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web/run.py 62.1 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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logHandler = logging.FileHandler(LOG_FILE)
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logHandler.setFormatter(logging.Formatter(
    "%(asctime)s - %(levelname)s - %(message)s"
))
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# set file messages depending on env var setting
if DEBUG:
    logHandler.setLevel(logging.DEBUG)
else:
    logHandler.setLevel(logging.ERROR)
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hp_logger.addHandler(logHandler)
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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
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                        - Jupiter
                        - Saturn
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                        - Mars
                        - MERCURY
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                        - Titan
                        - Io
                        - VENUS
                        - Ganymede
                        - Uranus
                        - Callisto
                        - Europa
7176ae9b   Goutte   Fix Myriam's cont...
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465
                        
                        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
9f57dceb   Goutte   Add half the brid...
466
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    :return: 
    """
11d86851   Goutte   Add support for s...
468
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    # Try out the form
    # http://voparis-tap-planeto.obspm.fr/__system__/adql/query/form

9f57dceb   Goutte   Add half the brid...
472
    api_url = "http://voparis-tap.obspm.fr/__system__/tap/run/tap/sync"
11d86851   Goutte   Add support for s...
473
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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()
9f57dceb   Goutte   Add half the brid...
482
483
    t_stopped_at = time.mktime(d_stopped_at.timetuple())

11d86851   Goutte   Add support for s...
484
    def timestamp_to_jday(timestamp):
9f57dceb   Goutte   Add half the brid...
485
486
        return timestamp / 86400.0 + 2440587.5

11d86851   Goutte   Add support for s...
487
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495
    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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496
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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...
505
506
AND   time_min >= {jday_start}
AND   time_min <= {jday_stop}
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507
508
509
ORDER BY time_min, granule_gid
""".format(
        target_name=target_name.replace("'", "\\'"),
11d86851   Goutte   Add support for s...
510
511
        jday_start=timestamp_to_jday(t_started_at),
        jday_stop=timestamp_to_jday(t_stopped_at)
9f57dceb   Goutte   Add half the brid...
512
    )
95155804   hitier   Reformat code
513
    # AND   processing_level = 4
9f57dceb   Goutte   Add half the brid...
514

95155804   hitier   Reformat code
515
516
517
    #     query = """
    # SELECT DISTINCT target_name FROM apis.epn_core
    # """
9f57dceb   Goutte   Add half the brid...
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    try:
        response = requests.post(api_url, {
            'REQUEST': 'doQuery',
34e94ae3   hitier   Code reformating
522
523
            'LANG': 'ADQL',
            'QUERY': query,
9f57dceb   Goutte   Add half the brid...
524
            'TIMEOUT': '30',
34e94ae3   hitier   Code reformating
525
            'FORMAT': 'VOTable/td'
9f57dceb   Goutte   Add half the brid...
526
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536
        })

        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...
537
538
                'time_min': jday_to_datetime(float(row[0].text)),
                'time_max': jday_to_datetime(float(row[1].text)),
9f57dceb   Goutte   Add half the brid...
539
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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.
551
def retrieve_amda_netcdf(orbiter, what, started_at, stopped_at):
8644387c   Goutte   Use real data.
552
    """
91c3d52d   Goutte   Add more logs.
553
554
    Handles remote querying AMDA's API for URLs, and then downloading,
    extracting and caching the netCDF files.
8644387c   Goutte   Use real data.
555
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566
    :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...
567
    hp_logger.info("Fetching remote gzip files list at '%s'." % url)
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568
569
    retries = 0
    success = False
92abc15b   Goutte   Mistrust the API ...
570
    errors = []
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571
572
573
    remote_gzip_files = []
    while not success and retries < 3:
        try:
3f9c36da   hitier   Change urllib import
574
            response = urllib_request.urlopen(url)
b2837a08   Goutte   Add three retries...
575
576
577
578
            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 ...
579
580
581
                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...
582
            if remote_gzip_files == ['OUTOFTIME']:  # it happens
80352490   Goutte   Multi model suppo...
583
584
                return []
                # raise Exception("API says it's out of time at '%s'." % url)
b2837a08   Goutte   Add three retries...
585
586
            success = True
        except Exception as e:
89c56528   hitier   Rename heliopropa...
587
            hp_logger.warning("Failed (%d/3) '%s' : %s" % (retries + 1, url, e.message))
92abc15b   Goutte   Mistrust the API ...
588
589
            remote_gzip_files = []
            errors.append(e)
b2837a08   Goutte   Add three retries...
590
591
592
        finally:
            retries += 1
    if not remote_gzip_files:
89c56528   hitier   Rename heliopropa...
593
594
595
        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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596
        abort(400, "Failed to fetch gzip files list for %s at '%s' : %s" %
34e94ae3   hitier   Code reformating
597
              (orbiter, url, errors))
08abc2d4   Goutte   Remove duplicate ...
598
599
    else:
        remote_gzip_files = list(set(remote_gzip_files))
9bfa6c42   Goutte   More bug hunting.
600

