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"pytest-mypy (>=0.9.1)", "pytest-ruff"] + +[metadata] +lock-version = "2.0" +python-versions = ">=3.9, <3.13" +content-hash = "cf6de5423ae462d82798362f48ec842367c50c1d806c5307860a0a2bc9ecad84" diff --git a/pyproject.toml b/pyproject.toml old mode 100644 new mode 100755 index 9f2cbfe..6872ab5 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,58 +1,60 @@ -[tool.poetry] -name = "snews-cs" -version = "2.2.0" -description = "An alert application for observing supernovas." -authors = ["Sebastian Torres-Lara ", "Melih Kara "] -license = "BSD 3-Clause" -readme = "README.md" -packages = [{include = "snews_cs"}] -homepage = "https://github.com/SNEWS2/SNEWS_Coincidence_System.git" -repository = "https://github.com/SNEWS2/SNEWS_Coincidence_System.git" -documentation = "https://snews-coincidence-system.readthedocs.io/" -classifiers = [ - "Development Status :: 2 - Pre-Alpha", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Intended Audience :: Science/Research", - "Intended Audience :: Developers", - "Natural Language :: English", - "Topic :: Scientific/Engineering", - "Topic :: Scientific/Engineering :: Astronomy", - "Topic :: Scientific/Engineering :: Physics", - "Operating System :: POSIX", - "Operating System :: Unix", - "Operating System :: MacOS", - "License :: OSI Approved :: BSD License", -] - -[tool.poetry.scripts] -snews_cs = "snews_cs.__main__:main" - -[tool.poetry.dependencies] -python = ">=3.9, <3.13" -click = "^8.1.7" -hop-client = "^0.8.0" -ipython = "<7.33.0" # Constrained by snews_pt -numpy = "^1.26.0" -pandas = "^2.1.1" -python-dotenv = "0.19.2" # Constrained by snews_pt -pymongo = "^4.5.0" -slack-sdk = "^3.22.0" -snews-pt = "^1.3.3" -matplotlib = "^3.8.0" -scipy = "^1.11.3" - -[tool.poetry.group.dev.dependencies] -autopep8 = "^2.0.4" -flake8 = "^6.1.0" -mongomock = "^4.1.2" -pytest = "<6.3.0" # Constrained by snews_pt - -[tool.poetry.group.docs.dependencies] -sphinx = "<5" # Constrained by snews_pt -sphinx-pdj-theme = "^0.4.0" - -[build-system] -requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" - +[tool.poetry] +name = "snews-cs" +version = "2.2.0" +description = "An alert application for observing supernovas." +authors = ["Sebastian Torres-Lara ", "Melih Kara "] +license = "BSD 3-Clause" +readme = "README.md" +packages = [{include = "snews_cs"}] +homepage = "https://github.com/SNEWS2/SNEWS_Coincidence_System.git" +repository = "https://github.com/SNEWS2/SNEWS_Coincidence_System.git" +documentation = "https://snews-coincidence-system.readthedocs.io/" +classifiers = [ + "Development Status :: 2 - Pre-Alpha", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Intended Audience :: Science/Research", + "Intended Audience :: Developers", + "Natural Language :: English", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Astronomy", + "Topic :: Scientific/Engineering :: Physics", + "Operating System :: POSIX", + "Operating System :: Unix", + "Operating System :: MacOS", + "License :: OSI Approved :: BSD License", +] + +[tool.poetry.scripts] +snews_cs = "snews_cs.__main__:main" + +[tool.poetry.dependencies] +python = ">=3.9, <3.13" +click = "^8.1.7" +hop-client = "^0.8.0" +ipython = "<7.33.0" # Constrained by snews_pt +numpy = "^1.26.0" +pandas = "^2.1.1" +python-dotenv = "0.19.2" # Constrained by snews_pt +pymongo = "^4.5.0" +slack-sdk = "^3.22.0" +snews-pt = "^1.3.3" +matplotlib = "^3.8.0" +scipy = "^1.11.3" +sqlalchemy = "^2.0.32" +tabulate = "^0.9.0" + +[tool.poetry.group.dev.dependencies] +autopep8 = "^2.0.4" +flake8 = "^6.1.0" +mongomock = "^4.1.2" +pytest = "<6.3.0" # Constrained by snews_pt + +[tool.poetry.group.docs.dependencies] +sphinx = "<5" # Constrained by snews_pt +sphinx-pdj-theme = "^0.4.0" + +[build-system] +requires = ["poetry-core"] +build-backend = "poetry.core.masonry.api" + diff --git a/snews_cs/_version.py b/snews_cs/_version.py index d4b750f..6c3c2c9 100644 --- a/snews_cs/_version.py +++ b/snews_cs/_version.py @@ -1 +1 @@ -version = '2.2.0' +version = '2.2.1' diff --git a/snews_cs/cs_stats.py b/snews_cs/cs_stats.py index d6598d3..2b5a153 100644 --- a/snews_cs/cs_stats.py +++ b/snews_cs/cs_stats.py @@ -3,6 +3,10 @@ def ncr(n, r): f = math.factorial + # if the HB cache is empty, n-r returns negative number for which factorial is not defined + # as a temporary fix, let's return 0 + if n-r < 0: + return 0 return int(f(n) / f(r) / f(n - r)) def cache_false_alarm_rate(cache_sub_list, hb_cache): diff --git a/snews_cs/heartbeat_feedbacks.py b/snews_cs/heartbeat_feedbacks.py index 3feee08..e54f296 100644 --- a/snews_cs/heartbeat_feedbacks.py +++ b/snews_cs/heartbeat_feedbacks.py @@ -7,7 +7,8 @@ from time import sleep from .core.logging import getLogger from .cs_email import send_warning_mail, send_feedback_mail -from .snews_hb import beats_path, mirror_csv +from .snews_hb import beats_path +from sqlalchemy import create_engine log = getLogger(__name__) @@ -24,6 +25,13 @@ # verbose print. Prints only if verbose=True vprint = lambda inp, _bool: print(inp) if _bool else None +# SQLite database for the cached heartbeats +cache_db = os.path.abspath(os.path.join(beats_path, 'cached_heartbeats_mirror.db')) +cache_engine = create_engine(f'sqlite:///{cache_db}') +cache_df = None + + + class FeedBack: """ Once every minute, check the HB of each detector If the last heartbeat is from longer than usual, send an email @@ -37,6 +45,7 @@ def __init__(self, verbose=False): self.last_feedback_time[k] = np.datetime64("2022-01-01") self.day_in_min = 1440 self.running_min = 0 + self.db_found = False self.verbose = verbose log.info(f"\t> Heartbeat tracking initiated.") @@ -48,15 +57,9 @@ def __call__(self): while True: # run every minute sleep(60) - try: - df = pd.read_csv(mirror_csv, parse_dates=['Received Times'], ) - except FileNotFoundError: - log.error(f"{mirror_csv} does not exist yet! Maybe `snews_cs run-coincidence` is not invoked?") - while not os.path.isfile(mirror_csv): - sleep(60) - df = pd.read_csv(mirror_csv, parse_dates=['Received Times'], ) - log.debug(f"OK {mirror_csv} found! Moving on") - + # The database is continuosly updated, read it every minute + # it will wait until it finds a database + df = self.read_database() # Received times are already parsed self.control(df) # check if a detector is taking longer than usual (mean+3*sigma>) self.running_min += 1 vprint(f"[DEBUG] >>>>> Running minute: {self.running_min}", self.verbose) @@ -66,6 +69,28 @@ def __call__(self): self.running_min = 0 # reset the counter delete_old_figures() + def read_database(self): + """ Try to read the database, if it is empty (or does not exist) wait + """ + try: + # - Try reading cached data from SQL DB + cache_df = pd.read_sql_table('cached_heartbeats', cache_engine, + parse_dates=['Received Times', 'Stamped Times']) + if len(cache_df) < 1: + raise FileNotFoundError + log.debug(f"OK DataBase found! Moving on") + except FileNotFoundError: + log.error(f"DataBase does not exist yet! Maybe `snews_cs run-coincidence` is not invoked?\n" + f"Sleeping until I find something") + sleep(60) + self.running_min += 1 + return self.read_database() + # if it passes, that means it found a non-empty database + if not self.db_found: + log.debug(f"OK DataBase found! Moving on") + # log it once, then set db found true + self.db_found=True + return cache_df def control(self, df): """ Check the current cache, check if any detector @@ -163,7 +188,8 @@ def plot_beats(df, detector, figname): from mpl_toolkits.axes_grid1 import make_axes_locatable from matplotlib.colors import LinearSegmentedColormap, Normalize - latency = pd.to_timedelta(df['Latency'].values).total_seconds() + # latency = pd.to_timedelta(df['Latency'].values).total_seconds() + latency = df['Latency'].values received_times = df['Received Times'] # should be numpy datetime object try: unique_days_np = np.unique(received_times.astype('datetime64[D]')) diff --git a/snews_cs/snews_hb.py b/snews_cs/snews_hb.py index 0de540c..3f15e80 100644 --- a/snews_cs/snews_hb.py +++ b/snews_cs/snews_hb.py @@ -4,9 +4,11 @@ """ import os, json +import numpy as np import pandas as pd from datetime import datetime -import numpy as np +from sqlalchemy import create_engine + from .cs_utils import set_env, make_beat_directory from .core.logging import getLogger @@ -14,13 +16,15 @@ # Check if detector name is in registered list. detector_file = os.path.abspath(os.path.join(os.path.dirname(__file__), 'auxiliary/detector_properties.json')) + with open(detector_file) as file: snews_detectors = json.load(file) + snews_detectors = list(snews_detectors.keys()) +#- Cache of old heartbeats beats_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "../beats")) -mirror_csv = os.path.abspath(os.path.join(beats_path, f"cached_heartbeats_mirror.csv")) -master_csv = os.path.abspath(os.path.join(beats_path, f"complete_heartbeat_log.csv")) +cache_db = os.path.abspath(os.path.join(beats_path, 'cached_heartbeats_mirror.db')) def get_data_strings(df_input): """ Convert datetime objects to strings @@ -47,6 +51,34 @@ def to_numpy_datetime(input_datetime): ## TODO: make a list of internal heartbeats, and send us = SERVER heartbeats. # How many times a day can server log these heartbeats, (what is the livetime of server) +def sanity_checks(message): + """ check if the message will crash the server + Check the following + - detector frequencies are reasonable + - latencies are reasonable + - At least one detector is operational + """ + issue = "no issue" + for key in ['detector_name', 'detector_status']: + if key not in message.keys(): + issue = f" {key} is not in message keys" + if issue == "no issue": + if not isinstance(message['Received Times'], np.datetime64): + issue = f" {message['Received Times']} is not a np.datetime64 object" + if not message['detector_status'].lower() in ['on','off']: + issue = f" {message['detector_status']} is neither ON nor OFF" + if not message['detector_name'] in snews_detectors: + issue = f" {message['detector_name']} is not a valid detector" + + if issue == "no issue": + # do not log each time + return True + else: + log.error(f"\t> {message} is received at snews_hb.py but not valid.\n" + f"issue is: {issue}") + return False + + class HeartBeat: """ Class to handle heartbeat message stream """ @@ -60,7 +92,6 @@ def __init__(self, env_path=None, store=True, firedrill_mode=True): self.store = store log.info(f"\t> Heartbeats are stored in {beats_path}.") make_beat_directory(beats_path) - self.stash_time = float(os.getenv("HB_STASH_TIME", "24")) # hours self.delete_after = float(os.getenv("HB_DELETE_AFTER", "7")) # days if firedrill_mode: self.heartbeat_topic = os.getenv("FIREDRILL_OBSERVATION_TOPIC") @@ -68,7 +99,17 @@ def __init__(self, env_path=None, store=True, firedrill_mode=True): self.heartbeat_topic = os.getenv("OBSERVATION_TOPIC") self.column_names = ["Received Times", "Detector", "Stamped Times", "Latency", "Time After Last", "Status"] - self.cache_df = pd.DataFrame(columns=self.column_names) + + #- Update the alert cache + self.cache_engine = create_engine(f'sqlite:///{cache_db}') + self.cache_df = None + try: + #- Try reading cached data from SQL DB + self.cache_df = pd.read_sql_table('cached_heartbeats', self.cache_engine, parse_dates=['Received Times', 'Stamped Times']) + except: + #- Fall-through if cache does not exist; create it + self.cache_df = pd.DataFrame(columns=self.column_names) + self._last_row = pd.DataFrame(columns=self.column_names) #pd.Series(index=self.column_names) def make_entry(self, message): @@ -79,10 +120,13 @@ def make_entry(self, message): msg = {"Received Times": message["Received Times"], "Detector": message["detector_name"]} - # stamped_time_obj = datetime.fromisoformat(message["sent_time"]) + # "sent_time" in the message has the following format; + # message["sent_time"] = np.datetime_as_string(np.datetime64(datetime.utcnow().isoformat()), unit='ns') stamped_time_obj = np.datetime64(message["sent_time"]) msg["Stamped Times"] = stamped_time_obj msg["Latency"] = msg["Received Times"] - msg["Stamped Times"] + # keep latency as integer seconds + msg["Latency"] = msg["Latency"].astype('timedelta64[s]').astype(int) # check the last message of given detector detector_df = self.cache_df[self.cache_df["Detector"] == msg['Detector']] @@ -99,121 +143,23 @@ def make_entry(self, message): else: self.cache_df = pd.concat([self.cache_df, self._last_row], ignore_index=True) - def store_beats(self): - """ log the heartbeats, and save locally - - """ - # for now store one master csv in any case - self.store_master_csv() - if self.store: - self.dump_csv() - self.dump_JSON() - def drop_old_messages(self): - """ Keep the heartbeats for 24 hours - Drop the earlier-than-24hours messages from cache - - """ - # first store a csv/JSON before dumping anything - # self.store_beats() - curr_time = datetime.utcnow() - existing_times = self.cache_df["Received Times"] - del_t = (curr_time - existing_times).dt.total_seconds() / 60 / 60 # in hours - locs = np.where(del_t < self.stash_time)[0] # keep only times within stash time e.g. 24 hours - self.cache_df = self.cache_df.reset_index(drop=True).loc[locs] - self.cache_df.sort_values(by=['Received Times'], inplace=True) - - def update_cache_csv(self): - """ The daily csv file is kept as a file per day - For heartbeat checks I need one that mirrors the current cache. + """ Keep the heartbeats for a time period delta. + Drop the earlier messages from cache """ - self.drop_old_messages() - self.cache_df.to_csv(mirror_csv, mode='w', header=True, index=False) + delta = f'{self.delete_after} day' - def dump_csv(self): - """ dump a local csv file once a day - and keep appending the messages within that day - into the same csv file + curr_time = np.datetime64(datetime.utcnow().isoformat()) #pd.to_datetime('now', utc=True) + delta_t = curr_time - pd.to_datetime(self.cache_df['Received Times']) + select = delta_t < pd.Timedelta(delta) - Note: - This is a temporary back up of the data. Ideally, we need only update_cache_csv - - """ - today = datetime.utcnow() - today_str = datetime.strftime(today, "%y-%m-%d") - output_csv_name = os.path.join(beats_path, f"{today_str}_heartbeat_log.csv") - if os.path.exists(output_csv_name): - self._last_row.to_csv(output_csv_name, mode='a', header=False, index=False) - else: - self.cache_df.to_csv(output_csv_name, mode='w', header=True, index=False) - - def dump_JSON(self): - """ dump a local JSON file once a day - and keep appending the messages within that day - into the same csv file - - Notes: - It is risky at the moment as I overwrite each time instead - Ideally we should compare the existing json file with the new one - and append the new ones. If the script is re-run in the same day, - current version would ignore the previous logs and overwrite a new one - - """ - # TODO: maybe not needed? - # df = get_data_strings(self.cache_df) # the object types need to be converted for json - # curr_data = df.to_json(orient='columns') - curr_data = self.cache_df.to_json(orient='columns') - today = datetime.utcnow() - today_str = datetime.strftime(today, "%y-%m-%d") - output_json_name = os.path.join(beats_path, f"{today_str}_heartbeat_log.json") - # if