: {}".format(str(exp)))) - return False diff --git a/autosubmit_api/experiment/common_requests.py b/autosubmit_api/experiment/common_requests.py index 5d29898..0028357 100644 --- a/autosubmit_api/experiment/common_requests.py +++ b/autosubmit_api/experiment/common_requests.py @@ -43,6 +43,7 @@ from autosubmit_api.logger import logger from autosubmit_api.performance.utils import calculate_SYPD_perjob from autosubmit_api.monitor.monitor import Monitor +from autosubmit_api.persistance.experiment import ExperimentPaths from autosubmit_api.statistics.statistics import Statistics @@ -212,10 +213,9 @@ def _is_exp_running(expid, time_condition=300): definite_log_path = None try: APIBasicConfig.read() - pathlog_aslog = APIBasicConfig.LOCAL_ROOT_DIR + '/' + expid + '/' + \ - APIBasicConfig.LOCAL_TMP_DIR + '/' + APIBasicConfig.LOCAL_ASLOG_DIR - pathlog_tmp = APIBasicConfig.LOCAL_ROOT_DIR + '/' + \ - expid + '/' + APIBasicConfig.LOCAL_TMP_DIR + exp_paths = ExperimentPaths(expid) + pathlog_aslog = exp_paths.tmp_as_logs_dir + pathlog_tmp = exp_paths.tmp_dir # Basic Configuration look_old_folder = False current_version = None @@ -480,7 +480,8 @@ def get_experiment_log_last_lines(expid): try: APIBasicConfig.read() - path = APIBasicConfig.LOCAL_ROOT_DIR + '/' + expid + '/' + APIBasicConfig.LOCAL_TMP_DIR + '/' + APIBasicConfig.LOCAL_ASLOG_DIR + exp_paths = ExperimentPaths(expid) + path = exp_paths.tmp_as_logs_dir reading = os.popen('ls -t ' + path + ' | grep "run.log"').read() if (os.path.exists(path)) else "" # Finding log files @@ -529,7 +530,8 @@ def get_job_log(expid, logfile, nlines=150): logcontent = [] reading = "" APIBasicConfig.read() - logfilepath = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, expid, APIBasicConfig.LOCAL_TMP_DIR, "LOG_{0}".format(expid), logfile) + exp_paths = ExperimentPaths(expid) + logfilepath = os.path.join(exp_paths.tmp_log_dir, logfile) try: if os.path.exists(logfilepath): current_stat = os.stat(logfilepath) @@ -817,7 +819,8 @@ def get_quick_view(expid): total_count = completed_count = failed_count = running_count = queuing_count = 0 try: APIBasicConfig.read() - path_to_logs = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, expid, "tmp", "LOG_" + expid) + exp_paths = ExperimentPaths(expid) + path_to_logs = exp_paths.tmp_log_dir # Retrieving packages now_ = time.time() @@ -906,7 +909,8 @@ def get_job_history(expid, job_name): result = None try: APIBasicConfig.read() - path_to_job_logs = os.path.join(APIBasicConfig.LOCAL_ROOT_DIR, expid, "tmp", "LOG_" + expid) + exp_paths = ExperimentPaths(expid) + path_to_job_logs = exp_paths.tmp_log_dir result = ExperimentHistoryDirector(ExperimentHistoryBuilder(expid)).build_reader_experiment_history().get_historic_job_data(job_name) except Exception as exp: print((traceback.format_exc())) diff --git a/autosubmit_api/history/database_managers/experiment_history_db_manager.py b/autosubmit_api/history/database_managers/experiment_history_db_manager.py index 0a821a3..f8a1e6b 100644 --- a/autosubmit_api/history/database_managers/experiment_history_db_manager.py +++ b/autosubmit_api/history/database_managers/experiment_history_db_manager.py @@ -19,6 +19,8 @@ import pysqlite3 as sqlite3 import os import traceback import textwrap + +from autosubmit_api.persistance.experiment import ExperimentPaths from .. import utils as HUtils from .. database_managers import database_models as Models from .. data_classes.job_data import JobData @@ -39,7 +41,8 @@ class ExperimentHistoryDbManager(DatabaseManager): super(ExperimentHistoryDbManager, self).__init__(expid, basic_config) self._set_schema_changes() self._set_table_queries() - self.historicaldb_file_path = os.path.join(self.JOBDATA_DIR, "job_data_{0}.db".format(self.expid)) # type : str + exp_paths = ExperimentPaths(expid) + self.historicaldb_file_path = exp_paths.job_data_db if self.my_database_exists(): self.set_db_version_models() diff --git a/autosubmit_api/history/strategies.py b/autosubmit_api/history/strategies.py deleted file mode 100644 index 8fdf88d..0000000 --- a/autosubmit_api/history/strategies.py +++ /dev/null @@ -1,220 +0,0 @@ -#!/usr/bin/env python - -# Copyright 2015-2020 Earth Sciences Department, BSC-CNS -# This file is part of Autosubmit. - -# Autosubmit is free software: you can redistribute it and/or modify -# it under the terms of the GNU General Public License as published by -# the Free Software Foundation, either version 3 of the License, or -# (at your option) any later version. - -# Autosubmit is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. - -# You should have received a copy of the GNU General Public License -# along with Autosubmit. If not, see . - -from abc import ABCMeta, abstractmethod -from .database_managers import database_models as Models -import traceback -from .internal_logging import Logging -from .database_managers.database_manager import DEFAULT_LOCAL_ROOT_DIR, DEFAULT_HISTORICAL_LOGS_DIR - -class PlatformInformationHandler(): - def __init__(self, strategy): - self._strategy = strategy - - @property - def strategy(self): - return self._strategy - - @strategy.setter - def strategy(self, strategy): - self._strategy = strategy - - def execute_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - return self._strategy.apply_distribution(job_data_dc, job_data_dcs_in_wrapper, slurm_monitor) - - -class Strategy(metaclass=ABCMeta): - """ Strategy Interface """ - - def __init__(self, historiclog_dir_path=DEFAULT_HISTORICAL_LOGS_DIR): - self.historiclog_dir_path = historiclog_dir_path - - @abstractmethod - def apply_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - pass - - def set_job_data_dc_as_processed(self, job_data_dc, original_ssh_output): - job_data_dc.platform_output = original_ssh_output - job_data_dc.rowstatus = Models.RowStatus.PROCESSED - return job_data_dc - - def set_job_data_dc_as_process_failed(self, job_data_dc, original_ssh_output): - job_data_dc.platform_output = original_ssh_output - job_data_dc.rowstatus = Models.RowStatus.FAULTY - return job_data_dc - - def get_calculated_weights_of_jobs_in_wrapper(self, job_data_dcs_in_wrapper): - """ Based on computational weight: running time in seconds * number of cpus. """ - total_weight = sum(job.computational_weight for job in job_data_dcs_in_wrapper) - return {job.job_name: round(job.computational_weight/total_weight, 4) for job in job_data_dcs_in_wrapper} - - -class SingleAssociationStrategy(Strategy): - - def __init__(self, historiclog_dir_path=DEFAULT_HISTORICAL_LOGS_DIR): - super(SingleAssociationStrategy, self).__init__(historiclog_dir_path=historiclog_dir_path) - - def apply_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - try: - if len(job_data_dcs_in_wrapper) > 0: - return [] - # job_data_dc.submit = slurm_monitor.header.submit - # job_data_dc.start = slurm_monitor.header.start - # job_data_dc.finish = slurm_monitor.header.finish - job_data_dc.ncpus = slurm_monitor.header.ncpus - job_data_dc.nnodes = slurm_monitor.header.nnodes - job_data_dc.energy = slurm_monitor.header.energy - job_data_dc.MaxRSS = max(slurm_monitor.header.MaxRSS, slurm_monitor.batch.MaxRSS if slurm_monitor.batch else 0, slurm_monitor.extern.MaxRSS if slurm_monitor.extern else 0) # TODO: Improve this rule - job_data_dc.AveRSS = max(slurm_monitor.header.AveRSS, slurm_monitor.batch.AveRSS if slurm_monitor.batch else 0, slurm_monitor.extern.AveRSS if slurm_monitor.extern else 0) - job_data_dc = self.set_job_data_dc_as_processed(job_data_dc, slurm_monitor.original_input) - return [job_data_dc] - except Exception as exp: - Logging("strategies", self.historiclog_dir_path).log("SingleAssociationStrategy failed for {0}. Using ssh_output: {1}. Exception message: {2}".format(job_data_dc.job_name, slurm_monitor.original_input, str(exp)), - traceback.format_exc()) - job_data_dc = self.set_job_data_dc_as_process_failed(job_data_dc, slurm_monitor.original_input) - return [job_data_dc] - -class StraightWrapperAssociationStrategy(Strategy): - - def __init__(self, historiclog_dir_path=DEFAULT_HISTORICAL_LOGS_DIR): - super(StraightWrapperAssociationStrategy, self).__init__(historiclog_dir_path=historiclog_dir_path) - - def apply_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - """ """ - try: - if len(job_data_dcs_in_wrapper) != slurm_monitor.step_count: - return [] - result = [] - computational_weights = self.get_calculated_weights_of_jobs_in_wrapper(job_data_dcs_in_wrapper) - for job_dc, step in zip(job_data_dcs_in_wrapper, slurm_monitor.steps): - job_dc.energy = step.energy + computational_weights.get(job_dc.job_name, 0) * slurm_monitor.extern.energy - job_dc.AveRSS = step.AveRSS - job_dc.MaxRSS = step.MaxRSS - job_dc.platform_output = "" - if job_dc.job_name == job_data_dc.job_name: - job_data_dc.energy = job_dc.energy - job_data_dc.AveRSS = job_dc.AveRSS - job_data_dc.MaxRSS = job_dc.MaxRSS - result.append(job_dc) - job_data_dc = self.set_job_data_dc_as_processed(job_data_dc, slurm_monitor.original_input) - result.append(job_data_dc) - return result - except Exception as exp: - Logging("strategies", self.historiclog_dir_path).log("StraightWrapperAssociationStrategy failed for {0}. Using ssh_output: {1}. Exception message: {2}".format(job_data_dc.job_name, - slurm_monitor.original_input, - str(exp)), - traceback.format_exc()) - job_data_dc = self.set_job_data_dc_as_process_failed(job_data_dc, slurm_monitor.original_input) - return [job_data_dc] - -class GeneralizedWrapperDistributionStrategy(Strategy): - - def __init__(self, historiclog_dir_path=DEFAULT_HISTORICAL_LOGS_DIR): - super(GeneralizedWrapperDistributionStrategy, self).__init__(historiclog_dir_path=historiclog_dir_path) - - def apply_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - try: - result = [] - computational_weights = self.get_calculated_weights_of_jobs_in_wrapper(job_data_dcs_in_wrapper) - for job_dc in job_data_dcs_in_wrapper: - job_dc.energy = round(computational_weights.get(job_dc.job_name, 0) * slurm_monitor.total_energy,2) - job_dc.platform_output = "" - if job_dc.job_name == job_data_dc.job_name: - job_data_dc.energy = job_dc.energy - result.append(job_dc) - job_data_dc = self.set_job_data_dc_as_processed(job_data_dc, slurm_monitor.original_input) - result.append(job_data_dc) - return result - except Exception as exp: - Logging("strategies", self.historiclog_dir_path).log("GeneralizedWrapperDistributionStrategy failed for {0}. Using ssh_output: {1}. Exception message: {2}".format(job_data_dc.job_name, slurm_monitor.original_input, str(exp)), - traceback.format_exc()) - job_data_dc = self.set_job_data_dc_as_process_failed(job_data_dc, slurm_monitor.original_input) - return [job_data_dc] - -class TwoDimWrapperDistributionStrategy(Strategy): - - def __init__(self, historiclog_dir_path=DEFAULT_HISTORICAL_LOGS_DIR): - super(TwoDimWrapperDistributionStrategy, self).__init__(historiclog_dir_path=historiclog_dir_path) - - def apply_distribution(self, job_data_dc, job_data_dcs_in_wrapper, slurm_monitor): - try: - result = [] - self.jobs_per_level = self.get_jobs_per_level(job_data_dcs_in_wrapper) - if len(self.jobs_per_level) != slurm_monitor.step_count: - return [] - comp_weight_per_level = self.get_comp_weight_per_level(self.jobs_per_level) - level_energy = [] - for i, step in enumerate(slurm_monitor.steps): - level_energy.append(step.energy + comp_weight_per_level[i] * slurm_monitor.extern.energy) - for i, jobs in enumerate(self.jobs_per_level): - weights = self.get_comp_weight_per_group_of_job_dcs(jobs) - for j, job_dc in enumerate(jobs): - job_dc.energy = round(level_energy[i] * weights[j], 2) - if job_dc.job_name == job_data_dc.job_name: - job_data_dc.energy = job_dc.energy - result.append(job_dc) - job_data_dc = self.set_job_data_dc_as_processed(job_data_dc, slurm_monitor.original_input) - result.append(job_data_dc) - return result - except Exception as exp: - Logging("strategies", self.historiclog_dir_path).log("TwoDimWrapperDistributionStrategy failed for {0}. Using ssh_output: {1}. Exception message: {2}".format(job_data_dc.job_name, slurm_monitor.original_input, str(exp)), - traceback.format_exc()) - job_data_dc = self.set_job_data_dc_as_process_failed(job_data_dc, slurm_monitor.original_input) - return [job_data_dc] - - def get_jobs_per_level(self, job_data_dcs_in_wrapper): - """ List of Lists, index of list is the level. """ - job_name_to_object = {job.job_name: job for job in job_data_dcs_in_wrapper} - levels = [] - roots_dcs = self._get_roots(job_data_dcs_in_wrapper) - levels.append(roots_dcs) - next_level = self.get_level(roots_dcs, job_name_to_object) - while len(next_level) > 0: - levels.append([job for job in next_level]) - next_level = self.get_level(next_level, job_name_to_object) - return levels - - def _get_roots(self, job_data_dcs_in_wrapper): - children_names = self._get_all_children(job_data_dcs_in_wrapper) - return [job for job in job_data_dcs_in_wrapper if job.job_name not in children_names] - - def _get_all_children(self, job_data_dcs_in_wrapper): - result = [] - for job_dc in job_data_dcs_in_wrapper: - result.extend(job_dc.children_list) - return result - - def get_comp_weight_per_group_of_job_dcs(self, jobs): - total = sum(job.computational_weight for job in jobs) - return [round(job.computational_weight/total, 4) for job in jobs] - - def get_comp_weight_per_level(self, jobs_per_level): - level_weight = [] - total_weight = 0 - for jobs in jobs_per_level: - computational_weight = sum(job.computational_weight for job in jobs) - total_weight += computational_weight - level_weight.append(computational_weight) - return [round(weight/total_weight, 4) for weight in level_weight] - - def get_level(self, previous_level_dcs, job_name_to_object): - children_names = [] - for job_dc in previous_level_dcs: - children_names.extend(job_dc.children_list) - level_dcs = [job_name_to_object[job_name] for job_name in children_names if job_name in job_name_to_object] - return level_dcs diff --git a/autosubmit_api/persistance/experiment.py b/autosubmit_api/persistance/experiment.py index d34370e..178c1b0 100644 --- a/autosubmit_api/persistance/experiment.py +++ b/autosubmit_api/persistance/experiment.py @@ -34,12 +34,33 @@ class ExperimentPaths: @property def tmp_dir(self): + """ + tmp dir + """ return os.path.join(self.exp_dir, APIBasicConfig.LOCAL_TMP_DIR) + + @property + def tmp_log_dir(self): + """ + tmp/LOG_{expid} dir + """ + return os.path.join(self.tmp_dir, f"LOG_{self.expid}") @property - def tmp_dir(self): - return os.path.join(self.exp_dir, APIBasicConfig.LOCAL_TMP_DIR) + def tmp_as_logs_dir(self): + """ + tmp/ASLOGS dir + """ + return os.path.join(self.tmp_dir, APIBasicConfig.LOCAL_ASLOG_DIR) @property - def tmp_log_dir(self): - return os.path.join(self.tmp_dir, f"LOG_{self.expid}") \ No newline at end of file + def job_data_db(self): + return os.path.join(APIBasicConfig.JOBDATA_DIR, f"job_data_{self.expid}.db") + + @property + def structure_db(self): + return os.path.join(APIBasicConfig.STRUCTURES_DIR, f"structure_{self.expid}.db") + + @property + def graph_data_db(self): + return os.path.join(APIBasicConfig.GRAPHDATA_DIR, f"graph_data_{self.expid}.db") diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 43bd6b66db7a106c2f556c68a50b9272caf871ae..cf469cc2ce4130f3744c12e19fb8d511d5d03f7d 100644 GIT binary patch delta 58 scmZp0XmFSy%{XhKj5Fh`jR{WjTxPn4=2j-gR)!{%*T^d%bFZOr0p(i{DF6Tf delta 58 scmZp0XmFSy&Db Date: Mon, 19 Feb 2024 11:24:42 +0100 Subject: [PATCH 15/18] update pysqlite3 to sqlite3 import --- CHANGELOG.md | 4 +++ autosubmit_api/app.py | 1 - autosubmit_api/database/db_common.py | 4 +-- autosubmit_api/database/db_jobdata.py | 2 +- autosubmit_api/database/db_structure.py | 4 +-- autosubmit_api/database/extended_db.py | 29 ------------------ .../database_managers/database_manager.py | 10 +++--- .../experiment_history_db_manager.py | 14 ++++----- tests/conftest.py | 14 +-------- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes 10 files changed, 21 insertions(+), 61 deletions(-) delete mode 100644 autosubmit_api/database/extended_db.py diff --git a/CHANGELOG.md b/CHANGELOG.md index ef0cfcd..2750192 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ ### Pre-release v4.0.0b4 - Release date: TBD +* The background task that updates the experiment status have refactored. Now, it keep the records of all the experiments +* **Major change:** `experiment_times` and `job_times` tables are removed. Background tasks related to them are also removed +* Fixed bug when performance metrics are not calculated when there is only one SIM job + ### Pre-release v4.0.0b3 - Release date: 2023-02-09 * Fix HPC value in the running endpoint diff --git a/autosubmit_api/app.py b/autosubmit_api/app.py index 6e63fa4..b191135 100644 --- a/autosubmit_api/app.py +++ b/autosubmit_api/app.py @@ -7,7 +7,6 @@ from autosubmit_api.bgtasks.scheduler import create_bind_scheduler from autosubmit_api.blueprints.v3 import create_v3_blueprint from autosubmit_api.blueprints.v4 import create_v4_blueprint from autosubmit_api.database import prepare_db -from autosubmit_api.database.extended_db import ExtendedDB from autosubmit_api.experiment import common_requests as CommonRequests from autosubmit_api.logger import get_app_logger from autosubmit_api.config.basicConfig import APIBasicConfig diff --git a/autosubmit_api/database/db_common.py b/autosubmit_api/database/db_common.py index 7b370b8..961bba6 100644 --- a/autosubmit_api/database/db_common.py +++ b/autosubmit_api/database/db_common.py @@ -22,7 +22,7 @@ Module containing functions to manage autosubmit's database. """ import os from sqlite3 import Connection, Cursor -import pysqlite3 as sqlite3 +import sqlite3 from bscearth.utils.log import Log from autosubmit_api.config.basicConfig import APIBasicConfig @@ -96,7 +96,7 @@ def open_conn(check_version=True) -> Tuple[Connection, Cursor]: return conn, cursor -def close_conn(conn, cursor): +def close_conn(conn: Connection, cursor): """ Commits changes and close connection to database diff --git a/autosubmit_api/database/db_jobdata.py b/autosubmit_api/database/db_jobdata.py index 44db432..cae28a8 100644 --- a/autosubmit_api/database/db_jobdata.py +++ b/autosubmit_api/database/db_jobdata.py @@ -21,7 +21,7 @@ import os import time import textwrap import traceback -import pysqlite3 as sqlite3 +import sqlite3 import collections import portalocker from datetime import datetime, timedelta diff --git a/autosubmit_api/database/db_structure.py b/autosubmit_api/database/db_structure.py index ea379e9..0866488 100644 --- a/autosubmit_api/database/db_structure.py +++ b/autosubmit_api/database/db_structure.py @@ -1,7 +1,7 @@ import os import textwrap import traceback -import pysqlite3 as sqlite3 +import sqlite3 from autosubmit_api.persistance.experiment import ExperimentPaths @@ -72,7 +72,7 @@ def create_connection(db_file): return None -def create_table(conn, create_table_sql): +def create_table(conn: sqlite3.Connection, create_table_sql): """ create a table from the create_table_sql statement :param conn: Connection object :param create_table_sql: a CREATE TABLE statement diff --git a/autosubmit_api/database/extended_db.py b/autosubmit_api/database/extended_db.py deleted file mode 100644 index 518941a..0000000 --- a/autosubmit_api/database/extended_db.py +++ /dev/null @@ -1,29 +0,0 @@ -from autosubmit_api.config.basicConfig import APIBasicConfig -from autosubmit_api.database.db_manager import DbManager -from autosubmit_api.database import prepare_db -from autosubmit_api.workers.populate_details.populate import DetailsProcessor - -class ExtendedDB: - def __init__(self, root_path: str, db_name: str, as_times_db_name: str) -> None: - self.root_path = root_path - self.db_name = db_name - self.main_db_manager = DbManager(root_path, db_name) - self.as_times_db_manager = DbManager(root_path, as_times_db_name) - - def prepare_db(self): - """ - Create tables and views that are required - """ - self.prepare_main_db() - prepare_db() - - - def prepare_main_db(self): - APIBasicConfig.read() - DetailsProcessor(APIBasicConfig).create_details_table_if_not_exists() - self.main_db_manager.create_view( - 'listexp', - 'select id,name,user,created,model,branch,hpc,description from experiment left join details on experiment.id = details.exp_id' - ) - - diff --git a/autosubmit_api/history/database_managers/database_manager.py b/autosubmit_api/history/database_managers/database_manager.py index 0bd01db..c7cb2d9 100644 --- a/autosubmit_api/history/database_managers/database_manager.py +++ b/autosubmit_api/history/database_managers/database_manager.py @@ -16,12 +16,12 @@ # You should have received a copy of the GNU General Public License # along with Autosubmit. If not, see . -import pysqlite3 as sqlite3 +import sqlite3 import os -from .. import utils as HUtils -from . import database_models as Models -from ...config.basicConfig import APIBasicConfig -from abc import ABCMeta, abstractmethod +from autosubmit_api.history import utils as HUtils +from autosubmit_api.history.database_managers import database_models as Models +from autosubmit_api.config.basicConfig import APIBasicConfig +from abc