89c56528   hitier   Rename heliopropa...
601
    hp_logger.debug("Fetched remote gzip files list : %s." % str(remote_gzip_files))
8644387c   Goutte   Use real data.
602

8644387c   Goutte   Use real data.
603
604
    local_gzip_files = []
    for remote_gzip_file in remote_gzip_files:
077980eb   Goutte   Improve availabil...
605
606
607
        # 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.
608
        if remote_gzip_file.endswith('/.gz'):
80352490   Goutte   Multi model suppo...
609
            continue  # this is just a plain bug
8644387c   Goutte   Use real data.
610
        remote_gzip_file = remote_gzip_file.replace('cdpp1', 'cdpp', 1)
077980eb   Goutte   Improve availabil...
611
        ################################################
e18701b6   Goutte   Cache clear (remo...
612
        local_gzip_file = join(CACHE_DIR, get_local_filename(remote_gzip_file))
8644387c   Goutte   Use real data.
613
614
        local_gzip_files.append(local_gzip_file)
        if not isfile(local_gzip_file):
89c56528   hitier   Rename heliopropa...
615
            hp_logger.debug("Retrieving '%s'..." % local_gzip_file)
3f9c36da   hitier   Change urllib import
616
            urllib_request.urlretrieve(remote_gzip_file, local_gzip_file)
89c56528   hitier   Rename heliopropa...
617
            hp_logger.debug("Retrieved '%s'." % local_gzip_file)
dc0be992   Goutte   Support having no...
618
        else:
89c56528   hitier   Rename heliopropa...
619
            hp_logger.debug("Found '%s' in the cache." % local_gzip_file)
8644387c   Goutte   Use real data.
620
621
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623

    local_netc_files = []
    for local_gzip_file in local_gzip_files:
        local_netc_file = local_gzip_file[0:-3]
89c56528   hitier   Rename heliopropa...
624
        hp_logger.debug("Unzipping '%s'..." % local_gzip_file)
3c064b17   Goutte   Ignore failures w...
625
626
        success = True
        try:
5ef50583   Goutte   Clean up.
627
            with gzip.open(local_gzip_file) as f:
3c064b17   Goutte   Ignore failures w...
628
629
630
631
632
                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...
633
634
            hp_logger.error("Cannot process gz file '%s' from '%s' : %s" %
                            (local_gzip_file, url, e))
dc0be992   Goutte   Support having no...
635
636
637
            # 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...
638
        if success:
dc0be992   Goutte   Support having no...
639
            local_netc_files.append(local_netc_file)
89c56528   hitier   Rename heliopropa...
640
            hp_logger.debug("Unzipped '%s'." % local_gzip_file)
8644387c   Goutte   Use real data.
641

ea6c8d5d   Goutte   Add interval cons...
642
    return list(set(local_netc_files))  # remove possible dupes
8644387c   Goutte   Use real data.
643
644


596da00d   Goutte   Add more exceptio...
645
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664
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689
# 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.
690
691
def get_data_for_target(target_config, input_slug,
                        started_at, stopped_at):
180d7d97   Goutte   Refactor heavily.
692
693
694
    """
    :return: dict whose keys are datetime as str, values tuples of data
    """
89c56528   hitier   Rename heliopropa...
695
    hp_logger.debug("Grabbing data for '%s'..." % target_config['slug'])
80352490   Goutte   Multi model suppo...
696

8644387c   Goutte   Use real data.
697
    try:
297a7dfc   Goutte   Add support for i...
698
        models = target_config['models'][input_slug]
077980eb   Goutte   Improve availabil...
699
700
    except Exception as e:
        abort(500, "Invalid model configuration for '%s' : %s"
180d7d97   Goutte   Refactor heavily.
701
702
              % (target_config['slug'], str(e)))
    try:
80352490   Goutte   Multi model suppo...
703
        orbits = target_config['orbit']['models']
d1c44c51   Goutte   Enable Earth
704
705
706
707
    except KeyError as e:
        orbits = []
        # abort(500, "Invalid orbit configuration for '%s' : %s"
        #       % (target_config['slug'], str(e)))
28ef3790   Goutte   Clean up.
708

80352490   Goutte   Multi model suppo...
709
    precision = "%Y-%m-%dT%H"  # model and orbits times are only equal-ish
180d7d97   Goutte   Refactor heavily.
710
    orbit_data = {}  # keys are datetime as str, values arrays of XY
ea6c8d5d   Goutte   Add interval cons...
711
712

    for orbit in orbits:
58bfe281   Goutte   Handle start and ...
713
        s0, s1 = _sta_sto(orbit, started_at, stopped_at)
ea6c8d5d   Goutte   Add interval cons...
714

d1c44c51   Goutte   Enable Earth
715
716
717
718
        nc_keys = default_nc_keys.copy()
        if 'parameters' in orbit:
            nc_keys.update(orbit['parameters'])

ea6c8d5d   Goutte   Add interval cons...
719
720
721
722
        orbit_files = retrieve_amda_netcdf(
            target_config['slug'], orbit['slug'], s0, s1
        )
        for orbit_file in orbit_files:
89c56528   hitier   Rename heliopropa...
723
724
            hp_logger.debug("%s: opening orbit NETCDF4 '%s'..." %
                            (target_config['name'], orbit_file))
ea6c8d5d   Goutte   Add interval cons...
725
726
            cdf_handle = Dataset(orbit_file, "r", format="NETCDF4")
            times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
d1c44c51   Goutte   Enable Earth
727
            data_hee = _read_var(cdf_handle, nc_keys, 'hee', mandatory=True)
ea6c8d5d   Goutte   Add interval cons...
728

89c56528   hitier   Rename heliopropa...
729
730
            hp_logger.debug("%s: aggregating data from '%s'..." %
                            (target_config['name'], orbit_file))
d1c44c51   Goutte   Enable Earth
731
            for ltime, datum_hee in zip(times, data_hee):
1324cc91   Goutte   Make the footer i...
732
                try:
d1c44c51   Goutte   Enable Earth
733
734
                    dtime = datetime_from_list(ltime)
                except Exception:
89c56528   hitier   Rename heliopropa...
735
                    hp_logger.error("Failed to parse time from get__data_for_target %s." % ltime)
d1c44c51   Goutte   Enable Earth
736
                    raise
81cb3ba6   Goutte   Fix an issue with...
737
                # Keep only what's in the interval
ea6c8d5d   Goutte   Add interval cons...
738
                if s0 <= dtime <= s1:
34e94ae3   hitier   Code reformating
739
                    dkey = round_time(dtime, 60 * 60).strftime(precision)
ea6c8d5d   Goutte   Add interval cons...
740
741
                    orbit_data[dkey] = datum_hee
            cdf_handle.close()
180d7d97   Goutte   Refactor heavily.
742

8644387c   Goutte   Use real data.
743
    all_data = {}  # keys are datetime as str, values tuples of data
81cb3ba6   Goutte   Fix an issue with...
744

58bfe281   Goutte   Handle start and ...
745
746
747
748
749
    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
750
751
752
753
        nc_keys = default_nc_keys.copy()
        if 'parameters' in model:
            nc_keys.update(model['parameters'])

129181a6   Goutte   Add more logs to ...
754
        if len(model_files) == 0:
89c56528   hitier   Rename heliopropa...
755
756
            hp_logger.warning("No model data for '%s' '%s'."
                              % (target_config['slug'], model['slug']))
129181a6   Goutte   Add more logs to ...
757

58bfe281   Goutte   Handle start and ...
758
        for model_file in model_files:
89c56528   hitier   Rename heliopropa...
759
760
            hp_logger.debug("%s: opening model NETCDF4 '%s'..." %
                            (target_config['name'], model_file))
58bfe281   Goutte   Handle start and ...
761
            cdf_handle = Dataset(model_file, "r", format="NETCDF4")
596da00d   Goutte   Add more exceptio...
762

d1c44c51   Goutte   Enable Earth
763
            # log.debug(cdf_handle.variables.keys())
596da00d   Goutte   Add more exceptio...
764

58bfe281   Goutte   Handle start and ...
765
            times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
d1c44c51   Goutte   Enable Earth
766
767
768
769
770
771
772
            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
773
774
775
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779
780
781
            # 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...
782
783
784
785
786
787
            # 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...
788
789
            hp_logger.debug("%s: aggregating data from '%s'..." %
                            (target_config['name'], model_file))
d1c44c51   Goutte   Enable Earth
790
791
792
            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 ...
793
                try:
d1c44c51   Goutte   Enable Earth
794
795
                    dtime = datetime_from_list(ltime)
                except Exception:
89c56528   hitier   Rename heliopropa...
796
                    hp_logger.error("Failed to parse time from %s." % ltime)
d1c44c51   Goutte   Enable Earth
797
                    raise
596da00d   Goutte   Add more exceptio...
798

81cb3ba6   Goutte   Fix an issue with...
799
800
801
                if not (s0 <= dtime <= s1):
                    continue  # Cull what's out of the interval

34e94ae3   hitier   Code reformating
802
                droundtime = round_time(dtime, 60 * 60)
81cb3ba6   Goutte   Fix an issue with...
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
                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...
832
                    if model['slug'] == 'ace_swepam_real_1h':
206d8d14   Goutte   Clean up.
833
                        datum_p = datum_n * vtot * vtot * 1.6726e-6
81cb3ba6   Goutte   Fix an issue with...
834
835
836
                    if vtot is None or isnan(vtot):
                        continue

7176ae9b   Goutte   Fix Myriam's cont...
837
838
839
840
841
                # 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...
842
843
                # Keep adding exceptions here until you can't or become mad

2be8e8a0   Goutte   Ignore bad data.
844
                # Ignore bad data
ff11e121   Goutte   Don't ignore bad ...
845
846
                # if numpy.isnan(datum_t):
                #     continue
2be8e8a0   Goutte   Ignore bad data.
847

81cb3ba6   Goutte   Fix an issue with...
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
                # 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...
863
864
                hp_logger.debug("    Ignored %d datum(s) during ~\"drizzling\"."
                                % ignored_count)
81cb3ba6   Goutte   Fix an issue with...
865

58bfe281   Goutte   Handle start and ...
866
            cdf_handle.close()
8644387c   Goutte   Use real data.
867

180d7d97   Goutte   Refactor heavily.
868
869
870
    return all_data


297a7dfc   Goutte   Add support for i...
871
def generate_csv_contents(target_slug, input_slug, started_at, stopped_at):
180d7d97   Goutte   Refactor heavily.
872
    target_config = get_target_config(target_slug)
89c56528   hitier   Rename heliopropa...
873
    hp_logger.debug("Crunching CSV contents for '%s'..." % target_config['name'])
b33d5f62   hitier   Change StringIO i...
874
    si = StringIO()
180d7d97   Goutte   Refactor heavily.
875
876
877
    cw = csv_writer(si)
    cw.writerow(PROPERTIES)

297a7dfc   Goutte   Add support for i...
878
879
880
881
    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.
882

89c56528   hitier   Rename heliopropa...
883
    hp_logger.debug("Writing and sorting CSV for '%s'..." % target_config['slug'])
8644387c   Goutte   Use real data.
884
885
    for dkey in sorted(all_data):
        cw.writerow(all_data[dkey])
2d2af24b   Goutte   Add a basic orbit...
886

89c56528   hitier   Rename heliopropa...
887
    hp_logger.info("Generated CSV contents for '%s'." % target_config['slug'])
2d2af24b   Goutte   Add a basic orbit...
888
889
    return si.getvalue()

8644387c   Goutte   Use real data.
890

dd6ae65b   hitier   Add new csvgenera...
891
892
def generate_csv_contents_spz(target_slug, input_slug, started_at, stopped_at):
    target_config = get_target_config(target_slug)
fc7cbbee   hitier   Move orbit parame...
893
894
    plasma_dict = target_config['models'][input_slug][0]['parameters']
    orbit_dict = target_config['orbit']['models'][0]['parameters']
ec483087   hitier   Fix dict merging
895
    parameters_dict = {**plasma_dict, **orbit_dict}
dd6ae65b   hitier   Add new csvgenera...
896

89c56528   hitier   Rename heliopropa...
897
    hp_logger.info(f"Aggregating dataframes speazy parameters for '{input_slug}' to '{target_slug}'")
dd6ae65b   hitier   Add new csvgenera...
898
    list_df = []
fc7cbbee   hitier   Move orbit parame...
899
    for _name, _id in parameters_dict.items():
89c56528   hitier   Rename heliopropa...
900
        hp_logger.debug(f"Getting parameter id '{_id}' for '{_name}'")
dd6ae65b   hitier   Add new csvgenera...
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
        _df = amda.get_data(_id, started_at, stopped_at).to_dataframe()
        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'})
        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)
    # Is ther a vtot param ? else build it
    if 'vtot' not in final_df.columns:
        final_df['vtot'] = final_df.apply(lambda x: sqrt(x.vtan * x.vtan + x.vrad * x.vrad), axis=1)

    cols_ordered = ['vrad', 'vtan', 'vtot', 'btan', 'brad', 'temp', 'pdyn', 'dens', 'atse', 'xhee', 'yhee']
    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.
933
934
def generate_csv_file_if_needed(target_slug, input_slug,
                                started_at, stopped_at):
297a7dfc   Goutte   Add support for i...
935
936
937
    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...
938
    local_csv_file = join(CACHE_DIR, filename)
80352490   Goutte   Multi model suppo...
939
940
941

    generate = True
    if isfile(local_csv_file):
297a7dfc   Goutte   Add support for i...
942
        # It needs to have more than one line to not be empty (headers)
80352490   Goutte   Multi model suppo...
943
944
945
946
947
948
949
950
        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...
951
    # temporary switch while migrating each target to spz
f85effea   hitier   Set all venus amd...
952
    if target_slug in ['mercury', 'venus', 'mars']:
dd6ae65b   hitier   Add new csvgenera...
953
954
955
956
        csv_generator = generate_csv_contents_spz
    else:
        csv_generator = generate_csv_contents

80352490   Goutte   Multi model suppo...
957
    if generate:
89c56528   hitier   Rename heliopropa...
958
        hp_logger.info("Generating CSV '%s'..." % local_csv_file)
c0df94bc   Goutte   Adding more logs.
959
960
        try:
            with open(local_csv_file, mode="w+") as f:
dd6ae65b   hitier   Add new csvgenera...
961
                f.write(csv_generator(
de97d643   Goutte   Fix more bugs.
962
963
964
                    target_slug=target_slug, input_slug=input_slug,
                    started_at=started_at, stopped_at=stopped_at
                ))
89c56528   hitier   Rename heliopropa...
965
            hp_logger.info("Generation of '%s' done." % filename)
c0df94bc   Goutte   Adding more logs.
966
        except Exception as e:
d1c44c51   Goutte   Enable Earth
967
968
969
            from sys import exc_info
            from traceback import extract_tb
            exc_type, exc_value, exc_traceback = exc_info()
89c56528   hitier   Rename heliopropa...
970
            hp_logger.error(e)
d1c44c51   Goutte   Enable Earth
971
            for trace in extract_tb(exc_traceback):
89c56528   hitier   Rename heliopropa...
972
                hp_logger.error(trace)
5ede388f   Goutte   Make sure failed ...
973
            if isfile(local_csv_file):
89c56528   hitier   Rename heliopropa...
974
                hp_logger.warning("Removing failed CSV '%s'..." % local_csv_file)
5ede388f   Goutte   Make sure failed ...
975
                removefile(local_csv_file)
9bfa6c42   Goutte   More bug hunting.
976
            abort(500, "Failed creating CSV '%s' : %s" % (filename, e))
c0df94bc   Goutte   Adding more logs.
977
978


e18701b6   Goutte   Cache clear (remo...
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
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...
1002
1003
def remove_files_created_before(date, in_directory):
    """
077980eb   Goutte   Improve availabil...
1004
1005
1006
    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...
1007
    :param date: datetime object
077980eb   Goutte   Improve availabil...
1008
    :param in_directory: absolute path to directory
28bb4b28   Goutte   API for the cache...
1009
1010
1011
1012
1013
1014
1015
    :return:
    """
    import os
    import time

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

077980eb   Goutte   Improve availabil...
1016
1017
    if not os.path.isdir(in_directory):
        raise ValueError("No directory to clean at '%s'.")
28bb4b28   Goutte   API for the cache...
1018
1019
1020
1021

    removed_files = []
    for file_name in os.listdir(in_directory):
        file_path = os.path.join(in_directory, file_name)
077980eb   Goutte   Improve availabil...
1022
1023
1024
1025
1026
        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...
1027
1028
1029
1030

    return removed_files


297a7dfc   Goutte   Add support for i...
1031
1032
def get_input_slug_from_query(inp=None):
    if inp is None:
b662fcc3   hitier   Change input name...
1033
        input_slug = request.args.get('input_slug', config['defaults']['input_slug'])
297a7dfc   Goutte   Add support for i...
1034
1035
    else:
        input_slug = inp
de97d643   Goutte   Fix more bugs.
1036
    if input_slug not in [i['slug'] for i in config['inputs']]:
b662fcc3   hitier   Change input name...
1037
        input_slug = config['defaults']['input_slug']  # be tolerant instead of yelling loudly
297a7dfc   Goutte   Add support for i...
1038
1039
1040
    return input_slug


284f4688   Goutte   Continue layers i...
1041
1042
1043
def get_interval_from_query():
    """
    Get the interval from the query, or from defaults.
3309d7c3   Goutte   Improve the date ...
1044
    Returns ISO date strings.
284f4688   Goutte   Continue layers i...
1045
    """
65b27161   hitier   Change default ti...
1046
    before = relativedelta(months=1)
284f4688   Goutte   Continue layers i...
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
    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 ...
1057
1058
1059
1060
1061
    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...
1062
1063
1064
    return started_at, stopped_at


1185f353   Goutte   Fix the CME Catal...
1065
def get_catalog_layers(input_slug, target_slug, started_at, stopped_at):
0332f168   Goutte   Initial support f...
1066
    """
284f4688   Goutte   Continue layers i...
1067
1068
    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...
1069
1070
1071
1072
1073
    
    :param input_slug: 
    :param target_slug: 
    :return: 
    """
0332f168   Goutte   Initial support f...
1074
    import json
2204c3f7   Goutte   Improve layers co...
1075
1076

    def _get_index_of_key(_data, _key):
2204c3f7   Goutte   Improve layers co...
1077
1078
1079
        try:
            index = _data['columns'].index(_key)
        except ValueError:
89c56528   hitier   Rename heliopropa...
1080
            hp_logger.error("Key %s not found in columns of %s" % (_key, _data))
2204c3f7   Goutte   Improve layers co...
1081
1082
1083
            raise
        return index

1185f353   Goutte   Fix the CME Catal...
1084
1085
1086
1087
1088
1089
1090
1091
1092
    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...
1093
    catalog_layers = {}
1ab47144   Goutte   Add new menus, up...
1094
    for config_layer in config['layers']['catalogs']:
0332f168   Goutte   Initial support f...
1095
1096
        if 'data' not in config_layer:
            continue
0332f168   Goutte   Initial support f...
1097
1098
1099
1100
1101
1102
        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 ...
1103
1104
1105
1106
1107
            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...
1108

0332f168   Goutte   Initial support f...
1109
1110
            with open(get_path("../data/catalog/%s" % cl_datum['file'])) as f:
                json_data = json.load(f)
284f4688   Goutte   Continue layers i...
1111
                if 'start' not in cl_datum:
89c56528   hitier   Rename heliopropa...
1112
                    hp_logger.error("Invalid configuration: 'start' is missing.")
284f4688   Goutte   Continue layers i...
1113
                    continue  # skip this
1185f353   Goutte   Fix the CME Catal...
1114
                if 'format' not in cl_datum:
54bb1311   Goutte   Bring back the CM...
1115
1116
1117
                    cl_datum['format'] = CME_DATE_FMT
                    # log.error("Invalid configuration: 'format' is missing.")
                    # continue  # skip this
284f4688   Goutte   Continue layers i...
1118
1119
1120
1121
1122
                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...
1123

0332f168   Goutte   Initial support f...
1124
                for json_datum in json_data['data']:
2204c3f7   Goutte   Improve layers co...
1125
                    validates_any_constraint = False
b03d5eb1   Goutte   Add the last CME ...
1126
1127
                    if 0 == len(constraints):
                        validates_any_constraint = True
2204c3f7   Goutte   Improve layers co...
1128
1129
                    for constraint in constraints:
                        validates_constraint = True
d4b3d381   hitier   Tiny python3 synt...
1130
                        for key, possible_values in iter(constraint.items()):
2204c3f7   Goutte   Improve layers co...
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
                            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...
1141
                        continue
284f4688   Goutte   Continue layers i...
1142
1143
                    start_time = json_datum[start_index]
                    stop_time = json_datum[stop_index]
1185f353   Goutte   Fix the CME Catal...
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154

                    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...
1155
                    catalog_layers[config_layer['slug']].append({
1185f353   Goutte   Fix the CME Catal...
1156
                        'start': start_time.strftime(MOMENT_DATE_FMT),
34e94ae3   hitier   Code reformating
1157
                        'stop': stop_time.strftime(MOMENT_DATE_FMT),
0332f168   Goutte   Initial support f...
1158
                    })
0332f168   Goutte   Initial support f...
1159
1160
1161
1162

    return catalog_layers


077980eb   Goutte   Improve availabil...
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
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...
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
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...
1190
1191
def update_spacepy():
    """
11d86851   Goutte   Add support for s...
1192
    Importing pycdf will fail if the toolbox is not up to date.
4aaf6874   Goutte   Try fixing the ge...
1193
    """
4aaf6874   Goutte   Try fixing the ge...
1194
    try:
89c56528   hitier   Rename heliopropa...
1195
        hp_logger.info("Updating spacepy's toolbox…")
4aaf6874   Goutte   Try fixing the ge...
1196
1197
1198
1199
        import spacepy.toolbox

        spacepy.toolbox.update()
    except Exception as e:
89c56528   hitier   Rename heliopropa...
1200
        hp_logger.error("Failed to update spacepy : %s." % e)
4aaf6874   Goutte   Try fixing the ge...
1201
1202


