# coding=utf-8
import StringIO
import datetime
import gzip
import json
import logging
import random
import tarfile
import time
import urllib
from csv import writer as csv_writer
from math import sqrt
from os import environ, remove as removefile
from os.path import isfile, join, abspath, dirname
from dateutil.relativedelta import relativedelta
from flask import Flask
from flask import request
from flask import url_for, send_from_directory, abort as abort_flask
from jinja2 import Environment, FileSystemLoader, Markup
from netCDF4 import Dataset, date2num
from yaml import load as yaml_load
# PATH RELATIVITY #############################################################
THIS_DIRECTORY = dirname(abspath(__file__))
def get_path(relative_path):
"""Get an absolute path from the relative path to this script directory."""
return abspath(join(THIS_DIRECTORY, relative_path))
# COLLECT GLOBAL INFORMATION FROM SOURCES #####################################
# VERSION
with open(get_path('../VERSION'), 'r') as version_file:
version = version_file.read().strip()
# CONFIG
with open(get_path('../config.yml'), 'r') as config_file:
config = yaml_load(config_file.read())
FILE_DATE_FMT = "%Y-%m-%dT%H:%M:%S"
# LOGGING #####################################################################
LOG_FILE = get_path('run.log')
log = logging.getLogger("HelioPropa")
log.setLevel(logging.DEBUG)
# log.setLevel(logging.ERROR) # <-- set log level here !
logHandler = logging.FileHandler(LOG_FILE)
logHandler.setFormatter(logging.Formatter(
"%(asctime)s - %(levelname)s - %(message)s"
))
log.addHandler(logHandler)
# HARDCODED CONFIGURATION #####################################################
# Absolute path to the installed CDF library from https://cdf.gsfc.nasa.gov/
CDF_LIB = '/usr/local/lib/libcdf'
# Absolute path to the data cache directory
CACHE_DIR = get_path('../cache')
# These two configs are not in the YAML config because adding a new parameter
# will not work as-is, you'd have to edit some netcdf-related code.
# The slugs of the available parameters in the generated CSV files.
# The order matters. If you change this you also need to change the
# innermost loop of `get_data_for_target`.
# The javascript knows the targets' properties under these names.
PROPERTIES = ('time', 'vrad', 'vtan', 'vtot', 'btan', 'temp', 'pdyn', 'dens',
'atse', 'xhee', 'yhee')
# The parameters that the users can handle.
# The slug MUST be one of the properties above.
PARAMETERS = {
'pdyn': {
'slug': 'pdyn',
'name': 'Dyn. Pressure',
'title': 'The dynamic pressure.',
'units': 'nPa',
'active': True,
'position': 10,
},
'vtot': {
'slug': 'vtot',
'name': 'Velocity',
'title': 'The velocity of the particles.',
'units': 'km/s',
'active': False,
'position': 20,
},
'btan': {
'slug': 'btan',
'name': 'B Tangential',
'title': 'B Tangential.',
'units': 'nT',
'active': False,
'position': 30,
},
'temp': {
'slug': 'temp',
'name': 'Temperature',
'title': 'The temperature.',
'units': 'eV',
'active': False,
'position': 40,
},
'dens': {
'slug': 'dens',
'name': 'Density',
'title': 'The density N.',
'units': 'cm^-3',
'active': False,
'position': 50,
},
'atse': {
'slug': 'atse',
'name': 'Angle T-S-E',
'title': 'Angle Target-Sun-Earth.',
'units': 'deg',
'active': False,
'position': 60,
},
}
# SETUP FLASK ENGINE ##########################################################
app = Flask(__name__, root_path=THIS_DIRECTORY)
app.debug = environ.get('DEBUG') == 'true'
if app.debug:
log.info("Starting Flask app IN DEBUG MODE...")
else:
log.info("Starting Flask app...")
# SETUP JINJA2 TEMPLATE ENGINE ################################################
def static_global(filename):
return url_for('static', filename=filename)
def shuffle_filter(seq):
"""
This shuffles the sequence it is applied to.
Jinja2 _should_ provide this.
"""
try:
result = list(seq)
random.shuffle(result)
return result
except:
return seq
def markdown_filter(value, nl2br=False, p=True):
"""
Converts markdown into html.
nl2br: set to True to replace line breaks with
tags
p: set to False to remove the enclosing
", "").replace(r"
", "") return markdowned _js_escapes = { '\\': '\\u005C', '\'': '\\u0027', '"': '\\u0022', '>': '\\u003E', '<': '\\u003C', '&': '\\u0026', '=': '\\u003D', '-': '\\u002D', ';': '\\u003B', u'\u2028': '\\u2028', u'\u2029': '\\u2029' } # Escape every ASCII character with a value less than 32. _js_escapes.update(('%c' % z, '\\u%04X' % z) for z in xrange(32)) def escapejs_filter(value): escaped = [] for letter in value: if letter in _js_escapes: escaped.append(_js_escapes[letter]) else: escaped.append(letter) return Markup("".join(escaped)) tpl_engine = Environment(loader=FileSystemLoader([get_path('view')]), trim_blocks=True, lstrip_blocks=True) tpl_engine.globals.update( url_for=url_for, static=static_global, ) tpl_engine.filters['markdown'] = markdown_filter tpl_engine.filters['md'] = markdown_filter tpl_engine.filters['shuffle'] = shuffle_filter tpl_engine.filters['escapejs'] = escapejs_filter tpl_global_vars = { 'request': request, 'version': version, 'config': config, 'now': datetime.datetime.now(), } # HELPERS ##################################################################### def abort(code, message): log.error(message) abort_flask(code, message) def render_view(view, context=None): """ A simple helper to render [view] template with [context] vars. It automatically adds the global template vars defined above, too. It returns a string, usually the HTML contents to display. """ context = {} if context is None else context return tpl_engine.get_template(view).render( dict(tpl_global_vars.items() + context.items()) ) # def render_page(page, title="My Page", context=None): # """ # A simple helper to render the md_page.html template with [context] vars & # the additional contents of `page/[page].md` in the `md_page` variable. # It automagically adds the global template vars defined above, too. # It returns a string, usually the HTML contents to display. # """ # if context is None: # context = {} # context['title'] = title # context['md_page'] = '' # with file(get_path('page/%s.md' % page)) as f: # context['md_page'] = f.read() # return tpl_engine.get_template('md_page.html').render( # dict(tpl_global_vars.items() + context.items()) # ) def is_list_in_list(needle, haystack): for n in needle: if n not in haystack: return False return True def round_time(dt=None, round_to=60): """ Round a datetime object to any time laps in seconds dt : datetime.datetime object, default now. roundTo : Closest number of seconds to round to, default 1 minute. """ if dt is None: dt = datetime.datetime.now() seconds = (dt.replace(tzinfo=None) - dt.min).seconds rounding = (seconds + round_to / 2) // round_to * round_to return dt + datetime.timedelta(0, rounding-seconds, -dt.microsecond) def datetime_from_list(time_list): """ Datetimes in retrieved CDFs are stored as lists of numbers, with DayOfYear starting at 0. We want it starting at 1 because it's what vendor parsers use, both in python and javascript. """ # Day Of Year starts at 0, but for our datetime parser it starts at 1 doy = '{:03d}'.format(int(''.join(time_list[4:7])) + 1) return datetime.datetime.strptime( "%s%s%s" % (''.join(time_list[0:4]), doy, ''.join(time_list[7:-1])), "%Y%j%H%M%S%f" ) def get_local_filename(url): """ Build the local cache filename for the distant file :param url: string :return: string """ from slugify import slugify n = len('http://') if url.startswith('https'): n += 1 s = url[n:] return slugify(s) def get_target_config(slug): for s in config['targets']: # dumb if s['slug'] == slug: return s raise Exception("No target found in configuration for '%s'." % slug) def check_target_config(slug): get_target_config(slug) def get_active_targets(): all_targets = config['targets'] return [t for t in all_targets if not ('locked' in t and t['locked'])] def retrieve_amda_netcdf(orbiter, what, started_at, stopped_at): """ Handles remote querying Myriam's API, downloading, extracting and caching the netCDF files. :param orbiter: key of the source in the YAML config :param what: either 'model' or 'orbit', a key in the config of the source :param started_at: :param stopped_at: :return: a list of local file paths to netCDF (.nc) files """ url = config['amda'].format( dataSet=what, startTime=started_at.isoformat(), stopTime=stopped_at.isoformat() ) log.info("Fetching remote gzip files list at '%s'." % url) retries = 0 success = False errors = [] remote_gzip_files = [] while not success and retries < 3: try: response = urllib.urlopen(url) remote_gzip_files = json.loads(response.read()) if not remote_gzip_files: raise Exception("Failed to fetch data at '%s'." % url) if remote_gzip_files == 'NODATASET': raise Exception("API says there's no dataset at '%s'." % url) if remote_gzip_files == 'ERROR': raise Exception("API returned an error at '%s'." % url) if remote_gzip_files == ['OUTOFTIME']: # it happens return [] # raise Exception("API says it's out of time at '%s'." % url) success = True except Exception as e: log.warn("Failed (%d/3) '%s' : %s" % (retries+1, url, e.message)) remote_gzip_files = [] errors.append(e) finally: retries += 1 if not remote_gzip_files: abort(400, "Failed to fetch gzip files list for %s at '%s' : %s" % (orbiter, url, errors)) else: remote_gzip_files = list(set(remote_gzip_files)) log.debug("Fetched remote gzip files list : %s." % str(remote_gzip_files)) local_gzip_files = [] for remote_gzip_file in remote_gzip_files: # hotfixes to remove when fixed upstream @Myriam if remote_gzip_file in ['OUTOFTIME', 'ERROR']: continue # sometimes half the response is okay, the other not if remote_gzip_file.endswith('/.gz'): continue # this is just a plain bug remote_gzip_file = remote_gzip_file.replace('cdpp1', 'cdpp', 1) ################################################ local_gzip_file = join(CACHE_DIR, get_local_filename(remote_gzip_file)) local_gzip_files.append(local_gzip_file) if not isfile(local_gzip_file): log.debug("Retrieving '%s'..." % local_gzip_file) urllib.urlretrieve(remote_gzip_file, local_gzip_file) log.debug("Retrieved '%s'." % local_gzip_file) else: log.debug("Found '%s' in the cache." % local_gzip_file) local_netc_files = [] for local_gzip_file in local_gzip_files: local_netc_file = local_gzip_file[0:-3] log.debug("Unzipping '%s'..." % local_gzip_file) success = True try: with gzip.open(local_gzip_file) as f: file_content = f.read() with open(local_netc_file, 'w+b') as g: g.write(file_content) except Exception as e: success = False log.error("Cannot process gz file '%s' from '%s' : %s" % (local_gzip_file, url, e)) # Sometimes, the downloaded gz is corrupted, and CRC checks fail. # We want to delete the local gz file and try again next time. removefile(local_gzip_file) if success: local_netc_files.append(local_netc_file) log.debug("Unzipped '%s'." % local_gzip_file) return list(set(local_netc_files)) # remove possible dupes def get_data_for_target(target_config, input_slug, started_at, stopped_at): """ :return: dict whose keys are datetime as str, values tuples of data """ log.debug("Grabbing data for '%s'..." % target_config['slug']) try: models = target_config['models'][input_slug] except Exception as e: abort(500, "Invalid model configuration for '%s' : %s" % (target_config['slug'], str(e))) try: orbits = target_config['orbit']['models'] except KeyError as e: orbits = [] # abort(500, "Invalid orbit configuration for '%s' : %s" # % (target_config['slug'], str(e))) def _sta_sto(_cnf, _sta, _sto): if 'started_at' in _cnf: _s0 = datetime.datetime.strptime(_cnf['started_at'], FILE_DATE_FMT) _s0 = max(_s0, _sta) else: _s0 = _sta if 'stopped_at' in _cnf: _s1 = datetime.datetime.strptime(_cnf['stopped_at'], FILE_DATE_FMT) _s1 = min(_s1, _sto) else: _s1 = _sto return _s0, _s1 def _read_var(_nc, _keys, _key, mandatory=False): try: return _nc.variables[_keys[_key]] except KeyError: pass if mandatory: raise Exception("No variable '%s' found in NetCDF." % _keys[_key]) return [None] * len(_nc.variables['Time']) # slow -- use numpy! # Override these using the model configuration default_nc_keys = { 'hee': 'HEE', 'vtot': 'V', 'magn': 'B', 'temp': 'T', 'dens': 'N', 'pdyn': 'P_dyn', 'atse': 'Delta_angle', } precision = "%Y-%m-%dT%H" # model and orbits times are only equal-ish orbit_data = {} # keys are datetime as str, values arrays of XY for orbit in orbits: s0, s1 = _sta_sto(orbit, started_at, stopped_at) nc_keys = default_nc_keys.copy() if 'parameters' in orbit: nc_keys.update(orbit['parameters']) orbit_files = retrieve_amda_netcdf( target_config['slug'], orbit['slug'], s0, s1 ) for orbit_file in orbit_files: log.debug("%s: opening orbit NETCDF4 '%s'..." % (target_config['name'], orbit_file)) cdf_handle = Dataset(orbit_file, "r", format="NETCDF4") times = cdf_handle.variables['Time'] # YYYY DOY HH MM SS .ms data_hee = _read_var(cdf_handle, nc_keys, 'hee', mandatory=True) log.debug("%s: aggregating data from '%s'..." % (target_config['name'], orbit_file)) for ltime, datum_hee in zip(times, data_hee): try: dtime = datetime_from_list(ltime) except Exception: log.error("Failed to parse time from %s." % ltime) raise if s0 <= dtime <= s1: dkey = round_time(dtime, 60*60).strftime(precision) orbit_data[dkey] = datum_hee cdf_handle.close() all_data = {} # keys are datetime as str, values tuples of data for model in models: s0, s1 = _sta_sto(model, started_at, stopped_at) model_files = retrieve_amda_netcdf( target_config['slug'], model['slug'], s0, s1 ) nc_keys = default_nc_keys.copy() if 'parameters' in model: nc_keys.update(model['parameters']) for model_file in model_files: log.debug("%s: opening model NETCDF4 '%s'..." % (target_config['name'], model_file)) cdf_handle = Dataset(model_file, "r", format="NETCDF4") # log.debug(cdf_handle.variables.keys()) times = cdf_handle.variables['Time'] # YYYY DOY HH MM SS .ms data_v = _read_var(cdf_handle, nc_keys, 'vtot') data_b = _read_var(cdf_handle, nc_keys, 'magn') data_t = _read_var(cdf_handle, nc_keys, 'temp') data_n = _read_var(cdf_handle, nc_keys, 'dens') data_p = _read_var(cdf_handle, nc_keys, 'pdyn') data_a = _read_var(cdf_handle, nc_keys, 'atse') # Usually: # Time, StartTime, StopTime, V, B, N, T, Delta_angle, P_dyn # Earth: # Time, BartelsNumber, ImfID, SwID, ImfPoints, # SwPoints, B_M_av, B_Vec_av, B_Theta_av, # B_Phi_av, B, T, N, V, Vlat, Vlon, # Alpha, RamP, E, Beta, Ma, Kp, R, DST, # AE, Flux, Flag, F10_Index, StartTime, StopTime log.debug("%s: aggregating data from '%s'..." % (target_config['name'], model_file)) for ltime, datum_v, datum_b, datum_t, datum_n, datum_p, datum_a \ in zip(times, data_v, data_b, data_t, data_n, data_p, data_a): try: dtime = datetime_from_list(ltime) except Exception: log.error("Failed to parse time from %s." % ltime) raise if s0 <= dtime <= s1: dkey = round_time(dtime, 60*60).strftime(precision) if hasattr(datum_v, '__len__'): vrad = datum_v[0] vtan = datum_v[1] vtot = sqrt(vrad * vrad + vtan * vtan) else: # eg: Earth vrad = None vtan = None vtot = datum_v x_hee = None y_hee = None if target_config['slug'] == 'earth': x_hee = 1 y_hee = 0 if dkey in orbit_data: x_hee = orbit_data[dkey][0] y_hee = orbit_data[dkey][1] all_data[dkey] = ( dtime.strftime("%Y-%m-%dT%H:%M:%S+00:00"), vrad, vtan, vtot, datum_b, datum_t, datum_n, datum_p, datum_a, x_hee, y_hee ) cdf_handle.close() return all_data def generate_csv_contents(target_slug, input_slug, started_at, stopped_at): target_config = get_target_config(target_slug) log.debug("Crunching CSV contents for '%s'..." % target_config['name']) si = StringIO.StringIO() cw = csv_writer(si) cw.writerow(PROPERTIES) all_data = get_data_for_target( target_config=target_config, input_slug=input_slug, started_at=started_at, stopped_at=stopped_at ) log.debug("Writing and sorting CSV for '%s'..." % target_config['slug']) for dkey in sorted(all_data): cw.writerow(all_data[dkey]) log.info("Generated CSV contents for '%s'." % target_config['slug']) return si.getvalue() def generate_csv_file_if_needed(target_slug, input_slug, started_at, stopped_at): filename = "%s_%s_%s_%s.csv" % (target_slug, input_slug, started_at.strftime(FILE_DATE_FMT), stopped_at.strftime(FILE_DATE_FMT)) local_csv_file = join(CACHE_DIR, filename) generate = True if isfile(local_csv_file): # It needs to have more than one line to not be empty (headers) with open(local_csv_file) as f: cnt = 0 for _ in f: cnt += 1 if cnt > 1: generate = False break if generate: log.info("Generating CSV '%s'..." % local_csv_file) try: with open(local_csv_file, mode="w+") as f: f.write(generate_csv_contents( target_slug=target_slug, input_slug=input_slug, started_at=started_at, stopped_at=stopped_at )) log.info("Generation of '%s' done." % filename) except Exception as e: from sys import exc_info from traceback import extract_tb exc_type, exc_value, exc_traceback = exc_info() log.error(e) for trace in extract_tb(exc_traceback): log.error(trace) if isfile(local_csv_file): log.warn("Removing failed CSV '%s'..." % local_csv_file) removefile(local_csv_file) abort(500, "Failed creating CSV '%s' : %s" % (filename, e)) def remove_all_files(in_directory): """ Will throw if something horrible happens. Does not remove recursively (could be done with os.walk if needed). Does not remove directories either. :param in_directory: absolute path to directory :return: """ import os if not os.path.isdir(in_directory): raise ValueError("No directory to clean at '%s'.") removed_files = [] for file_name in os.listdir(in_directory): file_path = os.path.join(in_directory, file_name) if os.path.isfile(file_path): os.remove(file_path) removed_files.append(file_path) return removed_files def remove_files_created_before(date, in_directory): """ Will throw if something horrible happens. Does not remove recursively (could be done with os.walk if needed). Does not remove directories either. :param date: datetime object :param in_directory: absolute path to directory :return: """ import os import time secs = time.mktime(date.timetuple()) if not os.path.isdir(in_directory): raise ValueError("No directory to clean at '%s'.") removed_files = [] for file_name in os.listdir(in_directory): file_path = os.path.join(in_directory, file_name) if os.path.isfile(file_path): t = os.stat(file_path) if t.st_ctime < secs: os.remove(file_path) removed_files.append(file_path) return removed_files def get_input_slug_from_query(inp=None): if inp is None: input_slug = request.args.get('input_slug', 'l1') else: input_slug = inp if input_slug not in [i['slug'] for i in config['inputs']]: input_slug = 'l1' # be tolerant instead of yelling loudly return input_slug def get_hit_counter(): hit_count_path = get_path("../VISITS") if isfile(hit_count_path): hit_count = int(open(hit_count_path).read()) else: hit_count = 1 return hit_count def increment_hit_counter(): hit_count_path = get_path("../VISITS") if isfile(hit_count_path): hit_count = int(open(hit_count_path).read()) hit_count += 1 else: hit_count = 1 hit_counter_file = open(hit_count_path, 'w') hit_counter_file.write(str(hit_count)) hit_counter_file.close() return hit_count tpl_global_vars['visits'] = get_hit_counter() # ROUTING ##################################################################### @app.route('/favicon.ico') def favicon(): # we want it served from the root, not from static/ return send_from_directory( join(app.root_path, 'static', 'img'), 'favicon.ico', mimetype='image/vnd.microsoft.icon' ) @app.route("/") @app.route("/home.html") @app.route("/index.html") def home(): increment_hit_counter() parameters = PARAMETERS.values() parameters.sort(key=lambda x: x['position']) input_slug = get_input_slug_from_query() return render_view('home.html.jinja2', { 'targets': config['targets'], 'parameters': parameters, 'input_slug': input_slug, 'planets': [s for s in config['targets'] if s['type'] == 'planet'], 'probes': [s for s in config['targets'] if s['type'] == 'probe'], 'comets': [s for s in config['targets'] if s['type'] == 'comet'], 'visits': get_hit_counter(), }) @app.route("/" + contents + "" @app.route("/log/clear") def log_clear(): with open(LOG_FILE, 'w') as f: f.truncate() return "Log cleared successfully." # DEV TOOLS ################################################################### # @app.route("/inspect") # def analyze_cdf(): # """ # For debug purposes. # """ # cdf_to_inspect = get_path("../res/dummy.nc") # cdf_to_inspect = get_path("../res/dummy_jupiter_coordinates.nc") # # si = StringIO.StringIO() # cw = csv.DictWriter(si, fieldnames=['Name', 'Shape', 'Length']) # cw.writeheader() # # # Time, StartTime, StopTime, V, B, N, T, Delta_angle, P_dyn, QualityFlag # cdf_handle = Dataset(cdf_to_inspect, "r", format="NETCDF4") # for variable in cdf_handle.variables: # v = cdf_handle.variables[variable] # cw.writerow({ # 'Name': variable, # 'Shape': v.shape, # 'Length': v.size, # }) # cdf_handle.close() # # return si.getvalue() # MAIN ######################################################################## if __name__ == "__main__": # Debug mode is on, as the production server does not use this but run.wsgi extra_files = [get_path('../config.yml')] app.run(debug=True, extra_files=extra_files)