import ABCMeta DEFAULT_JOBDATA_DIR = os.path.join('/esarchive', 'autosubmit', 'as_metadata', 'data') DEFAULT_HISTORICAL_LOGS_DIR = os.path.join('/esarchive', 'autosubmit', 'as_metadata', 'logs') diff --git a/autosubmit_api/history/database_managers/experiment_history_db_manager.py b/autosubmit_api/history/database_managers/experiment_history_db_manager.py index f8a1e6b..1f35a92 100644 --- a/autosubmit_api/history/database_managers/experiment_history_db_manager.py +++ b/autosubmit_api/history/database_managers/experiment_history_db_manager.py @@ -15,18 +15,16 @@ # You should have received a copy of the GNU General Public License # along with Autosubmit. If not, see . -import pysqlite3 as sqlite3 import os -import traceback import textwrap from autosubmit_api.persistance.experiment import ExperimentPaths -from .. import utils as HUtils -from .. database_managers import database_models as Models -from .. data_classes.job_data import JobData -from ..data_classes.experiment_run import ExperimentRun -from ...config.basicConfig import APIBasicConfig -from .database_manager import DatabaseManager, DEFAULT_JOBDATA_DIR +from autosubmit_api.history import utils as HUtils +from autosubmit_api.history.database_managers import database_models as Models +from autosubmit_api.history.data_classes.job_data import JobData +from autosubmit_api.history.data_classes.experiment_run import ExperimentRun +from autosubmit_api.config.basicConfig import APIBasicConfig +from autosubmit_api.history.database_managers.database_manager import DatabaseManager from typing import List from collections import namedtuple diff --git a/tests/conftest.py b/tests/conftest.py index 9d3f98e..be699e0 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,20 +22,8 @@ def fixture_disable_protection(monkeypatch: pytest.MonkeyPatch): @pytest.fixture def fixture_mock_basic_config(monkeypatch: pytest.MonkeyPatch): + # Get APIBasicConfig from file monkeypatch.setenv("AUTOSUBMIT_CONFIGURATION", os.path.join(FAKE_EXP_DIR, ".autosubmitrc")) - # Patch APIBasicConfig parent BasicConfig - # monkeypatch.setattr(BasicConfig, "read", custom_return_value(None)) - # monkeypatch.setattr(APIBasicConfig, "read", custom_return_value(None)) - # monkeypatch.setattr(BasicConfig, "LOCAL_ROOT_DIR", FAKE_EXP_DIR) - # monkeypatch.setattr(BasicConfig, "DB_DIR", FAKE_EXP_DIR) - # monkeypatch.setattr(BasicConfig, "DB_FILE", "autosubmit.db") - # monkeypatch.setattr( - # BasicConfig, "JOBDATA_DIR", os.path.join(FAKE_EXP_DIR, "metadata", "data") - # ) - # monkeypatch.setattr( - # BasicConfig, "DB_PATH", os.path.join(FAKE_EXP_DIR, "autosubmit.db") - # ) - # monkeypatch.setattr(BasicConfig, "AS_TIMES_DB", "as_times.db") yield APIBasicConfig diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index cf469cc2ce4130f3744c12e19fb8d511d5d03f7d..cc4cf74a4902e90ee22eebd09d244ca78646d699 100644 GIT binary patch delta 52 vcmZp0XmFSy&A4o$j5Fi1jR{Wj?3TKQhE_%}I-#=2j-glUK?s!`YYRmARneR)!`3k?sxU -- GitLab From 5be7b7f20ab741305018afbfd376b181a5f23b57 Mon Sep 17 00:00:00 2001 From: Bruno de Paula Kinoshita <777-bdepaula@users.noreply.earth.bsc.es> Date: Mon, 19 Feb 2024 11:28:10 +0100 Subject: [PATCH 16/18] Use dependency groups in setuptools --- README.md | 4 ++-- pytest.ini | 10 ++++++++++ setup.py | 58 +++++++++++++++++++++++++++++++++--------------------- 3 files changed, 48 insertions(+), 24 deletions(-) create mode 100644 pytest.ini diff --git a/README.md b/README.md index dc078e6..c33ed7c 100644 --- a/README.md +++ b/README.md @@ -70,13 +70,13 @@ The Autosubmit API have some configuration options that can be modified by setti ### Install pytest ```bash -pip install -U pytest pytest-cov +pip install -e .[test] ``` ### Run tests: ```bash -pytest tests/* +pytest ``` ### Run tests with coverage HTML report: diff --git a/pytest.ini b/pytest.ini new file mode 100644 index 0000000..da75339 --- /dev/null +++ b/pytest.ini @@ -0,0 +1,10 @@ +[pytest] +addopts = + --cov=autosubmit_api --cov-config=.coveragerc --cov-report=html +testpaths = + tests/ +doctest_optionflags = + NORMALIZE_WHITESPACE + IGNORE_EXCEPTION_DETAIL + ELLIPSIS + diff --git a/setup.py b/setup.py index 87d42ee..8eb87b2 100644 --- a/setup.py +++ b/setup.py @@ -19,6 +19,40 @@ def get_authors(): return autosubmit_api.