os.path.exists(output_json_name): - with open(output_json_name, 'w') as file: - # file_data = json.load(file) - # # append missing keys? - # OVERWRITE INSTEAD - file.seek(0) - json.dump(curr_data, file, indent=4) - - def store_master_csv(self): - """ For now, also keep a csv that doesn't distinguish dates - Append and save everything - - """ - if os.path.exists(master_csv): - self._last_row.to_csv(master_csv, mode='a', header=False, index=False) - else: - self.cache_df.to_csv(master_csv, mode='w', header=True, index=False) - - def burn_logs(self): - """ Remove the logs after pre-decided time + self.cache_df = self.cache_df[select] + self.cache_df.sort_values(by=['Received Times'], inplace=True) + def update_cache(self): + """Update the alert cache with whatever we decided to keep. """ - today_fulldate = datetime.utcnow() - today_str = datetime.strftime(today_fulldate, "%y-%m-%d") - today = datetime.strptime(today_str, "%y-%m-%d") - existing_logs = os.listdir(beats_path) - if self.store: - existing_logs = np.array([x for x in existing_logs if (x.endswith('log.json') or x.endswith('log.csv')) and - ("complete_heartbeat_log.csv" not in x)]) - - # take only dates - dates_str = [i.split('/')[-1].split("_heartbeat")[0] for i in existing_logs] - dates, files = [], [] - for d_str, logfile in zip(dates_str, existing_logs): - try: - dates.append(datetime.strptime(d_str, "%y-%m-%d")) - files.append(logfile) - except: - continue - - time_differences = np.array([(date - today).days for date in dates]) - older_than_limit = np.where(np.abs(time_differences) > self.delete_after) - files = np.array(files) - log.debug(f"\t> The following logs are older than {self.delete_after} days and will be removed; \n{files[older_than_limit[0]]}") - for file in files[older_than_limit[0]]: - filepath = os.path.join(beats_path, file) - os.remove(filepath) - log.debug(f"\t> {file} deleted.") + self.cache_df.to_sql('cached_heartbeats', self.cache_engine, if_exists='replace', index=False) def display_table(self): """ When printed out, these table can be read from the purdue servers @@ -222,44 +168,13 @@ def display_table(self): """ print(f"\nCurrent cache \n{'=' * 133}\n{self.cache_df.to_markdown()}\n{'=' * 133}\n") - - def sanity_checks(self, message): - """ check if the message will crash the server - Check the following - - detector frequencies are reasonable - - latencies are reasonable - - At least one detector is operational - """ - issue = "no issue" - for key in ['detector_name', 'detector_status']: - if key not in message.keys(): - issue = f" {key} is not in message keys" - if issue == "no issue": - if not isinstance(message['Received Times'], np.datetime64): - issue = f" {message['Received Times']} is not a np.datetime64 object" - if not message['detector_status'].lower() in ['on','off']: - issue = f" {message['detector_status']} is neither ON nor OFF" - if not message['detector_name'] in snews_detectors: - issue = f" {message['detector_name']} is not a valid detector" - - if issue == "no issue": - # do not log each time - return True - else: - log.error(f"\t> {message} is received at snews_hb.py but not valid.\n" - f"issue is: {issue}") - return False - - def electrocardiogram(self, message): try: - message["Received Times"] = np.datetime64('now', 'ns') #np.datetime_as_string(np.datetime64('now'), unit='ns') - if self.sanity_checks(message): + message["Received Times"] = np.datetime64(datetime.utcnow().isoformat()) #pd.to_datetime('now', utc=True) + if sanity_checks(message): self.make_entry(message) - self.store_beats() - self.update_cache_csv() - # self.drop_old_messages() - self.burn_logs() + self.update_cache() + self.drop_old_messages() # if all successful, return True. Not logging each time, not to overcrowd return True else: