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web/run.py 63.2 KB
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# coding=utf-8

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from io import StringIO
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import datetime
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import gzip
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import json
import logging
import random
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import tarfile
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import time
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import urllib.request as urllib_request
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import requests
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import re  # regex
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from csv import writer as csv_writer, DictWriter as csv_dict_writer
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from math import sqrt, isnan
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from os import environ, remove as removefile
from os.path import isfile, join, abspath, dirname

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# (i) Just ignore the requirements warning, we already require `dateutils`.
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from dateutil.relativedelta import relativedelta
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from dateutil import parser as dateparser

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from flask import Flask
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from flask import request
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from flask import url_for, send_from_directory, abort as abort_flask
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from jinja2 import Environment, FileSystemLoader
from jinja2.utils import markupsafe
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from yaml import load as yaml_load, dump
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from speasy import amda
import pandas as pd

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try:
    from yaml import CLoader as Loader
except ImportError:
    from yaml import Loader
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from netCDF4 import Dataset, date2num
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# PATH RELATIVITY #############################################################

THIS_DIRECTORY = dirname(abspath(__file__))


def get_path(relative_path):
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    """Get an absolute path from the relative path to this script directory."""
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    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
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with open(get_path('../config.yml'), 'r', encoding='utf8') as config_file:
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    config = yaml_load(config_file.read(), Loader=Loader)
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FILE_DATE_FMT = "%Y-%m-%dT%H:%M:%S"
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MOMENT_DATE_FMT = "%Y-%m-%dT%H:%M:%SZ"
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CME_DATE_FMT = "%Y-%m-%dT%H:%MZ"
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# Are we on the SSA instance for ESA?
SSA = environ.get('SSA') == 'true'
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DEBUG = environ.get('DEBUG') in ['true', 'True', 1, '1']
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# LOGGING #####################################################################

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LOG_FILE = get_path('run.log')

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hp_logger = logging.getLogger("HelioPropa")
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hp_logger.setLevel(logging.DEBUG)

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fileHandler = logging.FileHandler(LOG_FILE)
fileHandler.setFormatter(logging.Formatter(
    "%(asctime)s -  %(levelname)s - %(message)s"
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))
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# set file messages depending on env var setting
if DEBUG:
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    fileHandler.setLevel(logging.DEBUG)
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else:
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    fileHandler.setLevel(logging.ERROR)
hp_logger.addHandler(fileHandler)


def init_console_logger():
    consoleHandler = logging.StreamHandler()
    if DEBUG:
        consoleHandler.setLevel(logging.DEBUG)
    else:
        consoleHandler.setLevel(logging.ERROR)
    formatter = logging.Formatter('CONSOLE: %(levelname)s - %(message)s')
    consoleHandler.setFormatter(formatter)
    # Add handlers to the logger
    hp_logger.addHandler(consoleHandler)
    return hp_logger

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# HARDCODED CONFIGURATION #####################################################

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ASTRONOMICAL_UNIT_IN_KM = 1.496e8

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# Absolute path to the installed CDF library from https://cdf.gsfc.nasa.gov/
CDF_LIB = '/usr/local/lib/libcdf'

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# 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
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# will not work as-is, you'd have to edit some netcdf-related code.
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# 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.
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# PROPERTIES = ('time', 'vrad', 'vtan', 'vtot', 'btan', 'brad', 'temp', 'pdyn', 'dens',
#               'atse', 'xhee', 'yhee')
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PROPERTIES = ('time', 'vrad', 'vtan', 'vtot', 'btan', 'temp', 'pdyn', 'dens',
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              'atse', 'xhee', 'yhee')
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# 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,
    },
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    # 'brad': {
    #     'slug': 'brad',
    #     'name': 'B Radial',
    #     'title': 'B Radial.',
    #     'units': 'nT',
    #     'active': False,
    #     'position': 35,
    # },
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    'temp': {
        'slug': 'temp',
        'name': 'Temperature',
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        'title': 'The temperature.',
        'units': 'eV',
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        'active': False,
        'position': 40,
    },
    'dens': {
        'slug': 'dens',
        'name': 'Density',
        'title': 'The density N.',
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        'units': 'cm^-3',
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        'active': False,
        'position': 50,
    },
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    'atse': {
        'slug': 'atse',
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        'name': 'Angle T-S-E',
        'title': 'Angle Target-Sun-Earth.',
        'units': 'deg',
        'active': False,
        'position': 60,
    },
}

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# SETUP ENVIRONMENT ###########################################################
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environ['SPACEPY'] = CACHE_DIR
environ['CDF_LIB'] = CDF_LIB

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# SETUP FLASK ENGINE ##########################################################

app = Flask(__name__, root_path=THIS_DIRECTORY)
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app.debug = DEBUG
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if app.debug:
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    hp_logger.info("Starting Flask app IN DEBUG MODE...")
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else:
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    hp_logger.info("Starting Flask app...")
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def handle_error(e):
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    hp_logger.error(e)
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    return str(e)  # wish we could use the default error renderer here

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app.register_error_handler(Exception, handle_error)


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# 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.
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    Jinja2 _should_ provide this.
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    """
    try:
        result = list(seq)
        random.shuffle(result)
        return result
    except:
        return seq


def markdown_filter(value, nl2br=False, p=True):
    """
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    Converts markdown into html.
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    nl2br: set to True to replace line breaks with <br> tags
    p: set to False to remove the enclosing <p></p> tags
    """
    from markdown import markdown
    from markdown.extensions.nl2br import Nl2BrExtension
    from markdown.extensions.abbr import AbbrExtension
    extensions = [AbbrExtension()]
    if nl2br is True:
        extensions.append(Nl2BrExtension())
    markdowned = markdown(value, output_format='html5', extensions=extensions)
    if p is False:
        markdowned = markdowned.replace(r"<p>", "").replace(r"</p>", "")
    return markdowned


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_js_escapes = {
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    '\\': '\\u005C',
    '\'': '\\u0027',
    '"': '\\u0022',
    '>': '\\u003E',
    '<': '\\u003C',
    '&': '\\u0026',
    '=': '\\u003D',
    '-': '\\u002D',
    ';': '\\u003B',
    u'\u2028': '\\u2028',
    u'\u2029': '\\u2029'
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}
# Escape every ASCII character with a value less than 32.
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_js_escapes.update(('%c' % z, '\\u%04X' % z) for z in range(32))
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def escapejs_filter(value):
    escaped = []
    for letter in value:
        if letter in _js_escapes:
            escaped.append(_js_escapes[letter])
        else:
            escaped.append(letter)

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    return markupsafe.Markup("".join(escaped))
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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
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tpl_engine.filters['escapejs'] = escapejs_filter
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tpl_global_vars = {
    'request': request,
    'version': version,
    'config': config,
    'now': datetime.datetime.now(),
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    'is_esa': SSA,
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}


# HELPERS #####################################################################

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def abort(code, message):
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    hp_logger.error("Abort: " + message)
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    abort_flask(code, message)


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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(
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        dict(list(tpl_global_vars.items()) + list(context.items()))
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    )


# 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())
#     )

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def is_list_in_list(needle, haystack):
    for n in needle:
        if n not in haystack:
            return False
    return True


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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
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    return dt + datetime.timedelta(0, rounding - seconds, -dt.microsecond)
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def datetime_from_list(time_list):
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    """
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    Datetimes in retrieved CDFs are stored as lists of numbers,
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    with DayOfYear starting at 0. We want it starting at 1 because it's what
    vendor parsers use, both in python and javascript.
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    """
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    try:
        time_list = [str(i, 'UTF8') for i in time_list]
    except Exception as e:
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        hp_logger.error(e)
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    # 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(
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        "%s%s%s" % (''.join(time_list[0:4]), doy, ''.join(time_list[7:-1])),
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        "%Y%j%H%M%S%f"
    )
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# Override these using the model configuration in config.yml
default_nc_keys = {
    'hee': 'HEE',
    'vtot': 'V',
    'magn': 'B',
    'temp': 'T',
    'dens': 'N',
    'pdyn': 'P_dyn',
    'atse': 'Delta_angle',
}
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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:
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        return _nc.variables[_keys[_key]][:]
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    except KeyError:
        pass
    if mandatory:
        raise Exception("No variable '%s' found in NetCDF." % _keys[_key])
    return [None] * len(_nc.variables['Time'])  # slow -- use numpy!


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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)


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def get_target_config(slug):
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    for s in config['targets']:  # dumb
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        if s['slug'] == slug:
            return s
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    raise Exception("No target found in configuration for '%s'." % slug)
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def check_target_config(slug):
    get_target_config(slug)


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def get_active_targets():
    all_targets = config['targets']
    return [t for t in all_targets if not ('locked' in t and t['locked'])]


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def validate_tap_target_config(target):
    tc = get_target_config(target)
    if 'tap' not in tc:
        raise Exception("No `tap` configuration for target `%s`." % target)
    if 'target_name' not in tc['tap']:
        raise Exception("No `target_name` in the `tap` configuration for target `%s`." % target)
    return tc


# Using pyvo would be best.
# def retrieve_auroral_emissions_vopy(target_name):
#     api_url = "http://voparis-tap.obspm.fr/__system__/tap/run/tap/sync"
#     import pyvo as vo
#     service = vo.dal.TAPService(api_url)
#     # … can't figure out how to install pyvo and spacepy alongside (forking?)


def retrieve_auroral_emissions(target_name, d_started_at=None, d_stopped_at=None):
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    """
    Work In Progress.
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    :param target_name: You should probably not let users define this value,
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                        as our sanitizing for ADQL may not be 100% safe.
                        Use values from YAML configuration, instead.
                        Below is a list of the ids we found to be existing.
                        > SELECT DISTINCT target_name FROM apis.epn_core
7176ae9b   Goutte   Fix Myriam's cont...
463
464
                        - Jupiter
                        - Saturn
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465
466
                        - Mars
                        - MERCURY
9f57dceb   Goutte   Add half the brid...
467
468
469
470
471
472
473
                        - Titan
                        - Io
                        - VENUS
                        - Ganymede
                        - Uranus
                        - Callisto
                        - Europa
7176ae9b   Goutte   Fix Myriam's cont...
474
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476
477
478
479
                        
                        https://pdssbn.astro.umd.edu/holdings/nh-p-rex-2-pluto-v1.0/document/codmac_level_definitions.pdf
                        processing_level == 3
                        
                        API doc and sandbox:
                        http://voparis-tap-planeto.obspm.fr/__system__/tap/run/info
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    :return: 
    """
11d86851   Goutte   Add support for s...
482
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    # Try out the form
    # http://voparis-tap-planeto.obspm.fr/__system__/adql/query/form

9f57dceb   Goutte   Add half the brid...
486
    api_url = "http://voparis-tap.obspm.fr/__system__/tap/run/tap/sync"
11d86851   Goutte   Add support for s...
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    if d_started_at is None:
        d_started_at = datetime.datetime.now()
        t_started_at = time.mktime(d_started_at.timetuple()) - 3600 * 24 * 365 * 2
        # t_started_at = 1
    else:
        t_started_at = time.mktime(d_started_at.timetuple())

    if d_stopped_at is None:
        d_stopped_at = datetime.datetime.now()
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    t_stopped_at = time.mktime(d_stopped_at.timetuple())

11d86851   Goutte   Add support for s...
498
    def timestamp_to_jday(timestamp):
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499
500
        return timestamp / 86400.0 + 2440587.5

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501
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509
    def jday_to_timestamp(jday):
        return (jday - 2440587.5) * 86400.0

    def jday_to_datetime(jday):
        return datetime.datetime.utcfromtimestamp(jday_to_timestamp(jday))

    # SELECT DISTINCT dataproduct_type FROM apis.epn_core
    # > im sp sc

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    query = """
SELECT
  time_min,
  time_max,
  thumbnail_url,
  external_link
FROM apis.epn_core
WHERE target_name='{target_name}'
AND   dataproduct_type='im'
11d86851   Goutte   Add support for s...
519
520
AND   time_min >= {jday_start}
AND   time_min <= {jday_stop}
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521
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523
ORDER BY time_min, granule_gid
""".format(
        target_name=target_name.replace("'", "\\'"),
11d86851   Goutte   Add support for s...
524
525
        jday_start=timestamp_to_jday(t_started_at),
        jday_stop=timestamp_to_jday(t_stopped_at)
9f57dceb   Goutte   Add half the brid...
526
    )
95155804   hitier   Reformat code
527
    # AND   processing_level = 4
9f57dceb   Goutte   Add half the brid...
528

95155804   hitier   Reformat code
529
530
531
    #     query = """
    # SELECT DISTINCT target_name FROM apis.epn_core
    # """
9f57dceb   Goutte   Add half the brid...
532
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    try:
        response = requests.post(api_url, {
            'REQUEST': 'doQuery',
34e94ae3   hitier   Code reformating
536
537
            'LANG': 'ADQL',
            'QUERY': query,
9f57dceb   Goutte   Add half the brid...
538
            'TIMEOUT': '30',
34e94ae3   hitier   Code reformating
539
            'FORMAT': 'VOTable/td'
9f57dceb   Goutte   Add half the brid...
540
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        })

        response_xml = response.text

        import xml.etree.ElementTree as ET
        root = ET.fromstring(response_xml)
        namespaces = {'vo': 'http://www.ivoa.net/xml/VOTable/v1.3'}
        rows_xpath = "./vo:RESOURCE/vo:TABLE/vo:DATA/vo:TABLEDATA/vo:TR"
        rows = []
        for row in root.findall(rows_xpath, namespaces):
            rows.append({
11d86851   Goutte   Add support for s...
551
552
                'time_min': jday_to_datetime(float(row[0].text)),
                'time_max': jday_to_datetime(float(row[1].text)),
9f57dceb   Goutte   Add half the brid...
553
554
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                'thumbnail_url': row[2].text,
                'external_link': row[3].text,
            })

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        return rows
    except Exception as e:
        print("Failed to retrieve auroral emissions :")
        print(e)

    # print(query)


180d7d97   Goutte   Refactor heavily.
565
def retrieve_amda_netcdf(orbiter, what, started_at, stopped_at):
8644387c   Goutte   Use real data.
566
    """
91c3d52d   Goutte   Add more logs.
567
568
    Handles remote querying AMDA's API for URLs, and then downloading,
    extracting and caching the netCDF files.
8644387c   Goutte   Use real data.
569
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    :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()
    )
89c56528   hitier   Rename heliopropa...
581
    hp_logger.info("Fetching remote gzip files list at '%s'." % url)
b2837a08   Goutte   Add three retries...
582
583
    retries = 0
    success = False
92abc15b   Goutte   Mistrust the API ...
584
    errors = []
b2837a08   Goutte   Add three retries...
585
586
587
    remote_gzip_files = []
    while not success and retries < 3:
        try:
3f9c36da   hitier   Change urllib import
588
            response = urllib_request.urlopen(url)
b2837a08   Goutte   Add three retries...
589
590
591
592
            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':
92abc15b   Goutte   Mistrust the API ...
593
594
595
                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)
077980eb   Goutte   Improve availabil...
596
            if remote_gzip_files == ['OUTOFTIME']:  # it happens
80352490   Goutte   Multi model suppo...
597
598
                return []
                # raise Exception("API says it's out of time at '%s'." % url)
b2837a08   Goutte   Add three retries...
599
600
            success = True
        except Exception as e:
89c56528   hitier   Rename heliopropa...
601
            hp_logger.warning("Failed (%d/3) '%s' : %s" % (retries + 1, url, e.message))
92abc15b   Goutte   Mistrust the API ...
602
603
            remote_gzip_files = []
            errors.append(e)
b2837a08   Goutte   Add three retries...
604
605
606
        finally:
            retries += 1
    if not remote_gzip_files:
89c56528   hitier   Rename heliopropa...
607
608
609
        hp_logger.error("Failed to retrieve data from AMDA.")
        hp_logger.error("Failed to fetch gzip files list for %s at '%s' : %s" %
                        (orbiter, url, errors))
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610
        abort(400, "Failed to fetch gzip files list for %s at '%s' : %s" %
34e94ae3   hitier   Code reformating
611
              (orbiter, url, errors))
08abc2d4   Goutte   Remove duplicate ...
612
613
    else:
        remote_gzip_files = list(set(remote_gzip_files))
9bfa6c42   Goutte   More bug hunting.
614

89c56528   hitier   Rename heliopropa...
615
    hp_logger.debug("Fetched remote gzip files list : %s." % str(remote_gzip_files))
8644387c   Goutte   Use real data.
616

8644387c   Goutte   Use real data.
617
618
    local_gzip_files = []
    for remote_gzip_file in remote_gzip_files:
077980eb   Goutte   Improve availabil...
619
620
621
        # hotfixes to remove when fixed upstream @Myriam
        if remote_gzip_file in ['OUTOFTIME', 'ERROR']:
            continue  # sometimes half the response is okay, the other not
8644387c   Goutte   Use real data.
622
        if remote_gzip_file.endswith('/.gz'):
80352490   Goutte   Multi model suppo...
623
            continue  # this is just a plain bug
8644387c   Goutte   Use real data.
624
        remote_gzip_file = remote_gzip_file.replace('cdpp1', 'cdpp', 1)
077980eb   Goutte   Improve availabil...
625
        ################################################
e18701b6   Goutte   Cache clear (remo...
626
        local_gzip_file = join(CACHE_DIR, get_local_filename(remote_gzip_file))
8644387c   Goutte   Use real data.
627
628
        local_gzip_files.append(local_gzip_file)
        if not isfile(local_gzip_file):
89c56528   hitier   Rename heliopropa...
629
            hp_logger.debug("Retrieving '%s'..." % local_gzip_file)
3f9c36da   hitier   Change urllib import
630
            urllib_request.urlretrieve(remote_gzip_file, local_gzip_file)
89c56528   hitier   Rename heliopropa...
631
            hp_logger.debug("Retrieved '%s'." % local_gzip_file)
dc0be992   Goutte   Support having no...
632
        else:
89c56528   hitier   Rename heliopropa...
633
            hp_logger.debug("Found '%s' in the cache." % local_gzip_file)
8644387c   Goutte   Use real data.
634
635
636
637

    local_netc_files = []
    for local_gzip_file in local_gzip_files:
        local_netc_file = local_gzip_file[0:-3]
89c56528   hitier   Rename heliopropa...
638
        hp_logger.debug("Unzipping '%s'..." % local_gzip_file)
3c064b17   Goutte   Ignore failures w...
639
640
        success = True
        try:
5ef50583   Goutte   Clean up.
641
            with gzip.open(local_gzip_file) as f:
3c064b17   Goutte   Ignore failures w...
642
643
644
645
646
                file_content = f.read()
                with open(local_netc_file, 'w+b') as g:
                    g.write(file_content)
        except Exception as e:
            success = False
89c56528   hitier   Rename heliopropa...
647
648
            hp_logger.error("Cannot process gz file '%s' from '%s' : %s" %
                            (local_gzip_file, url, e))
dc0be992   Goutte   Support having no...
649
650
651
            # 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)
3c064b17   Goutte   Ignore failures w...
652
        if success:
dc0be992   Goutte   Support having no...
653
            local_netc_files.append(local_netc_file)
89c56528   hitier   Rename heliopropa...
654
            hp_logger.debug("Unzipped '%s'." % local_gzip_file)
8644387c   Goutte   Use real data.
655

ea6c8d5d   Goutte   Add interval cons...
656
    return list(set(local_netc_files))  # remove possible dupes
8644387c   Goutte   Use real data.
657
658


596da00d   Goutte   Add more exceptio...
659
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703
# class DataParser:
#     """
#     Default data parser
#     A wip to try to handle code exeptions sanely.
#     """
#
#     # 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',
#     }
#
#     def __init__(self, target, model):
#         self.target = target
#         self.model = model
#         pass
#
#     def _read_var(self, 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?
#
#     def parse(self, cdf_handle):
#         nc_keys = self.default_nc_keys.copy()
#
#         times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
#         data_v = self._read_var(cdf_handle, nc_keys, 'vtot')
#         data_b = self._read_var(cdf_handle, nc_keys, 'magn')
#         data_t = self._read_var(cdf_handle, nc_keys, 'temp')
#         data_n = self._read_var(cdf_handle, nc_keys, 'dens')
#         data_p = self._read_var(cdf_handle, nc_keys, 'pdyn')
#         data_a = self._read_var(cdf_handle, nc_keys, 'atse')
#
#         return zip()


de97d643   Goutte   Fix more bugs.
704
705
def get_data_for_target(target_config, input_slug,
                        started_at, stopped_at):
180d7d97   Goutte   Refactor heavily.
706
707
708
    """
    :return: dict whose keys are datetime as str, values tuples of data
    """
89c56528   hitier   Rename heliopropa...
709
    hp_logger.debug("Grabbing data for '%s'..." % target_config['slug'])
80352490   Goutte   Multi model suppo...
710

8644387c   Goutte   Use real data.
711
    try:
297a7dfc   Goutte   Add support for i...
712
        models = target_config['models'][input_slug]
077980eb   Goutte   Improve availabil...
713
714
    except Exception as e:
        abort(500, "Invalid model configuration for '%s' : %s"
180d7d97   Goutte   Refactor heavily.
715
716
              % (target_config['slug'], str(e)))
    try:
80352490   Goutte   Multi model suppo...
717
        orbits = target_config['orbit']['models']
d1c44c51   Goutte   Enable Earth
718
719
720
721
    except KeyError as e:
        orbits = []
        # abort(500, "Invalid orbit configuration for '%s' : %s"
        #       % (target_config['slug'], str(e)))
28ef3790   Goutte   Clean up.
722

80352490   Goutte   Multi model suppo...
723
    precision = "%Y-%m-%dT%H"  # model and orbits times are only equal-ish
180d7d97   Goutte   Refactor heavily.
724
    orbit_data = {}  # keys are datetime as str, values arrays of XY
ea6c8d5d   Goutte   Add interval cons...
725
726

    for orbit in orbits:
58bfe281   Goutte   Handle start and ...
727
        s0, s1 = _sta_sto(orbit, started_at, stopped_at)
ea6c8d5d   Goutte   Add interval cons...
728

d1c44c51   Goutte   Enable Earth
729
730
731
732
        nc_keys = default_nc_keys.copy()
        if 'parameters' in orbit:
            nc_keys.update(orbit['parameters'])

ea6c8d5d   Goutte   Add interval cons...
733
734
735
736
        orbit_files = retrieve_amda_netcdf(
            target_config['slug'], orbit['slug'], s0, s1
        )
        for orbit_file in orbit_files:
89c56528   hitier   Rename heliopropa...
737
738
            hp_logger.debug("%s: opening orbit NETCDF4 '%s'..." %
                            (target_config['name'], orbit_file))
ea6c8d5d   Goutte   Add interval cons...
739
740
            cdf_handle = Dataset(orbit_file, "r", format="NETCDF4")
            times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
d1c44c51   Goutte   Enable Earth
741
            data_hee = _read_var(cdf_handle, nc_keys, 'hee', mandatory=True)
ea6c8d5d   Goutte   Add interval cons...
742

89c56528   hitier   Rename heliopropa...
743
744
            hp_logger.debug("%s: aggregating data from '%s'..." %
                            (target_config['name'], orbit_file))
d1c44c51   Goutte   Enable Earth
745
            for ltime, datum_hee in zip(times, data_hee):
1324cc91   Goutte   Make the footer i...
746
                try:
d1c44c51   Goutte   Enable Earth
747
748
                    dtime = datetime_from_list(ltime)
                except Exception:
89c56528   hitier   Rename heliopropa...
749
                    hp_logger.error("Failed to parse time from get__data_for_target %s." % ltime)
d1c44c51   Goutte   Enable Earth
750
                    raise
81cb3ba6   Goutte   Fix an issue with...
751
                # Keep only what's in the interval
ea6c8d5d   Goutte   Add interval cons...
752
                if s0 <= dtime <= s1:
34e94ae3   hitier   Code reformating
753
                    dkey = round_time(dtime, 60 * 60).strftime(precision)
ea6c8d5d   Goutte   Add interval cons...
754
755
                    orbit_data[dkey] = datum_hee
            cdf_handle.close()
180d7d97   Goutte   Refactor heavily.
756

8644387c   Goutte   Use real data.
757
    all_data = {}  # keys are datetime as str, values tuples of data
81cb3ba6   Goutte   Fix an issue with...
758

58bfe281   Goutte   Handle start and ...
759
760
761
762
763
    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
        )
d1c44c51   Goutte   Enable Earth
764
765
766
767
        nc_keys = default_nc_keys.copy()
        if 'parameters' in model:
            nc_keys.update(model['parameters'])

129181a6   Goutte   Add more logs to ...
768
        if len(model_files) == 0:
89c56528   hitier   Rename heliopropa...
769
770
            hp_logger.warning("No model data for '%s' '%s'."
                              % (target_config['slug'], model['slug']))
129181a6   Goutte   Add more logs to ...
771

58bfe281   Goutte   Handle start and ...
772
        for model_file in model_files:
89c56528   hitier   Rename heliopropa...
773
774
            hp_logger.debug("%s: opening model NETCDF4 '%s'..." %
                            (target_config['name'], model_file))
58bfe281   Goutte   Handle start and ...
775
            cdf_handle = Dataset(model_file, "r", format="NETCDF4")
596da00d   Goutte   Add more exceptio...
776

d1c44c51   Goutte   Enable Earth
777
            # log.debug(cdf_handle.variables.keys())
596da00d   Goutte   Add more exceptio...
778

58bfe281   Goutte   Handle start and ...
779
            times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
d1c44c51   Goutte   Enable Earth
780
781
782
783
784
785
786
            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')

d1c44c51   Goutte   Enable Earth
787
788
789
790
791
792
793
794
795
            # 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

81cb3ba6   Goutte   Fix an issue with...
796
797
798
799
800
801
            # Don't ignore, but instead, compute a mean ?
            # Look for discretisation ? temporal drizzling ? 1D drizzling ?
            # The easy linear mean feels a bit rough too. Running mean too.
            # FIXME
            ignored_count = 0

89c56528   hitier   Rename heliopropa...
802
803
            hp_logger.debug("%s: aggregating data from '%s'..." %
                            (target_config['name'], model_file))
d1c44c51   Goutte   Enable Earth
804
805
806
            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):

58bfe281   Goutte   Handle start and ...
807
                try:
d1c44c51   Goutte   Enable Earth
808
809
                    dtime = datetime_from_list(ltime)
                except Exception:
89c56528   hitier   Rename heliopropa...
810
                    hp_logger.error("Failed to parse time from %s." % ltime)
d1c44c51   Goutte   Enable Earth
811
                    raise
596da00d   Goutte   Add more exceptio...
812

81cb3ba6   Goutte   Fix an issue with...
813
814
815
                if not (s0 <= dtime <= s1):
                    continue  # Cull what's out of the interval

34e94ae3   hitier   Code reformating
816
                droundtime = round_time(dtime, 60 * 60)
81cb3ba6   Goutte   Fix an issue with...
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
                dkey = droundtime.strftime(precision)

                x_hee = None
                y_hee = None
                if dkey in orbit_data:
                    x_hee = orbit_data[dkey][0] / ASTRONOMICAL_UNIT_IN_KM
                    y_hee = orbit_data[dkey][1] / ASTRONOMICAL_UNIT_IN_KM

                # First exception: V may be a vector instead of a scalar
                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

                # Second exception: Earth is always at (1, 0)
                if target_config['slug'] == 'earth':
                    x_hee = 1
                    y_hee = 0

                # Third exception: B is a Vector3 or a Vector2 for Earth
                if target_config['slug'] == 'earth':
                    if model['slug'] == 'omni_hour_all':  # Vector3
                        datum_b = datum_b[0]
                    # if model['slug'] == 'ace_swepam_real':  # Vector2
                    #     datum_b = datum_b[0]
56028f6d   Myriam Bouchemit   bug for dyn press...
846
                    if model['slug'] == 'ace_swepam_real_1h':
206d8d14   Goutte   Clean up.
847
                        datum_p = datum_n * vtot * vtot * 1.6726e-6
81cb3ba6   Goutte   Fix an issue with...
848
849
850
                    if vtot is None or isnan(vtot):
                        continue

7176ae9b   Goutte   Fix Myriam's cont...
851
852
853
854
855
                # Fourth exception: Earth temp is in K, not eV
                # @nandre: à vérifier ! Where is la constante de Boltzmann ?
                if target_config['slug'] == 'earth' and datum_t:
                    datum_t = datum_t / 11605.0

81cb3ba6   Goutte   Fix an issue with...
856
857
                # Keep adding exceptions here until you can't or become mad

2be8e8a0   Goutte   Ignore bad data.
858
                # Ignore bad data
ff11e121   Goutte   Don't ignore bad ...
859
860
                # if numpy.isnan(datum_t):
                #     continue
2be8e8a0   Goutte   Ignore bad data.
861

81cb3ba6   Goutte   Fix an issue with...
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
                # Crude/Bad drizzling condition : first found datum in the hour
                # gets to set the data. Improve this.
                if dkey not in all_data:
                    # /!. The Set value MUST be in the same order as PROPERTIES
                    all_data[dkey] = (
                        dtime.strftime("%Y-%m-%dT%H:%M:%S+00:00"),
                        vrad, vtan, vtot,
                        datum_b, datum_t, datum_p, datum_n, datum_a,
                        x_hee, y_hee
                    )
                else:
                    ignored_count += 1

            # Improve this loop so as to remove this stinky debug log
            if ignored_count > 0:
89c56528   hitier   Rename heliopropa...
877
878
                hp_logger.debug("    Ignored %d datum(s) during ~\"drizzling\"."
                                % ignored_count)
81cb3ba6   Goutte   Fix an issue with...
879

58bfe281   Goutte   Handle start and ...
880
            cdf_handle.close()
8644387c   Goutte   Use real data.
881

180d7d97   Goutte   Refactor heavily.
882
883
884
    return all_data


297a7dfc   Goutte   Add support for i...
885
def generate_csv_contents(target_slug, input_slug, started_at, stopped_at):
180d7d97   Goutte   Refactor heavily.
886
    target_config = get_target_config(target_slug)
89c56528   hitier   Rename heliopropa...
887
    hp_logger.debug("Crunching CSV contents for '%s'..." % target_config['name'])
b33d5f62   hitier   Change StringIO i...
888
    si = StringIO()
180d7d97   Goutte   Refactor heavily.
889
890
891
    cw = csv_writer(si)
    cw.writerow(PROPERTIES)

297a7dfc   Goutte   Add support for i...
892
893
894
895
    all_data = get_data_for_target(
        target_config=target_config, input_slug=input_slug,
        started_at=started_at, stopped_at=stopped_at
    )
180d7d97   Goutte   Refactor heavily.
896

89c56528   hitier   Rename heliopropa...
897
    hp_logger.debug("Writing and sorting CSV for '%s'..." % target_config['slug'])
8644387c   Goutte   Use real data.
898
899
    for dkey in sorted(all_data):
        cw.writerow(all_data[dkey])
2d2af24b   Goutte   Add a basic orbit...
900

89c56528   hitier   Rename heliopropa...
901
    hp_logger.info("Generated CSV contents for '%s'." % target_config['slug'])
2d2af24b   Goutte   Add a basic orbit...
902
903
    return si.getvalue()

8644387c   Goutte   Use real data.
904

dd6ae65b   hitier   Add new csvgenera...
905
906
def generate_csv_contents_spz(target_slug, input_slug, started_at, stopped_at):
    target_config = get_target_config(target_slug)
c992a282   hitier   Read parameters i...
907
908
909
910
911
912
913
    plasma_params = {}
    for plasma_struct in target_config['models'][input_slug]:
        plasma_params = {**plasma_params, **plasma_struct['parameters']}
    orbit_params = {}
    for orbit_struct in target_config['orbit']['models']:
        orbit_params = {**orbit_params, **orbit_struct['parameters']}
    parameters_dict = {**plasma_params, **orbit_params}
dd6ae65b   hitier   Add new csvgenera...
914

89c56528   hitier   Rename heliopropa...
915
    hp_logger.info(f"Aggregating dataframes speazy parameters for '{input_slug}' to '{target_slug}'")
dd6ae65b   hitier   Add new csvgenera...
916
    list_df = []
fc7cbbee   hitier   Move orbit parame...
917
    for _name, _id in parameters_dict.items():
89c56528   hitier   Rename heliopropa...
918
        hp_logger.debug(f"Getting parameter id '{_id}' for '{_name}'")
ea48da74   hitier   Go on building da...
919
920
921
922
        amda_dataset = amda.get_data(_id, started_at, stopped_at)
        if amda_dataset is None:
            continue
        _df = amda_dataset.to_dataframe()
dd6ae65b   hitier   Add new csvgenera...
923
924
925
926
927
        if _name == 'xy_v':
            _df = _df.rename(columns={_df.columns[0]: 'vrad', _df.columns[1]: 'vtan'})
        elif _name == 'xy_hee':
            _df = _df.drop(_df.columns[2], axis=1)
            _df = _df.rename(columns={_df.columns[0]: 'xhee', _df.columns[1]: 'yhee'})
3a5138b2   hitier   Set all earth amd...
928
929
930
        elif _name == 'xy_b':
            _df = _df.drop(_df.columns[2], axis=1)
            _df = _df.rename(columns={_df.columns[0]: 'brad', _df.columns[1]: 'btan'})
dd6ae65b   hitier   Add new csvgenera...
931
932
933
934
935
936
937
938
939
940
941
942
943
944
        else:
            _df = _df.rename(columns={_df.columns[0]: _name})

        # _df = _df[~_df.index.duplicated()]

        # resample to frequency, for later concatenation
        _df = _df.resample('1H').mean()

        # _df = _df.loc[_df.first_valid_index():_df.last_valid_index()]

        list_df.append(_df)

    from math import sqrt
    final_df = pd.concat(list_df, axis=1)
0c75436e   hitier   Better check in v...
945
946
947
948
    # build vtot param  if doesnt exist
    if 'vtot' not in final_df.columns \
            and 'vtan' in final_df.columns \
            and 'vrad' in final_df.columns:
dd6ae65b   hitier   Add new csvgenera...
949
950
        final_df['vtot'] = final_df.apply(lambda x: sqrt(x.vtan * x.vtan + x.vrad * x.vrad), axis=1)

3a5138b2   hitier   Set all earth amd...
951
952
953
954
955
    # Hardcoded earth coordinates
    if target_slug == 'earth':
        final_df['xhee'] = 1
        final_df['yhee'] = 0

dd6ae65b   hitier   Add new csvgenera...
956
    cols_ordered = ['vrad', 'vtan', 'vtot', 'btan', 'brad', 'temp', 'pdyn', 'dens', 'atse', 'xhee', 'yhee']
db050046   hitier   Order cols even i...
957
    cols_ordered = [_c for _c in cols_ordered if _c in final_df.columns]
dd6ae65b   hitier   Add new csvgenera...
958
959
960
961
962
963
964
    final_df = final_df[cols_ordered]
    final_df.index.name = 'time'
    return final_df.to_csv(date_format='%Y-%m-%dT%H:%M:%S+00:00', float_format="%.5f",
                           header=True,
                           sep=",")


de97d643   Goutte   Fix more bugs.
965
966
def generate_csv_file_if_needed(target_slug, input_slug,
                                started_at, stopped_at):
297a7dfc   Goutte   Add support for i...
967
968
969
    filename = "%s_%s_%s_%s.csv" % (target_slug, input_slug,
                                    started_at.strftime(FILE_DATE_FMT),
                                    stopped_at.strftime(FILE_DATE_FMT))
e18701b6   Goutte   Cache clear (remo...
970
    local_csv_file = join(CACHE_DIR, filename)
80352490   Goutte   Multi model suppo...
971
972
973

    generate = True
    if isfile(local_csv_file):
297a7dfc   Goutte   Add support for i...
974
        # It needs to have more than one line to not be empty (headers)
80352490   Goutte   Multi model suppo...
975
976
977
978
979
980
981
982
        with open(local_csv_file) as f:
            cnt = 0
            for _ in f:
                cnt += 1
                if cnt > 1:
                    generate = False
                    break

8eb47b5f   hitier   Set all mercury a...
983
    # temporary switch while migrating each target to spz
3a5138b2   hitier   Set all earth amd...
984
    if target_slug in ['mercury', 'venus', 'mars', 'earth']:
dd6ae65b   hitier   Add new csvgenera...
985
986
987
988
        csv_generator = generate_csv_contents_spz
    else:
        csv_generator = generate_csv_contents

80352490   Goutte   Multi model suppo...
989
    if generate:
89c56528   hitier   Rename heliopropa...
990
        hp_logger.info("Generating CSV '%s'..." % local_csv_file)
c0df94bc   Goutte   Adding more logs.
991
992
        try:
            with open(local_csv_file, mode="w+") as f:
dd6ae65b   hitier   Add new csvgenera...
993
                f.write(csv_generator(
de97d643   Goutte   Fix more bugs.
994
995
996
                    target_slug=target_slug, input_slug=input_slug,
                    started_at=started_at, stopped_at=stopped_at
                ))
89c56528   hitier   Rename heliopropa...
997
            hp_logger.info("Generation of '%s' done." % filename)
c0df94bc   Goutte   Adding more logs.
998
        except Exception as e:
d1c44c51   Goutte   Enable Earth
999
1000
1001
            from sys import exc_info
            from traceback import extract_tb
            exc_type, exc_value, exc_traceback = exc_info()
89c56528   hitier   Rename heliopropa...
1002
            hp_logger.error(e)
d1c44c51   Goutte   Enable Earth
1003
            for trace in extract_tb(exc_traceback):
89c56528   hitier   Rename heliopropa...
1004
                hp_logger.error(trace)
5ede388f   Goutte   Make sure failed ...
1005
            if isfile(local_csv_file):
89c56528   hitier   Rename heliopropa...
1006
                hp_logger.warning("Removing failed CSV '%s'..." % local_csv_file)
5ede388f   Goutte   Make sure failed ...
1007
                removefile(local_csv_file)
9bfa6c42   Goutte   More bug hunting.
1008
            abort(500, "Failed creating CSV '%s' : %s" % (filename, e))
c0df94bc   Goutte   Adding more logs.
1009
1010


e18701b6   Goutte   Cache clear (remo...
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
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


28bb4b28   Goutte   API for the cache...
1034
1035
def remove_files_created_before(date, in_directory):
    """
077980eb   Goutte   Improve availabil...
1036
1037
1038
    Will throw if something horrible happens.
    Does not remove recursively (could be done with os.walk if needed).
    Does not remove directories either.
28bb4b28   Goutte   API for the cache...
1039
    :param date: datetime object
077980eb   Goutte   Improve availabil...
1040
    :param in_directory: absolute path to directory
28bb4b28   Goutte   API for the cache...
1041
1042
1043
1044
1045
1046
1047
    :return:
    """
    import os
    import time

    secs = time.mktime(date.timetuple())

077980eb   Goutte   Improve availabil...
1048
1049
    if not os.path.isdir(in_directory):
        raise ValueError("No directory to clean at '%s'.")
28bb4b28   Goutte   API for the cache...
1050
1051
1052
1053

    removed_files = []
    for file_name in os.listdir(in_directory):
        file_path = os.path.join(in_directory, file_name)
077980eb   Goutte   Improve availabil...
1054
1055
1056
1057
1058
        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)
28bb4b28   Goutte   API for the cache...
1059
1060
1061
1062

    return removed_files


297a7dfc   Goutte   Add support for i...
1063
1064
def get_input_slug_from_query(inp=None):
    if inp is None:
b662fcc3   hitier   Change input name...
1065
        input_slug = request.args.get('input_slug', config['defaults']['input_slug'])
297a7dfc   Goutte   Add support for i...
1066
1067
    else:
        input_slug = inp
de97d643   Goutte   Fix more bugs.
1068
    if input_slug not in [i['slug'] for i in config['inputs']]:
b662fcc3   hitier   Change input name...
1069
        input_slug = config['defaults']['input_slug']  # be tolerant instead of yelling loudly
297a7dfc   Goutte   Add support for i...
1070
1071
1072
    return input_slug


284f4688   Goutte   Continue layers i...
1073
1074
1075
def get_interval_from_query():
    """
    Get the interval from the query, or from defaults.
3309d7c3   Goutte   Improve the date ...
1076
    Returns ISO date strings.
284f4688   Goutte   Continue layers i...
1077
    """
65b27161   hitier   Change default ti...
1078
    before = relativedelta(months=1)
284f4688   Goutte   Continue layers i...
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
    after = relativedelta(months=1)
    today = datetime.datetime.now().replace(hour=0, minute=0, second=0)
    started_at = today - before
    stopped_at = today + after
    default_started_at = started_at.strftime(FILE_DATE_FMT)
    default_stopped_at = stopped_at.strftime(FILE_DATE_FMT)

    started_at = request.args.get('started_at', default_started_at)
    stopped_at = request.args.get('stopped_at', default_stopped_at)

3309d7c3   Goutte   Improve the date ...
1089
1090
1091
1092
1093
    d_started_at = dateparser.isoparse(started_at)
    d_stopped_at = dateparser.isoparse(stopped_at)
    started_at = d_started_at.strftime(FILE_DATE_FMT)
    stopped_at = d_stopped_at.strftime(FILE_DATE_FMT)

284f4688   Goutte   Continue layers i...
1094
1095
1096
    return started_at, stopped_at


1185f353   Goutte   Fix the CME Catal...
1097
def get_catalog_layers(input_slug, target_slug, started_at, stopped_at):
0332f168   Goutte   Initial support f...
1098
    """
284f4688   Goutte   Continue layers i...
1099
1100
    In the JSON file we have "columns" and "data".
    Of course, each JSON file has its own columns, with different conventions.
0332f168   Goutte   Initial support f...
1101
1102
1103
1104
1105
    
    :param input_slug: 
    :param target_slug: 
    :return: 
    """
0332f168   Goutte   Initial support f...
1106
    import json
2204c3f7   Goutte   Improve layers co...
1107
1108

    def _get_index_of_key(_data, _key):
2204c3f7   Goutte   Improve layers co...
1109
1110
1111
        try:
            index = _data['columns'].index(_key)
        except ValueError:
89c56528   hitier   Rename heliopropa...
1112
            hp_logger.error("Key %s not found in columns of %s" % (_key, _data))
2204c3f7   Goutte   Improve layers co...
1113
1114
1115
            raise
        return index

1185f353   Goutte   Fix the CME Catal...
1116
1117
1118
1119
1120
1121
1122
1123
1124
    try:
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)

0332f168   Goutte   Initial support f...
1125
    catalog_layers = {}
1ab47144   Goutte   Add new menus, up...
1126
    for config_layer in config['layers']['catalogs']:
0332f168   Goutte   Initial support f...
1127
1128
        if 'data' not in config_layer:
            continue
0332f168   Goutte   Initial support f...
1129
1130
1131
1132
1133
1134
        catalog_layers[config_layer['slug']] = []
        for cl_datum in config_layer['data']:
            if input_slug not in cl_datum:
                continue
            if target_slug not in cl_datum[input_slug]:
                continue
b03d5eb1   Goutte   Add the last CME ...
1135
1136
1137
1138
1139
            if cl_datum[input_slug][target_slug] is None:
                # We used ~ in the config, there are no constraints
                constraints = []
            else:
                constraints = cl_datum[input_slug][target_slug]['constraints']
1185f353   Goutte   Fix the CME Catal...
1140

0332f168   Goutte   Initial support f...
1141
1142
            with open(get_path("../data/catalog/%s" % cl_datum['file'])) as f:
                json_data = json.load(f)
284f4688   Goutte   Continue layers i...
1143
                if 'start' not in cl_datum:
89c56528   hitier   Rename heliopropa...
1144
                    hp_logger.error("Invalid configuration: 'start' is missing.")
284f4688   Goutte   Continue layers i...
1145
                    continue  # skip this
1185f353   Goutte   Fix the CME Catal...
1146
                if 'format' not in cl_datum:
54bb1311   Goutte   Bring back the CM...
1147
1148
1149
                    cl_datum['format'] = CME_DATE_FMT
                    # log.error("Invalid configuration: 'format' is missing.")
                    # continue  # skip this
284f4688   Goutte   Continue layers i...
1150
1151
1152
1153
1154
                start_index = _get_index_of_key(json_data, cl_datum['start'])
                if 'stop' not in cl_datum:
                    stop_index = start_index
                else:
                    stop_index = _get_index_of_key(json_data, cl_datum['stop'])
2204c3f7   Goutte   Improve layers co...
1155

0332f168   Goutte   Initial support f...
1156
                for json_datum in json_data['data']:
2204c3f7   Goutte   Improve layers co...
1157
                    validates_any_constraint = False
b03d5eb1   Goutte   Add the last CME ...
1158
1159
                    if 0 == len(constraints):
                        validates_any_constraint = True
2204c3f7   Goutte   Improve layers co...
1160
1161
                    for constraint in constraints:
                        validates_constraint = True
d4b3d381   hitier   Tiny python3 synt...
1162
                        for key, possible_values in iter(constraint.items()):
2204c3f7   Goutte   Improve layers co...
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
                            actual_value = json_datum[_get_index_of_key(
                                json_data, key
                            )]
                            if actual_value not in possible_values:
                                validates_constraint = False
                                break
                        if validates_constraint:
                            validates_any_constraint = True
                            break
                    if not validates_any_constraint:
0332f168   Goutte   Initial support f...
1173
                        continue
284f4688   Goutte   Continue layers i...
1174
1175
                    start_time = json_datum[start_index]
                    stop_time = json_datum[stop_index]
1185f353   Goutte   Fix the CME Catal...
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186

                    start_time = datetime.datetime.strptime(
                        start_time, cl_datum['format']
                    )
                    stop_time = datetime.datetime.strptime(
                        stop_time, cl_datum['format']
                    )

                    if start_time < started_at:
                        continue

0332f168   Goutte   Initial support f...
1187
                    catalog_layers[config_layer['slug']].append({
1185f353   Goutte   Fix the CME Catal...
1188
                        'start': start_time.strftime(MOMENT_DATE_FMT),
34e94ae3   hitier   Code reformating
1189
                        'stop': stop_time.strftime(MOMENT_DATE_FMT),
0332f168   Goutte   Initial support f...
1190
                    })
0332f168   Goutte   Initial support f...
1191
1192
1193
1194

    return catalog_layers


077980eb   Goutte   Improve availabil...
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
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


a4a9ef03   Goutte   Cache generated C...
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
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


4aaf6874   Goutte   Try fixing the ge...
1222
1223
def update_spacepy():
    """
11d86851   Goutte   Add support for s...
1224
    Importing pycdf will fail if the toolbox is not up to date.
4aaf6874   Goutte   Try fixing the ge...
1225
    """
4aaf6874   Goutte   Try fixing the ge...
1226
    try:
89c56528   hitier   Rename heliopropa...
1227
        hp_logger.info("Updating spacepy's toolbox…")
4aaf6874   Goutte   Try fixing the ge...
1228
1229
1230
1231
        import spacepy.toolbox

        spacepy.toolbox.update()
    except Exception as e:
89c56528   hitier   Rename heliopropa...
1232
        hp_logger.error("Failed to update spacepy : %s." % e)
4aaf6874   Goutte   Try fixing the ge...
1233
1234


077980eb   Goutte   Improve availabil...
1235
1236
1237
tpl_global_vars['visits'] = get_hit_counter()


a4a9ef03   Goutte   Cache generated C...
1238
1239
1240
# ROUTING #####################################################################

@app.route('/favicon.ico')
bde97e4d   Goutte   Add more changes ...
1241
def favicon():  # we want it served from the root, not from static/
a4a9ef03   Goutte   Cache generated C...
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
    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():
077980eb   Goutte   Improve availabil...
1252
    increment_hit_counter()
bde97e4d   Goutte   Add more changes ...
1253
    parameters = PARAMETERS.values()
d4b3d381   hitier   Tiny python3 synt...
1254
    parameters = sorted(parameters, key=lambda x: x['position'])
297a7dfc   Goutte   Add support for i...
1255
    input_slug = get_input_slug_from_query()
0332f168   Goutte   Initial support f...
1256
    targets = [t for t in config['targets'] if not t['locked']]
284f4688   Goutte   Continue layers i...
1257
    started_at, stopped_at = get_interval_from_query()
0332f168   Goutte   Initial support f...
1258
1259
    for i, target in enumerate(targets):
        targets[i]['catalog_layers'] = get_catalog_layers(
1185f353   Goutte   Fix the CME Catal...
1260
            input_slug, target['slug'], started_at, stopped_at
0332f168   Goutte   Initial support f...
1261
        )
a4a9ef03   Goutte   Cache generated C...
1262
    return render_view('home.html.jinja2', {
0332f168   Goutte   Initial support f...
1263
1264
        # 'targets': config['targets'],
        'targets': targets,
bde97e4d   Goutte   Add more changes ...
1265
        'parameters': parameters,
297a7dfc   Goutte   Add support for i...
1266
        'input_slug': input_slug,
284f4688   Goutte   Continue layers i...
1267
1268
        'started_at': started_at,
        'stopped_at': stopped_at,
a4a9ef03   Goutte   Cache generated C...
1269
        'planets': [s for s in config['targets'] if s['type'] == 'planet'],
34e94ae3   hitier   Code reformating
1270
1271
1272
        '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(),
a4a9ef03   Goutte   Cache generated C...
1273
1274
1275
    })


64a671cd   Goutte   Add an About page.
1276
1277
@app.route("/about.html")
def about():
36961d6f   Goutte   Slightly improve ...
1278
    import uuid
64a671cd   Goutte   Add an About page.
1279
1280
    increment_hit_counter()
    return render_view('about.html.jinja2', {
36961d6f   Goutte   Slightly improve ...
1281
1282
1283
        'authors_emails': [a['mail'] for a in config['authors']],
        'uuid4': str(uuid.uuid4())[0:3],
        'visits': get_hit_counter(),
64a671cd   Goutte   Add an About page.
1284
1285
1286
    })


6288347a   Goutte   Add the HELP page...
1287
1288
1289
1290
1291
1292
1293
@app.route("/help.html")
def help():
    return render_view('help.html.jinja2', {
        'visits': get_hit_counter(),
    })


297a7dfc   Goutte   Add support for i...
1294
1295
@app.route("/<target>_<inp>_<started_at>_<stopped_at>.csv")
def download_target_csv(target, inp, started_at, stopped_at):
a4a9ef03   Goutte   Cache generated C...
1296
1297
1298
1299
    """
    Grab data and orbit data for the specified `target`,
    rearrange it and return it as a CSV file.
    `started_at` and `stopped_at` should be UTC.
b662fcc3   hitier   Change input name...
1300
    `inp` is the input slug, omni or sa or sb.
a4a9ef03   Goutte   Cache generated C...
1301
    """
180d7d97   Goutte   Refactor heavily.
1302
    check_target_config(target)
a4a9ef03   Goutte   Cache generated C...
1303
    try:
c0df94bc   Goutte   Adding more logs.
1304
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
1305
1306
1307
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
c0df94bc   Goutte   Adding more logs.
1308
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
1309
1310
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
297a7dfc   Goutte   Add support for i...
1311
    input_slug = get_input_slug_from_query(inp=inp)
a4a9ef03   Goutte   Cache generated C...
1312

297a7dfc   Goutte   Add support for i...
1313
1314
1315
    filename = "%s_%s_%s_%s.csv" % (target, input_slug,
                                    started_at.strftime(FILE_DATE_FMT),
                                    stopped_at.strftime(FILE_DATE_FMT))
e18701b6   Goutte   Cache clear (remo...
1316
    local_csv_file = join(CACHE_DIR, filename)
297a7dfc   Goutte   Add support for i...
1317
1318
1319
1320
    generate_csv_file_if_needed(
        target_slug=target, input_slug=input_slug,
        started_at=started_at, stopped_at=stopped_at
    )
a4a9ef03   Goutte   Cache generated C...
1321
1322
1323
    if not isfile(local_csv_file):
        abort(500, "Could not cache CSV file at '%s'." % local_csv_file)

e18701b6   Goutte   Cache clear (remo...
1324
    return send_from_directory(CACHE_DIR, filename)
a4a9ef03   Goutte   Cache generated C...
1325
1326


297a7dfc   Goutte   Add support for i...
1327
1328
@app.route("/<targets>_<inp>_<started_at>_<stopped_at>.tar.gz")
def download_targets_tarball(targets, inp, started_at, stopped_at):
b2837a08   Goutte   Add three retries...
1329
    """
bc18b96c   Goutte   Implement first (...
1330
1331
1332
    Grab data and orbit data for each of the specified `targets`,
    in their own CSV file, and make a tarball of them.
    `started_at` and `stopped_at` should be UTC strings.
b2837a08   Goutte   Add three retries...
1333

ea6c8d5d   Goutte   Add interval cons...
1334
1335
    Note: we do not use this route anymore, but let's keep it shelved for now.

2fedd73b   Goutte   Initial implement...
1336
    targets: string list of targets' slugs, separated by `-`.
b2837a08   Goutte   Add three retries...
1337
    """
2fedd73b   Goutte   Initial implement...
1338
    separator = '-'
0511eed7   Goutte   Tarball generatio...
1339
    targets = targets.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1340
    targets.sorty()
2fedd73b   Goutte   Initial implement...
1341
1342
    targets_configs = []
    for target in targets:
b2837a08   Goutte   Add three retries...
1343
1344
        if not target:
            abort(400, "Invalid targets format : `%s`." % targets)
180d7d97   Goutte   Refactor heavily.
1345
        targets_configs.append(get_target_config(target))
2fedd73b   Goutte   Initial implement...
1346
    if 0 == len(targets_configs):
b2837a08   Goutte   Add three retries...
1347
1348
        abort(400, "No valid targets specified. What are you doing?")

b2837a08   Goutte   Add three retries...
1349
    try:
ea6c8d5d   Goutte   Add interval cons...
1350
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1351
1352
1353
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
ea6c8d5d   Goutte   Add interval cons...
1354
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1355
1356
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
ea6c8d5d   Goutte   Add interval cons...
1357
1358
    sta = started_at.strftime(FILE_DATE_FMT)
    sto = stopped_at.strftime(FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1359

297a7dfc   Goutte   Add support for i...
1360
1361
1362
1363
1364
    input_slug = get_input_slug_from_query(inp=inp)

    gzip_filename = "%s_%s_%s_%s.tar.gz" % (
        separator.join(targets), input_slug, sta, sto
    )
e18701b6   Goutte   Cache clear (remo...
1365
    local_gzip_file = join(CACHE_DIR, gzip_filename)
2fedd73b   Goutte   Initial implement...
1366
1367

    if not isfile(local_gzip_file):
89c56528   hitier   Rename heliopropa...
1368
        hp_logger.debug("Creating the CSV files for the tarball...")
2fedd73b   Goutte   Initial implement...
1369
        for target_config in targets_configs:
297a7dfc   Goutte   Add support for i...
1370
1371
1372
            filename = "%s_%s_%s_%s.csv" % (
                target_config['slug'], input_slug, sta, sto
            )
e18701b6   Goutte   Cache clear (remo...
1373
            local_csv_file = join(CACHE_DIR, filename)
2fedd73b   Goutte   Initial implement...
1374
1375
            if not isfile(local_csv_file):
                with open(local_csv_file, mode="w+") as f:
297a7dfc   Goutte   Add support for i...
1376
1377
1378
1379
1380
1381
                    f.write(generate_csv_contents(
                        target_slug=target_config['slug'],
                        started_at=started_at,
                        stopped_at=stopped_at,
                        input_slug=input_slug
                    ))
2fedd73b   Goutte   Initial implement...
1382

89c56528   hitier   Rename heliopropa...
1383
        hp_logger.debug("Creating the tarball '%s'..." % local_gzip_file)
2fedd73b   Goutte   Initial implement...
1384
1385
        with tarfile.open(local_gzip_file, "w:gz") as tar:
            for target_config in targets_configs:
297a7dfc   Goutte   Add support for i...
1386
1387
1388
                filename = "%s_%s_%s_%s.csv" % (
                    target_config['slug'], input_slug, sta, sto
                )
e18701b6   Goutte   Cache clear (remo...
1389
                local_csv_file = join(CACHE_DIR, filename)
2fedd73b   Goutte   Initial implement...
1390
1391
1392
                tar.add(local_csv_file, arcname=filename)

    if not isfile(local_gzip_file):
0511eed7   Goutte   Tarball generatio...
1393
        abort(500, "No tarball to serve. Looked at '%s'." % local_gzip_file)
2fedd73b   Goutte   Initial implement...
1394

e18701b6   Goutte   Cache clear (remo...
1395
    return send_from_directory(CACHE_DIR, gzip_filename)
b2837a08   Goutte   Add three retries...
1396

28bb4b28   Goutte   API for the cache...
1397

297a7dfc   Goutte   Add support for i...
1398
1399
@app.route("/<targets>_<inp>_<params>_<started_at>_<stopped_at>.nc")
def download_targets_netcdf(targets, inp, params, started_at, stopped_at):
bc18b96c   Goutte   Implement first (...
1400
    """
4aaf6874   Goutte   Try fixing the ge...
1401
1402
    NOTE : This is not used anymore.
    
bc18b96c   Goutte   Implement first (...
1403
    Grab data and orbit data for the specified `target`,
aa7247d6   Goutte   Generate a CDF fi...
1404
    rearrange it and return it as a NetCDF file.
e18701b6   Goutte   Cache clear (remo...
1405
    `started_at` and `stopped_at` are expected to be UTC.
bc18b96c   Goutte   Implement first (...
1406
1407
1408
1409

    targets: string list of targets' slugs, separated by `-`.
    params: string list of targets' parameters, separated by `-`.
    """
e18701b6   Goutte   Cache clear (remo...
1410
    separator = '-'  # /!\ this char should never be in target's slugs
bc18b96c   Goutte   Implement first (...
1411
    targets = targets.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1412
    targets.sorty()
bc18b96c   Goutte   Implement first (...
1413
1414
1415
1416
1417
1418
1419
    targets_configs = []
    for target in targets:
        if not target:
            abort(400, "Invalid targets format : `%s`." % targets)
        targets_configs.append(get_target_config(target))
    if 0 == len(targets_configs):
        abort(400, "No valid targets specified. What are you doing?")
4aaf6874   Goutte   Try fixing the ge...
1420

bc18b96c   Goutte   Implement first (...
1421
    params = params.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1422
    params.sorty()
bc18b96c   Goutte   Implement first (...
1423
1424
1425
1426
1427
    if 0 == len(params):
        abort(400, "No valid parameters specified. What are you doing?")
    if not is_list_in_list(params, PARAMETERS.keys()):
        abort(400, "Some parameters are not recognized in '%s'." % str(params))

57493104   Goutte   Add the time to t...
1428
    date_fmt = FILE_DATE_FMT
bc18b96c   Goutte   Implement first (...
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
    try:
        started_at = datetime.datetime.strptime(started_at, date_fmt)
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
        stopped_at = datetime.datetime.strptime(stopped_at, date_fmt)
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
    sta = started_at.strftime(date_fmt)
    sto = stopped_at.strftime(date_fmt)

297a7dfc   Goutte   Add support for i...
1440
1441
1442
1443
1444
    input_slug = get_input_slug_from_query(inp=inp)

    nc_filename = "%s_%s_%s_%s_%s.nc" % (
        separator.join(targets), separator.join(params), input_slug, sta, sto
    )
e18701b6   Goutte   Cache clear (remo...
1445
    nc_path = join(CACHE_DIR, nc_filename)
bc18b96c   Goutte   Implement first (...
1446
1447

    if not isfile(nc_path):
89c56528   hitier   Rename heliopropa...
1448
        hp_logger.debug("Creating the NetCDF file '%s'..." % nc_filename)
bc18b96c   Goutte   Implement first (...
1449
1450
        nc_handle = Dataset(nc_path, "w", format="NETCDF4")
        try:
ea6c8d5d   Goutte   Add interval cons...
1451
            nc_handle.description = "Model and orbit data for targets"  # todo
bc18b96c   Goutte   Implement first (...
1452
            nc_handle.history = "Created " + time.ctime(time.time())
ea6c8d5d   Goutte   Add interval cons...
1453
            nc_handle.source = "Heliopropa (CDDP)"
bc18b96c   Goutte   Implement first (...
1454
1455
1456
            available_params = list(PROPERTIES)
            for target in targets_configs:
                target_slug = target['slug']
89c56528   hitier   Rename heliopropa...
1457
                hp_logger.debug("Adding group '%s' to the NetCDF..." % target_slug)
bc18b96c   Goutte   Implement first (...
1458
                nc_group = nc_handle.createGroup(target_slug)
297a7dfc   Goutte   Add support for i...
1459
1460
1461
1462
                data = get_data_for_target(
                    target_config=target, input_slug=input_slug,
                    started_at=started_at, stopped_at=stopped_at
                )
bc18b96c   Goutte   Implement first (...
1463
                dkeys = sorted(data)
34e94ae3   hitier   Code reformating
1464
                dimension = 'dim_' + target_slug
ceeb2f4a   Goutte   Add the target co...
1465
                nc_handle.createDimension(dimension, len(dkeys))
57493104   Goutte   Add the time to t...
1466
1467

                # TIME #
ceeb2f4a   Goutte   Add the target co...
1468
                nc_time = nc_group.createVariable('time', 'i8', (dimension,))
57493104   Goutte   Add the time to t...
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
                nc_time.units = "hours since 1970-01-01 00:00:00"
                nc_time.calendar = "standard"
                times = []
                for dkey in dkeys:
                    time_as_string = data[dkey][0][:-6]  # remove +00:00 tail
                    date = datetime.datetime.strptime(time_as_string, date_fmt)
                    times.append(date2num(
                        date, units=nc_time.units, calendar=nc_time.calendar
                    ))
                nc_time[:] = times

                # SELECTED PARAMETERS #
bc18b96c   Goutte   Implement first (...
1481
1482
1483
1484
                nc_vars = []
                indices = []
                for param in params:
                    indices.append(available_params.index(param))
ceeb2f4a   Goutte   Add the target co...
1485
                    nc_var = nc_group.createVariable(param, 'f8', (dimension,))
5a6d4498   Goutte   Add a title to ea...
1486
                    nc_var.units = PARAMETERS[param]['units']
bc18b96c   Goutte   Implement first (...
1487
1488
1489
1490
1491
1492
1493
1494
                    nc_vars.append(nc_var)
                for i, nc_var in enumerate(nc_vars):
                    index = indices[i]
                    values = []
                    for dkey in dkeys:
                        dval = data[dkey]
                        values.append(dval[index])
                    nc_var[:] = values
ceeb2f4a   Goutte   Add the target co...
1495
1496

                # ORBIT #
6491a1f1   Goutte   Fix up the bugs l...
1497
                nc_x = nc_group.createVariable('xhee', 'f8', (dimension,))
ceeb2f4a   Goutte   Add the target co...
1498
                nc_x.units = 'Au'
6491a1f1   Goutte   Fix up the bugs l...
1499
                nc_y = nc_group.createVariable('yhee', 'f8', (dimension,))
ceeb2f4a   Goutte   Add the target co...
1500
1501
1502
                nc_y.units = 'Au'
                values_x = []
                values_y = []
6491a1f1   Goutte   Fix up the bugs l...
1503
1504
                index_x = available_params.index('xhee')
                index_y = available_params.index('yhee')
ceeb2f4a   Goutte   Add the target co...
1505
1506
1507
1508
1509
1510
                for dkey in dkeys:
                    dval = data[dkey]
                    values_x.append(dval[index_x])
                    values_y.append(dval[index_y])
                nc_x[:] = values_x
                nc_y[:] = values_y
89c56528   hitier   Rename heliopropa...
1511
            hp_logger.debug("Writing NetCDF '%s'..." % nc_filename)
ceeb2f4a   Goutte   Add the target co...
1512

d1c44c51   Goutte   Enable Earth
1513
        except Exception:
89c56528   hitier   Rename heliopropa...
1514
            hp_logger.error("Failed to generate NetCDF '%s'." % nc_filename)
d1c44c51   Goutte   Enable Earth
1515
            raise
bc18b96c   Goutte   Implement first (...
1516
1517
1518
1519
1520
1521
        finally:
            nc_handle.close()

    if not isfile(nc_path):
        abort(500, "No NetCDF to serve. Looked at '%s'." % nc_path)

e18701b6   Goutte   Cache clear (remo...
1522
    return send_from_directory(CACHE_DIR, nc_filename)
bc18b96c   Goutte   Implement first (...
1523
1524


297a7dfc   Goutte   Add support for i...
1525
1526
@app.route("/<targets>_<inp>_<started_at>_<stopped_at>.cdf")
def download_targets_cdf(targets, inp, started_at, stopped_at):
aa7247d6   Goutte   Generate a CDF fi...
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
    """
    Grab data and orbit data for the specified `target`,
    rearrange it and return it as a CDF file.
    `started_at` and `stopped_at` are expected to be UTC.

    targets: string list of targets' slugs, separated by `-`.
    params: string list of targets' parameters, separated by `-`.
    """
    separator = '-'  # /!\ this char should never be in target's slugs
    targets = targets.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1537
    targets.sorty()
aa7247d6   Goutte   Generate a CDF fi...
1538
1539
1540
1541
1542
1543
1544
1545
1546
    targets_configs = []
    for target in targets:
        if not target:
            abort(400, "Invalid targets format : `%s`." % targets)
        targets_configs.append(get_target_config(target))
    if 0 == len(targets_configs):
        abort(400, "No valid targets specified. What are you doing?")

    params = PARAMETERS.keys()
aa7247d6   Goutte   Generate a CDF fi...
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558

    try:
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
    sta = started_at.strftime(FILE_DATE_FMT)
    sto = stopped_at.strftime(FILE_DATE_FMT)

297a7dfc   Goutte   Add support for i...
1559
1560
1561
1562
1563
    input_slug = get_input_slug_from_query(inp=inp)

    cdf_filename = "%s_%s_%s_%s.cdf" % (
        separator.join(targets), input_slug, sta, sto
    )
aa7247d6   Goutte   Generate a CDF fi...
1564
1565
1566
    cdf_path = join(CACHE_DIR, cdf_filename)

    if not isfile(cdf_path):
89c56528   hitier   Rename heliopropa...
1567
        hp_logger.debug("Creating the CDF file '%s'..." % cdf_filename)
604616e4   Goutte   Misc changes from...
1568
        try:
8a48d5fa   Goutte   Make sure spacepy...
1569
            from spacepy import pycdf
4aaf6874   Goutte   Try fixing the ge...
1570
1571
1572
1573
1574
1575
1576
        except ImportError:
            # If spacepy's toolbox is not up-to-date, importing will fail.
            # So, let's update and try again !
            update_spacepy()
            try:
                from spacepy import pycdf
            except ImportError as e:
89c56528   hitier   Rename heliopropa...
1577
                hp_logger.error("Failed to import pycdf from spacepy : %s" % e)
4aaf6874   Goutte   Try fixing the ge...
1578
                raise
2fe06b17   Goutte   Move the ENV dire...
1579
        except Exception as e:
89c56528   hitier   Rename heliopropa...
1580
            hp_logger.error("Failed to import pycdf from spacepy : %s" % e)
2fe06b17   Goutte   Move the ENV dire...
1581
            raise
4aaf6874   Goutte   Try fixing the ge...
1582

8a48d5fa   Goutte   Make sure spacepy...
1583
        try:
952e3d8f   Goutte   Move to another s...
1584
            cdf_handle = pycdf.CDF(cdf_path, masterpath='')
54bb1311   Goutte   Bring back the CM...
1585
1586
            targets_names = ', '.join([t['name'] for t in targets_configs])
            description = "Model and orbit data for %s." % targets_names
952e3d8f   Goutte   Move to another s...
1587
1588
1589
            cdf_handle.attrs['Description'] = description
            cdf_handle.attrs['Author'] = "Heliopropa.irap.omp.eu (CDPP)"
            cdf_handle.attrs['Created'] = str(time.ctime(time.time()))
aa7247d6   Goutte   Generate a CDF fi...
1590

54bb1311   Goutte   Bring back the CM...
1591
1592
1593
1594
            # fixme: Try changing the name from 00 to something relevant
            cdf_handle.attrs['Title'] = "Heliopropa - %s" % targets_names
            #######

aa7247d6   Goutte   Generate a CDF fi...
1595
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1597
            available_params = list(PROPERTIES)
            for target in targets_configs:
                target_slug = target['slug']
297a7dfc   Goutte   Add support for i...
1598
1599
1600
1601
                data = get_data_for_target(
                    target_config=target, input_slug=input_slug,
                    started_at=started_at, stopped_at=stopped_at
                )
aa7247d6   Goutte   Generate a CDF fi...
1602
1603
1604
                dkeys = sorted(data)

                values = []
aa7247d6   Goutte   Generate a CDF fi...
1605
                for dkey in dkeys:
952e3d8f   Goutte   Move to another s...
1606
1607
1608
1609
                    time_str = data[dkey][0][:-6]  # remove +00:00 tail
                    date = datetime.datetime.strptime(time_str, FILE_DATE_FMT)
                    values.append(date)
                kt = "%s_time" % target_slug
4aaf6874   Goutte   Try fixing the ge...
1610
                cdf_handle.new(kt, type=pycdf.const.CDF_EPOCH)
952e3d8f   Goutte   Move to another s...
1611
                cdf_handle[kt] = values
4aaf6874   Goutte   Try fixing the ge...
1612
                # cdf_handle[kt].attrs['FIELDNAM'] = "Time since 0 A.D"
aa7247d6   Goutte   Generate a CDF fi...
1613
1614
1615

                for param in params:
                    k = "%s_%s" % (target_slug, param)
aa7247d6   Goutte   Generate a CDF fi...
1616
1617
                    values = []
                    i = available_params.index(param)
4aaf6874   Goutte   Try fixing the ge...
1618
                    has_nones = False
aa7247d6   Goutte   Generate a CDF fi...
1619
                    for dkey in dkeys:
4aaf6874   Goutte   Try fixing the ge...
1620
1621
1622
1623
1624
1625
1626
1627
1628
                        value = data[dkey][i]
                        if value is None:
                            has_nones = True
                        values.append(value)
                    if has_nones:
                        # PyCDF hates it when there are Nones.
                        # Since we don't know what value to set instead,
                        # let's skip the param altogether.
                        continue
aa7247d6   Goutte   Generate a CDF fi...
1629
                    cdf_handle[k] = values
952e3d8f   Goutte   Move to another s...
1630
1631
1632
1633
1634
1635
1636
1637
1638
1639
                    attrs = cdf_handle[k].attrs
                    attrs['UNITS'] = PARAMETERS[param]['units']
                    attrs['LABLAXIS'] = PARAMETERS[param]['name']
                    attrs['FIELDNAM'] = PARAMETERS[param]['title']
                    if values:
                        attrs['VALIDMIN'] = min(values)
                        attrs['VALIDMAX'] = max(values)

                kx = "%s_xhee" % target_slug
                ky = "%s_yhee" % target_slug
aa7247d6   Goutte   Generate a CDF fi...
1640
1641
1642
1643
1644
                values_xhee = []
                values_yhee = []
                index_x = available_params.index('xhee')
                index_y = available_params.index('yhee')
                for dkey in dkeys:
391d581c   Goutte   Make the CDF down...
1645
1646
1647
                    value_xhee = data[dkey][index_x]
                    value_yhee = data[dkey][index_y]
                    # We've got some `None`s cropping up in the data sometimes.
4aaf6874   Goutte   Try fixing the ge...
1648
                    # PyCDF does not digest Nones at all.
391d581c   Goutte   Make the CDF down...
1649
1650
1651
1652
1653
                    # While they solve this upstream, let's make an ugly fix!
                    if (value_xhee is not None) and (value_yhee is not None):
                        values_xhee.append(value_xhee)
                        values_yhee.append(value_yhee)
                    else:
4aaf6874   Goutte   Try fixing the ge...
1654
1655
                        values_xhee.append(0)
                        values_yhee.append(0)
89c56528   hitier   Rename heliopropa...
1656
                        hp_logger.warning("Orbit data for %s has NaNs." % target_slug)
952e3d8f   Goutte   Move to another s...
1657
1658
1659
1660
                cdf_handle[kx] = values_xhee
                cdf_handle[ky] = values_yhee
                cdf_handle[kx].attrs['UNITS'] = 'Au'
                cdf_handle[ky].attrs['UNITS'] = 'Au'
aa7247d6   Goutte   Generate a CDF fi...
1661

89c56528   hitier   Rename heliopropa...
1662
            hp_logger.debug("Writing CDF '%s'..." % cdf_filename)
952e3d8f   Goutte   Move to another s...
1663
            cdf_handle.close()
89c56528   hitier   Rename heliopropa...
1664
            hp_logger.debug("Wrote CDF '%s'." % cdf_filename)
aa7247d6   Goutte   Generate a CDF fi...
1665
1666

        except Exception as e:
89c56528   hitier   Rename heliopropa...
1667
            hp_logger.error("Failed to generate CDF '%s'." % cdf_filename)
952e3d8f   Goutte   Move to another s...
1668
1669
            if isfile(cdf_path):
                removefile(cdf_path)
aa7247d6   Goutte   Generate a CDF fi...
1670
1671
            raise

aa7247d6   Goutte   Generate a CDF fi...
1672
1673
1674
1675
1676
1677
    if not isfile(cdf_path):
        abort(500, "No CDF to serve. Looked at '%s'." % cdf_path)

    return send_from_directory(CACHE_DIR, cdf_filename)


11d86851   Goutte   Add support for s...
1678
1679
1680
@app.route("/<target>_auroral_catalog.csv")
def download_auroral_catalog_csv(target):
    tc = validate_tap_target_config(target)
89c56528   hitier   Rename heliopropa...
1681
    hp_logger.debug("Requesting auroral emissions CSV for %s..." % tc['name'])
11d86851   Goutte   Add support for s...
1682
1683
1684
1685

    filename = "%s_auroral_catalog.csv" % (target)
    local_csv_file = join(CACHE_DIR, filename)

11d86851   Goutte   Add support for s...
1686
1687
1688
1689
1690
1691
1692
1693
1694
    target_name = tc['tap']['target_name']
    emissions = retrieve_auroral_emissions(target_name)

    # Be careful with regexes in python 2 ; best always use the ^$
    thumbnail_url_filter = re.compile("^.*proc(?:_small)?\\.(?:jpe?g|png|webp|gif|bmp|tiff)$")

    # Filter the emissions
    def _keep_emission(emission):
        ok = thumbnail_url_filter.match(emission['thumbnail_url'])
11d86851   Goutte   Add support for s...
1695
1696
1697
1698
1699
1700
1701
        return bool(ok)

    emissions = [e for e in emissions if _keep_emission(e)]

    header = ('time_min', 'time_max', 'thumbnail_url', 'external_link')
    if len(emissions):
        header = emissions[0].keys()
b33d5f62   hitier   Change StringIO i...
1702
    si = StringIO()
11d86851   Goutte   Add support for s...
1703
1704
1705
    cw = csv_dict_writer(si, fieldnames=header)
    cw.writeheader()
    # 'time_min', 'time_max', 'thumbnail_url', 'external_link'
34e94ae3   hitier   Code reformating
1706
    # cw.writerow(head)
11d86851   Goutte   Add support for s...
1707

89c56528   hitier   Rename heliopropa...
1708
    hp_logger.debug("Writing auroral emissions CSV for %s..." % tc['name'])
11d86851   Goutte   Add support for s...
1709
1710
    cw.writerows(emissions)

89c56528   hitier   Rename heliopropa...
1711
    hp_logger.info("Generated auroral emissions CSV contents for %s." % tc['name'])
11d86851   Goutte   Add support for s...
1712
1713
1714
1715
1716
1717
1718
1719
    return si.getvalue()

    # if not isfile(local_csv_file):
    #     abort(500, "Could not cache CSV file at '%s'." % local_csv_file)
    #
    # return send_from_directory(CACHE_DIR, filename)


11d86851   Goutte   Add support for s...
1720
1721
1722
1723
1724
1725
1726
1727
1728
@app.route("/test/auroral/<target>")
def test_auroral_emissions(target):
    tc = validate_tap_target_config(target)
    target_name = tc['tap']['target_name']
    retrieved = retrieve_auroral_emissions(target_name)

    return "%d results:\n%s" % (len(retrieved), str(retrieved))


28bb4b28   Goutte   API for the cache...
1729
1730
# API #########################################################################

e18701b6   Goutte   Cache clear (remo...
1731
1732
1733
1734
1735
1736
1737
1738
1739
@app.route("/cache/clear")
def cache_clear():
    """
    Removes all files from the cache.
    Note: It also removes the .gitkeep file. Not a problem for prod.
    """
    removed_files = remove_all_files(CACHE_DIR)
    count = len(removed_files)
    return "Cache cleared! Removed %d file%s." \
95155804   hitier   Reformat code
1740
        % (count, 's' if count != 1 else '')
e18701b6   Goutte   Cache clear (remo...
1741
1742


d9710a98   Goutte   Rename the cleanu...
1743
1744
@app.route("/cache/cleanup")
def cache_cleanup():
28bb4b28   Goutte   API for the cache...
1745
1746
    """
    Removes all files from the cache that are older than roughly one month.
e18701b6   Goutte   Cache clear (remo...
1747
    Note: It also removes the .gitkeep file. Maybe it should not, but hey.
28bb4b28   Goutte   API for the cache...
1748
1749
    """
    a_month_ago = datetime.datetime.now() - datetime.timedelta(days=32)
e18701b6   Goutte   Cache clear (remo...
1750
    removed_files = remove_files_created_before(a_month_ago, CACHE_DIR)
d9710a98   Goutte   Rename the cleanu...
1751
1752
    count = len(removed_files)
    return "Cache cleaned! Removed %d old file%s." \
95155804   hitier   Reformat code
1753
        % (count, 's' if count != 1 else '')
28bb4b28   Goutte   API for the cache...
1754
1755


b500e561   Goutte   Invert the orbits...
1756
1757
1758
1759
@app.route("/cache/warmup")
def cache_warmup():
    """
    Warms up the cache for the current day.
b500e561   Goutte   Invert the orbits...
1760
    """
390a3587   Goutte   Add a CRON config...
1761
    warmup_started_at = datetime.datetime.now()
284f4688   Goutte   Continue layers i...
1762
    sta, sto = get_interval_from_query()
b662fcc3   hitier   Change input name...
1763
    inp = config['defaults']['input_slug']  # default input, maybe warm them all up ?
fb383448   Goutte   Implement the cac...
1764
1765

    targets = get_active_targets()
fb383448   Goutte   Implement the cac...
1766
    targets_slugs = [target['slug'] for target in targets]
d4b3d381   hitier   Tiny python3 synt...
1767
    targets_slugs.sorty()
4aaf6874   Goutte   Try fixing the ge...
1768
1769
1770
1771

    update_spacepy()
    for target in targets:
        download_target_csv(target['slug'], inp, sta, sto)
297a7dfc   Goutte   Add support for i...
1772
    download_targets_cdf('-'.join(targets_slugs), inp, sta, sto)
fb383448   Goutte   Implement the cac...
1773

390a3587   Goutte   Add a CRON config...
1774
1775
1776
1777
    warmup_ended_at = datetime.datetime.now()
    warmup_timedelta = warmup_ended_at - warmup_started_at

    return "Done in %s." % str(warmup_timedelta)
b500e561   Goutte   Invert the orbits...
1778
1779


1324cc91   Goutte   Make the footer i...
1780
@app.route("/log")
596da00d   Goutte   Add more exceptio...
1781
@app.route("/log.html")
1324cc91   Goutte   Make the footer i...
1782
1783
def log_show():
    with open(LOG_FILE, 'r') as f:
bde97e4d   Goutte   Add more changes ...
1784
        contents = f.read()
fb383448   Goutte   Implement the cac...
1785
    return "<pre>" + contents + "</pre>"
bde97e4d   Goutte   Add more changes ...
1786
1787


1324cc91   Goutte   Make the footer i...
1788
1789
1790
1791
1792
1793
1794
@app.route("/log/clear")
def log_clear():
    with open(LOG_FILE, 'w') as f:
        f.truncate()
    return "Log cleared successfully."


1754789b   Goutte   Decorate and clea...
1795
1796
1797
1798
# DEV TOOLS ###################################################################

# @app.route("/inspect")
# def analyze_cdf():
a4a9ef03   Goutte   Cache generated C...
1799
#     """
1754789b   Goutte   Decorate and clea...
1800
#     For debug purposes.
a4a9ef03   Goutte   Cache generated C...
1801
#     """
1754789b   Goutte   Decorate and clea...
1802
1803
#     cdf_to_inspect = get_path("../res/dummy.nc")
#     cdf_to_inspect = get_path("../res/dummy_jupiter_coordinates.nc")
a4a9ef03   Goutte   Cache generated C...
1804
#
b33d5f62   hitier   Change StringIO i...
1805
#     si = StringIO()
1754789b   Goutte   Decorate and clea...
1806
1807
#     cw = csv.DictWriter(si, fieldnames=['Name', 'Shape', 'Length'])
#     cw.writeheader()
a4a9ef03   Goutte   Cache generated C...
1808
#
1754789b   Goutte   Decorate and clea...
1809
1810
1811
1812
1813
1814
1815
1816
1817
1818
#     # 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()
a4a9ef03   Goutte   Cache generated C...
1819
1820
1821
1822
#
#     return si.getvalue()


9390ec89   Goutte   Initial experimen...
1823
1824
1825
# MAIN ########################################################################

if __name__ == "__main__":
952e3d8f   Goutte   Move to another s...
1826
    # Debug mode is on, as the production server does not use this but run.wsgi
9390ec89   Goutte   Initial experimen...
1827
1828
    extra_files = [get_path('../config.yml')]
    app.run(debug=True, extra_files=extra_files)