077980eb   Goutte   Improve availabil...
1203
1204
1205
tpl_global_vars['visits'] = get_hit_counter()


a4a9ef03   Goutte   Cache generated C...
1206
1207
1208
# ROUTING #####################################################################

@app.route('/favicon.ico')
bde97e4d   Goutte   Add more changes ...
1209
def favicon():  # we want it served from the root, not from static/
a4a9ef03   Goutte   Cache generated C...
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
    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...
1220
    increment_hit_counter()
bde97e4d   Goutte   Add more changes ...
1221
    parameters = PARAMETERS.values()
d4b3d381   hitier   Tiny python3 synt...
1222
    parameters = sorted(parameters, key=lambda x: x['position'])
297a7dfc   Goutte   Add support for i...
1223
    input_slug = get_input_slug_from_query()
0332f168   Goutte   Initial support f...
1224
    targets = [t for t in config['targets'] if not t['locked']]
284f4688   Goutte   Continue layers i...
1225
    started_at, stopped_at = get_interval_from_query()
0332f168   Goutte   Initial support f...
1226
1227
    for i, target in enumerate(targets):
        targets[i]['catalog_layers'] = get_catalog_layers(
1185f353   Goutte   Fix the CME Catal...
1228
            input_slug, target['slug'], started_at, stopped_at
0332f168   Goutte   Initial support f...
1229
        )
a4a9ef03   Goutte   Cache generated C...
1230
    return render_view('home.html.jinja2', {
0332f168   Goutte   Initial support f...
1231
1232
        # 'targets': config['targets'],
        'targets': targets,
bde97e4d   Goutte   Add more changes ...
1233
        'parameters': parameters,
297a7dfc   Goutte   Add support for i...
1234
        'input_slug': input_slug,
284f4688   Goutte   Continue layers i...
1235
1236
        'started_at': started_at,
        'stopped_at': stopped_at,
a4a9ef03   Goutte   Cache generated C...
1237
        'planets': [s for s in config['targets'] if s['type'] == 'planet'],
34e94ae3   hitier   Code reformating
1238
1239
1240
        '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...
1241
1242
1243
    })


64a671cd   Goutte   Add an About page.
1244
1245
@app.route("/about.html")
def about():
36961d6f   Goutte   Slightly improve ...
1246
    import uuid
64a671cd   Goutte   Add an About page.
1247
1248
    increment_hit_counter()
    return render_view('about.html.jinja2', {
36961d6f   Goutte   Slightly improve ...
1249
1250
1251
        '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.
1252
1253
1254
    })


6288347a   Goutte   Add the HELP page...
1255
1256
1257
1258
1259
1260
1261
@app.route("/help.html")
def help():
    return render_view('help.html.jinja2', {
        'visits': get_hit_counter(),
    })


297a7dfc   Goutte   Add support for i...
1262
1263
@app.route("/<target>_<inp>_<started_at>_<stopped_at>.csv")
def download_target_csv(target, inp, started_at, stopped_at):
a4a9ef03   Goutte   Cache generated C...
1264
1265
1266
1267
    """
    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...
1268
    `inp` is the input slug, omni or sa or sb.
a4a9ef03   Goutte   Cache generated C...
1269
    """
180d7d97   Goutte   Refactor heavily.
1270
    check_target_config(target)
a4a9ef03   Goutte   Cache generated C...
1271
    try:
c0df94bc   Goutte   Adding more logs.
1272
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
1273
1274
1275
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
c0df94bc   Goutte   Adding more logs.
1276
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
1277
1278
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
297a7dfc   Goutte   Add support for i...
1279
    input_slug = get_input_slug_from_query(inp=inp)
a4a9ef03   Goutte   Cache generated C...
1280

297a7dfc   Goutte   Add support for i...
1281
1282
1283
    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...
1284
    local_csv_file = join(CACHE_DIR, filename)
297a7dfc   Goutte   Add support for i...
1285
1286
1287
1288
    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...
1289
1290
1291
    if not isfile(local_csv_file):
        abort(500, "Could not cache CSV file at '%s'." % local_csv_file)

e18701b6   Goutte   Cache clear (remo...
1292
    return send_from_directory(CACHE_DIR, filename)
a4a9ef03   Goutte   Cache generated C...
1293
1294


297a7dfc   Goutte   Add support for i...
1295
1296
@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...
1297
    """
bc18b96c   Goutte   Implement first (...
1298
1299
1300
    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...
1301

ea6c8d5d   Goutte   Add interval cons...
1302
1303
    Note: we do not use this route anymore, but let's keep it shelved for now.

