diff --git a/docs/source/jwql_monitors.rst b/docs/source/jwql_monitors.rst index 3d2d6feac..0d37eb25a 100644 --- a/docs/source/jwql_monitors.rst +++ b/docs/source/jwql_monitors.rst @@ -2,6 +2,12 @@ jwql_monitors ************* +monitor_cron_jobs.py +-------------------- +.. automodule:: jwql.jwql_monitors.monitor_cron_jobs + :members: + :undoc-members: + monitor_filesystem.py --------------------- .. automodule:: jwql.jwql_monitors.monitor_filesystem diff --git a/environment.yml b/environment.yml index 9215b3c19..f640cfda4 100644 --- a/environment.yml +++ b/environment.yml @@ -1,15 +1,15 @@ name: jwql channels: -- defaults - http://ssb.stsci.edu/astroconda-dev +- defaults dependencies: -- astropy=4.0 +- astropy - astroquery=0.3.8 - bokeh=1.0.1 - django=2.1.2 - ipython=6.4.0 - jinja2=2.10 -- jwst=0.7.8rc9 +- jwst - matplotlib=2.1.1 - numpy=1.14.0 - numpydoc=0.8.0 diff --git a/jwql/jwql_monitors/monitor_cron_jobs.py b/jwql/jwql_monitors/monitor_cron_jobs.py new file mode 100644 index 000000000..6b5c6de95 --- /dev/null +++ b/jwql/jwql_monitors/monitor_cron_jobs.py @@ -0,0 +1,326 @@ +#! /usr/bin/env python + +"""This module monitors the status of the ``jwql`` monitors via their +log files. Basic results (e.g. ``success``, ``failure``) are collected +and placed in a ``bokeh`` table for display on the web app. + +Authors +------- + + - Bryan Hilbert + +Use +--- + + This module can be executed as such: + + :: + + from jwql.jwql_monitors import monitor_cron_jobs + monitor_cron_jobs.status() + +Dependencies +------------ + + The user must have a configuration file named ``config.json`` + placed in the ``utils`` directory. +""" + +from datetime import datetime +import logging +import numpy as np +import os +import time + +from bokeh.io import save, output_file +from bokeh.models import ColumnDataSource +from bokeh.models.widgets import DataTable, DateFormatter, HTMLTemplateFormatter, TableColumn + +from jwql.utils.logging_functions import configure_logging, log_info, log_fail +from jwql.utils.permissions import set_permissions +from jwql.utils.utils import get_config + + +def create_table(status_dict): + """Create interactive ``bokeh`` table containing the logfile status + results. + + Parameters + ---------- + status_dict : dict + Nested dictionary with status results from all logfiles + """ + # Rearrange the nested dictionary into a non-nested dict for the table + filenames = [] + dates = [] + missings = [] + results = [] + for key in status_dict: + filenames.append(status_dict[key]['logname']) + dates.append(datetime.fromtimestamp(status_dict[key]['latest_time'])) + missings.append(str(status_dict[key]['missing_file'])) + results.append(status_dict[key]['status']) + + # div to color the boxes in the status column + success_template = """ +
; + color: white"> + <%= value %>
+ """ + + # div to color the boxes in the column for possibly late logfiles + missing_template = """ +
; + color: white"> + <%= value %>
+ """ + success_formatter = HTMLTemplateFormatter(template=success_template) + missing_formatter = HTMLTemplateFormatter(template=missing_template) + + data = dict(name=list(status_dict.keys()), filename=filenames, date=dates, missing=missings, + result=results) + source = ColumnDataSource(data) + + datefmt = DateFormatter(format="RFC-2822") + columns = [ + TableColumn(field="name", title="Monitor Name", width=200), + TableColumn(field="filename", title="Most Recent File", width=350), + TableColumn(field="date", title="Most Recent Time", width=200, formatter=datefmt), + TableColumn(field="missing", title="Possible Missing File", width=200, formatter=missing_formatter), + TableColumn(field="result", title="Status", width=100, formatter=success_formatter), + ] + data_table = DataTable(source=source, columns=columns, width=800, height=280, index_position=None) + + # Get output directory for saving the table files + output_dir = get_config()['outputs'] + output_filename = 'cron_status_table' + + # Save full html + html_outfile = os.path.join(output_dir, 'monitor_cron_jobs', '{}.html'.format(output_filename)) + output_file(html_outfile) + save(data_table) + try: + set_permissions(html_outfile) + except PermissionError: + logging.warning('Unable to set permissions for {}'.format(html_outfile)) + logging.info('Saved Bokeh full HTML file: {}'.format(html_outfile)) + + +def find_latest(logfiles): + """Given a list of log files in a directory, identify the most + recent. The way that ``jwql.utils.logging_functions.make_log_file`` + is set up, log files for all monitors are guaranteed to be the name + of the monitor followed by the datetime that they were run, so we + should be able to simply sort the filenames and the last will be the + most recent. + + Parameters + ---------- + logfiles : list + List of logfiles in the directory + + Returns + ------- + latest : str + Filename of the most recent file + + latest_time : float + Time associated with the most recent log file + """ + latest = sorted(logfiles)[-1] + latest_time = os.path.getctime(latest) + return (latest, latest_time) + + +def get_cadence(filenames): + """Calculate the cadence of the log files in a given directory. + Use timestamps + + Parameters + --------- + filenames : list + List of log files to examine + + Returns + ------- + mean_delta : float + Mean time in seconds between the appearance of consecutive log + files + + stdev_delta : float + Standard deviation in seconds between the appearance of + consecutive log files + """ + minimum_log_num = 3 # Set to a low value for now since we don't have many logfiles + times = [os.path.getctime(filename) for filename in filenames] + if len(times) >= minimum_log_num: + sorted_times = np.array(sorted(times)) + delta_times = sorted_times[1:] - sorted_times[0:-1] + mean_delta = np.mean(delta_times) + stdev_delta = np.std(delta_times) + else: + # If there are < minimum_log_num logfiles, then let's assume we can't + # get a reliable measure of cadence. Fall back to a value of + # 1 year between files, to avoid accidentally flagging this monitor + # as running late in the subsequent check + mean_delta = 31556736.0 # sec per year + stdev_delta = 31556736.0 # sec per year + return mean_delta, stdev_delta + + +def missing_file_check(avg_time_between, uncertainty, latest_file): + """Given the name of the most recent log file, along with the + historical average time between files and the stdev of the time + between files, determine whether we expect a more recent log file + than the file given. This could hint at a problem with the cron job + used to create the log files. + + Parameters + ---------- + avg_time_between : float + Average number of seconds between log files + + uncertainty : float + Standard deviation of the number of seconds between log files + + latest_file : str + Name of the most recent log file + + Returns + ------- + late : bool + True = We expect a more recent file than that given + False = It is reasonable that the file given is the most + recent + """ + latest_time = os.path.getctime(latest_file) + now = time.time() + time_since_latest = now - latest_time + if time_since_latest > (avg_time_between + 3 * uncertainty): + late = True + else: + late = False + return late + + +@log_fail +@log_info +def status(production_mode=True): + """Main function: determine the status of the instrument montiors + by examining log files. + + Parameters + ---------- + production_mode : bool + If ``True``, look in the main log directory. If ``False``, look + in the ``dev`` log file directory. + + Returns + ------- + logfile_status : dict + Nested dictionary containing the status for all monitors. Top + level keys include all monitors. Within a given monitor, the + value is a dictionary containing 'missing_file' and 'status' + keys. 