__author__ +install_requires = [ + "Flask~=2.2.5", + "pyjwt~=2.8.0", + "requests~=2.28.1", + "flask_cors~=3.0.10", + "bscearth.utils~=0.5.2", + "pysqlite-binary", + "pydotplus~=2.0.2", + "portalocker~=2.6.0", + "networkx~=2.6.3", + "scipy~=1.7.3", + "paramiko~=2.12.0", + "python-dotenv", + "autosubmitconfigparser~=1.0.48", + "autosubmit>=3.13", + "Flask-APScheduler", + "gunicorn", + "pydantic~=2.5.2", + "SQLAlchemy~=2.0.23", + "python-cas>=1.6.0", + "Authlib>=1.3.0" +] + +# Test dependencies +test_requires = [ + "pytest", + "pytest-cov" +] + +extras_require = { + 'test': test_requires, + 'all': install_requires + test_requires +} + setup( name="autosubmit_api", version=get_version(), @@ -32,28 +66,8 @@ setup( packages=find_packages(), keywords=["autosubmit", "API"], python_requires=">=3.8", - install_requires=[ - "Flask~=2.2.5", - "pyjwt~=2.8.0", - "requests~=2.28.1", - "flask_cors~=3.0.10", - "bscearth.utils~=0.5.2", - "pysqlite-binary", - "pydotplus~=2.0.2", - "portalocker~=2.6.0", - "networkx~=2.6.3", - "scipy~=1.7.3", - "paramiko~=2.12.0", - "python-dotenv", - "autosubmitconfigparser~=1.0.48", - "autosubmit>=3.13", - "Flask-APScheduler", - "gunicorn", - "pydantic~=2.5.2", - "SQLAlchemy~=2.0.23", - "python-cas>=1.6.0", - "Authlib>=1.3.0" - ], + install_requires=install_requires, + extras_require=extras_require, include_package_data=True, package_data={"autosubmit-api": ["README", "VERSION", "LICENSE"]}, classifiers=[ -- GitLab From 5958ee1bb7a566d64dcfbcceea6f3f77c55437b1 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Thu, 22 Feb 2024 09:41:43 +0100 Subject: [PATCH 17/18] fix graph background task parser --- autosubmit_api/database/db_jobdata.py | 7 +- autosubmit_api/database/tables.py | 12 +++ tests/experiments/as_times.db | Bin 8192 -> 8192 bytes .../experiments/calculation_in_progress.lock | 0 .../metadata/graph/graph_data_a003.db | Bin 8192 -> 8192 bytes tests/test_graph.py | 75 ++++++++++++++++++ 6 files changed, 91 insertions(+), 3 deletions(-) delete mode 100644 tests/experiments/calculation_in_progress.lock create mode 100644 tests/test_graph.py diff --git a/autosubmit_api/database/db_jobdata.py b/autosubmit_api/database/db_jobdata.py index cae28a8..25a70ad 100644 --- a/autosubmit_api/database/db_jobdata.py +++ b/autosubmit_api/database/db_jobdata.py @@ -622,9 +622,10 @@ class ExperimentGraphDrawing(MainDataBase): result = graph.create('dot', format="plain") for u in result.split(b"\n"): splitList = u.split(b" ") - if len(splitList) > 1 and splitList[0] == "node": - self.coordinates.append((splitList[1], int( - float(splitList[2]) * 90), int(float(splitList[3]) * -90))) + if len(splitList) > 1 and splitList[0].decode() == "node": + + self.coordinates.append((splitList[1].decode(), int( + float(splitList[2].decode()) * 90), int(float(splitList[3].decode()) * -90))) # self.coordinates[splitList[1]] = ( # int(float(splitList[2]) * 90), int(float(splitList[3]) * -90)) self.insert_coordinates() diff --git a/autosubmit_api/database/tables.py b/autosubmit_api/database/tables.py index e4929c6..7a42573 100644 --- a/autosubmit_api/database/tables.py +++ b/autosubmit_api/database/tables.py @@ -37,3 +37,15 @@ experiment_status_table = Table( Column("seconds_diff", Integer, nullable=False), Column("modified", Text, nullable=False), ) + + +# Graph Data TABLES + +graph_data_table = Table( + "experiment_graph_draw", + metadata_obj, + Column("id", Integer, primary_key=True), + Column("job_name", Text, nullable=False), + Column("x", Integer, nullable=False), + Column("y", Integer, nullable=False), +) diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index cc4cf74a4902e90ee22eebd09d244ca78646d699..4c5bbb7fe7429ad841f559522f44241d10055b91 100644 GIT binary patch delta 61 scmZp0XmFSy&A4Wwj5Fh!jR}tO+(t&a29{RFMph=Klh??j@~@%t0T?F_-~a#s delta 61 scmZp0XmFSy&A4o$j5Fi1jR}tO+=iCAhK5!~CRTN9B*V`WMp7sU>Kj4Y!Dw3>y;2Y zD}y3bjkAxdqaVYp2|{eF4Dw7&V0{7p!66K@{+lVVvNBjh#Zb&LiVybmWtjEvjsgps ziVT=_hEOF2>0 C6$;Y; diff --git a/tests/test_graph.py b/tests/test_graph.py new file mode 100644 index 0000000..0dc5bed --- /dev/null +++ b/tests/test_graph.py @@ -0,0 +1,75 @@ +import os + +from sqlalchemy import create_engine +from autosubmit_api.builders.configuration_facade_builder import ( + AutosubmitConfigurationFacadeBuilder, + ConfigurationFacadeDirector, +) +from autosubmit_api.builders.joblist_loader_builder import ( + JobListLoaderBuilder, + JobListLoaderDirector, +) +from autosubmit_api.database import tables +from autosubmit_api.database.db_jobdata import ExperimentGraphDrawing +from autosubmit_api.monitor.monitor import Monitor +from autosubmit_api.persistance.experiment import ExperimentPaths + + +class TestPopulateDB: + + def test_monitor_dot(self, fixture_mock_basic_config): + expid = "a003" + job_list_loader = JobListLoaderDirector( + JobListLoaderBuilder(expid) + ).build_loaded_joblist_loader() + + monitor = Monitor() + graph = monitor.create_tree_list( + expid, + job_list_loader.jobs, + None, + dict(), + False, + job_list_loader.job_dictionary, + ) + assert graph + + result = graph.create("dot", format="plain") + assert result and len(result) > 0 + + def test_process_graph(self, fixture_mock_basic_config): + expid = "a003" + experimentGraphDrawing = ExperimentGraphDrawing(expid) + job_list_loader = JobListLoaderDirector( + JobListLoaderBuilder(expid) + ).build_loaded_joblist_loader() + + autosubmit_configuration_facade = ConfigurationFacadeDirector( + AutosubmitConfigurationFacadeBuilder(expid) + ).build_autosubmit_configuration_facade() + + exp_paths = ExperimentPaths(expid) + with create_engine( + f"sqlite:///{ os.path.abspath(exp_paths.graph_data_db)}" + ).connect() as conn: + conn.execute(tables.graph_data_table.delete()) + conn.commit() + + experimentGraphDrawing.calculate_drawing( + allJobs=job_list_loader.jobs, + independent=False, + num_chunks=autosubmit_configuration_facade.chunk_size, + job_dictionary=job_list_loader.job_dictionary, + ) + + assert ( + experimentGraphDrawing.coordinates + and len(experimentGraphDrawing.coordinates) == 8 + ) + + rows = conn.execute(tables.graph_data_table.select()).all() + + assert len(rows) == 8 + for job in rows: + job_name: str = job.job_name + assert job_name.startswith(expid) -- GitLab From 973d6da3d889a1fc16aade429772264d8db48ea5 Mon Sep 17 00:00:00 2001 From: Luiggi Tenorio Date: Fri, 23 Feb 2024 11:38:34 +0100 Subject: [PATCH 18/18] update changelog --- CHANGELOG.md | 12 ++++++++---- tests/experiments/as_times.db | Bin 8192 -> 8192 bytes .../metadata/graph/graph_data_a003.db | Bin 8192 -> 8192 bytes 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2750192..e491adb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,12 +1,16 @@ # CHANGELOG -### Pre-release v4.0.0b4 - Release date: TBD +### Pre-release v4.0.0b4 - Release date: 2024-02-23 -* The background task that updates the experiment status have refactored. Now, it keep the records of all the experiments -* **Major change:** `experiment_times` and `job_times` tables are removed. Background tasks related to them are also removed +* The background task that updates the experiment status has been refactored. Now, it keeps the records of all the experiments +* **Major change:** Removed `experiment_times` and `job_times` tables and background tasks related to them * Fixed bug when performance metrics are not calculated when there is only one SIM job +* Multiple tests have been added +* Testing module configuration fixtures have been fixed +* A lot of dead code has been removed +* Fix the decoding issue on graph coordinates generation on the background task -### Pre-release v4.0.0b3 - Release date: 2023-02-09 +### Pre-release v4.0.0b3 - Release date: 2024-02-09 * Fix HPC value in the running endpoint * **Major change:** Updated all route names. Versioning path prefix is included: diff --git a/tests/experiments/as_times.db b/tests/experiments/as_times.db index 4c5bbb7fe7429ad841f559522f44241d10055b91..0f8be2ec756ee0c158c810bbb21ecc5baa5089d0 100644 GIT binary patch delta 58 scmZp0XmFSy&A5J|j5FiPEmR80_RwkyC*T^d%bFZOr0qc|xN&o-= diff --git a/tests/experiments/metadata/graph/graph_data_a003.db b/tests/experiments/metadata/graph/graph_data_a003.db index 5083d17c32f839b7956f4a0380e12877978e504b..ed0362b552850f04244080a7fe51840c7fdaf54c 100755 GIT binary patch delta 17 YcmZp0XmFSy%_uuj#+gxeW5NP?0519kC;$Ke delta 17 YcmZp0XmFSy%_ucd#+gxSW5NP?04~i1A^-pY -- GitLab