'missing_file' is a boolean describing whether or not + there is a suspected missing log file based on the timestamps + of the existing files. 'status' is a string that is either + 'success' or 'failure'. + """ + # Begin logging + logging.info("Beginning cron job status monitor") + + # Get main logfile path + log_path = get_config()['log_dir'] + + # If we are in development mode, the log files are in a slightly + # different location than in production mode + if not production_mode: + log_path = os.path.join(log_path, 'dev') + + # Set up a dictionary to keep track of results + logfile_status = {} + + # Get a list of the directories under the main logging directory. + generator = os.walk(log_path, topdown=True) + + # Loop over monitors + for subdir, subsubdir, filenames in generator: + # When running in production mode, skip the 'dev' subdirectory, + # as it contains the development version of the monitor logs + if production_mode: + subsubdir[:] = [dirname for dirname in subsubdir if dirname != 'dev'] + + if len(filenames) > 0: + monitor_name = subdir.split('/')[-1] + + # Avoid monitor_cron_jobs itseft + if monitor_name != 'monitor_cron_jobs': + + log_file_list = [os.path.join(subdir, filename) for filename in filenames] + + # Find the cadence of the monitor + delta_time, stdev_time = get_cadence(log_file_list) + + # Identify the most recent log file + latest_log, latest_log_time = find_latest(log_file_list) + + # Check to see if we expect a file more recent than the latest + missing_file = missing_file_check(delta_time, stdev_time, latest_log) + if missing_file: + logging.warning('Expected a more recent {} logfile than {}' + .format(monitor_name, os.path.basename(latest_log))) + + # Check the file for success/failure + result = success_check(latest_log) + logging.info('{}: Latest log file indicates {}'.format(monitor_name, result)) + + # Add results to the dictionary + logfile_status[monitor_name] = {'logname': os.path.basename(latest_log), + 'latest_time': latest_log_time, + 'missing_file': missing_file, 'status': result} + + # Create table of results using Bokeh + create_table(logfile_status) + logging.info('Cron job status monitor completed successfully.') + + +def success_check(filename): + """Parse the given log file and check whether the script execution + was successful or not + + Parameters + ---------- + filename : str + Name of the log file to parse + + Returns + ------- + execution : str + ``success`` or ``failure`` + """ + with open(filename, 'r') as file_obj: + all_lines = file_obj.readlines() + final_line = all_lines[-1] + if 'complete' in final_line.lower(): + execution = 'success' + else: + execution = 'failure' + return execution + + +if __name__ == '__main__': + + module = os.path.basename(__file__).strip('.py') + configure_logging(module, production_mode=True) + + status() diff --git a/jwql/utils/utils.py b/jwql/utils/utils.py index dc9eb1f1d..3ff27a967 100644 --- a/jwql/utils/utils.py +++ b/jwql/utils/utils.py @@ -78,7 +78,6 @@ def get_config(): settings : dict A dictionary that holds the contents of the config file. """ - with open(os.path.join(__location__, 'config.json'), 'r') as config_file: settings = json.load(config_file) diff --git a/jwql/website/apps/jwql/data_containers.py b/jwql/website/apps/jwql/data_containers.py index fe06bc646..bafa1b5e5 100644 --- a/jwql/website/apps/jwql/data_containers.py +++ b/jwql/website/apps/jwql/data_containers.py @@ -28,6 +28,7 @@ from astroquery.mast import Mast import numpy as np +from jwql.jwql_monitors import monitor_cron_jobs from jwql.utils.preview_image import PreviewImage from jwql.utils.utils import get_config, filename_parser, MONITORS @@ -90,13 +91,15 @@ def get_all_proposals(): def get_dashboard_components(): - """Build and return a dictionary containing components needed for - the dashboard. + """Build and return dictionaries containing components and html + needed for the dashboard. Returns ------- dashboard_components : dict A dictionary containing components needed for the dashboard. + dashboard_components : dict + A dictionary containing full HTML needed for the dashboard. """ output_dir = get_config()['outputs'] @@ -110,27 +113,41 @@ def get_dashboard_components(): 'filecount': 'Total File Counts', 'system_stats': 'System Statistics'} + # Exclude monitors that can't be saved as components + exclude_list = ['monitor_cron_jobs'] + + # Run the cron job monitor to produce an updated table + monitor_cron_jobs.status(production_mode=True) + + # Build dictionary of components dashboard_components = {} for dir_name, subdir_list, file_list in os.walk(output_dir): monitor_name = os.path.basename(dir_name) - dashboard_components[name_dict[monitor_name]] = {} - for fname in file_list: - if 'component' in fname: - full_fname = '{}/{}'.format(monitor_name, fname) - plot_name = fname.split('_component')[0] - - # Get the div - html_file = full_fname.split('.')[0] + '.html' - with open(os.path.join(output_dir, html_file)) as f: - div = f.read() - - # Get the script - js_file = full_fname.split('.')[0] + '.js' - with open(os.path.join(output_dir, js_file)) as f: - script = f.read() - dashboard_components[name_dict[monitor_name]][name_dict[plot_name]] = [div, script] - - return dashboard_components + if monitor_name not in exclude_list: + dashboard_components[name_dict[monitor_name]] = {} + for fname in file_list: + if 'component' in fname: + full_fname = '{}/{}'.format(monitor_name, fname) + plot_name = fname.split('_component')[0] + + # Get the div + html_file = full_fname.split('.')[0] + '.html' + with open(os.path.join(output_dir, html_file)) as f: + div = f.read() + + # Get the script + js_file = full_fname.split('.')[0] + '.js' + with open(os.path.join(output_dir, js_file)) as f: + script = f.read() + dashboard_components[name_dict[monitor_name]][name_dict[plot_name]] = [div, script] + + # Add HTML that cannot be saved as components to the dictionary + with open(os.path.join(output_dir, 'monitor_cron_jobs', 'cron_status_table.html')) as f: + cron_status_table_html = f.read() + dashboard_html = {} + dashboard_html['Cron Job Monitor'] = cron_status_table_html + + return dashboard_components, dashboard_html def get_filenames_by_instrument(instrument): diff --git a/jwql/website/apps/jwql/templates/base.html b/jwql/website/apps/jwql/templates/base.html index 783414e5f..bcf679994 100644 --- a/jwql/website/apps/jwql/templates/base.html +++ b/jwql/website/apps/jwql/templates/base.html @@ -19,8 +19,8 @@ - - + + {% block preamble %} diff --git a/jwql/website/apps/jwql/templates/dashboard.html b/jwql/website/apps/jwql/templates/dashboard.html index a956c434d..0250fd416 100644 --- a/jwql/website/apps/jwql/templates/dashboard.html +++ b/jwql/website/apps/jwql/templates/dashboard.html @@ -5,7 +5,7 @@ Dashboard - JWQL - + {% for monitor_name, plots in dashboard_components.items() %} {% for plot_name, components in plots.items() %} {{ components[1] | safe}} @@ -21,6 +21,14 @@

JWQL Dashboard

+ +
+ {% for monitor_name, plot in dashboard_html.items() %} + {{ plot | safe }} + {% endfor %} +
+ +
{% for monitor_name, plots in dashboard_components.items() %} diff --git a/jwql/website/apps/jwql/templates/filesystem_monitor_full.html b/jwql/website/apps/jwql/templates/filesystem_monitor_full.html index 5145f4221..02043c0af 100755 --- a/jwql/website/apps/jwql/templates/filesystem_monitor_full.html +++ b/jwql/website/apps/jwql/templates/filesystem_monitor_full.html @@ -5,9 +5,9 @@ Bokeh Plot - + - + @@ -33,7 +33,7 @@ (function() { var fn = function() { Bokeh.safely(function() { - var docs_json = 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return render(request, template, context) @@ -215,7 +216,7 @@ def instrument(request, inst): doc_url = url_dict[inst] - context = {'inst': inst, + context = {'inst': inst, 'tools': MONITORS, 'doc_url': doc_url}