2fedd73b   Goutte   Initial implement...
1304
    targets: string list of targets' slugs, separated by `-`.
b2837a08   Goutte   Add three retries...
1305
    """
2fedd73b   Goutte   Initial implement...
1306
    separator = '-'
0511eed7   Goutte   Tarball generatio...
1307
    targets = targets.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1308
    targets.sorty()
2fedd73b   Goutte   Initial implement...
1309
1310
    targets_configs = []
    for target in targets:
b2837a08   Goutte   Add three retries...
1311
1312
        if not target:
            abort(400, "Invalid targets format : `%s`." % targets)
180d7d97   Goutte   Refactor heavily.
1313
        targets_configs.append(get_target_config(target))
2fedd73b   Goutte   Initial implement...
1314
    if 0 == len(targets_configs):
b2837a08   Goutte   Add three retries...
1315
1316
        abort(400, "No valid targets specified. What are you doing?")

b2837a08   Goutte   Add three retries...
1317
    try:
ea6c8d5d   Goutte   Add interval cons...
1318
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1319
1320
1321
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
ea6c8d5d   Goutte   Add interval cons...
1322
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1323
1324
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)
ea6c8d5d   Goutte   Add interval cons...
1325
1326
    sta = started_at.strftime(FILE_DATE_FMT)
    sto = stopped_at.strftime(FILE_DATE_FMT)
b2837a08   Goutte   Add three retries...
1327

297a7dfc   Goutte   Add support for i...
1328
1329
1330
1331
1332
    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...
1333
    local_gzip_file = join(CACHE_DIR, gzip_filename)
2fedd73b   Goutte   Initial implement...
1334
1335

    if not isfile(local_gzip_file):
89c56528   hitier   Rename heliopropa...
1336
        hp_logger.debug("Creating the CSV files for the tarball...")
2fedd73b   Goutte   Initial implement...
1337
        for target_config in targets_configs:
297a7dfc   Goutte   Add support for i...
1338
1339
1340
            filename = "%s_%s_%s_%s.csv" % (
                target_config['slug'], input_slug, sta, sto
            )
e18701b6   Goutte   Cache clear (remo...
1341
            local_csv_file = join(CACHE_DIR, filename)
2fedd73b   Goutte   Initial implement...
1342
1343
            if not isfile(local_csv_file):
                with open(local_csv_file, mode="w+") as f:
297a7dfc   Goutte   Add support for i...
1344
1345
1346
1347
1348
1349
                    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...
1350

89c56528   hitier   Rename heliopropa...
1351
        hp_logger.debug("Creating the tarball '%s'..." % local_gzip_file)
2fedd73b   Goutte   Initial implement...
1352
1353
        with tarfile.open(local_gzip_file, "w:gz") as tar:
            for target_config in targets_configs:
297a7dfc   Goutte   Add support for i...
1354
1355
1356
                filename = "%s_%s_%s_%s.csv" % (
                    target_config['slug'], input_slug, sta, sto
                )
e18701b6   Goutte   Cache clear (remo...
1357
                local_csv_file = join(CACHE_DIR, filename)
2fedd73b   Goutte   Initial implement...
1358
1359
1360
                tar.add(local_csv_file, arcname=filename)

    if not isfile(local_gzip_file):
0511eed7   Goutte   Tarball generatio...
1361
        abort(500, "No tarball to serve. Looked at '%s'." % local_gzip_file)
2fedd73b   Goutte   Initial implement...
1362

e18701b6   Goutte   Cache clear (remo...
1363
    return send_from_directory(CACHE_DIR, gzip_filename)
b2837a08   Goutte   Add three retries...
1364

28bb4b28   Goutte   API for the cache...
1365

297a7dfc   Goutte   Add support for i...
1366
1367
@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 (...
1368
    """
4aaf6874   Goutte   Try fixing the ge...
1369
1370
    NOTE : This is not used anymore.
    
bc18b96c   Goutte   Implement first (...
1371
    Grab data and orbit data for the specified `target`,
aa7247d6   Goutte   Generate a CDF fi...
1372
    rearrange it and return it as a NetCDF file.
e18701b6   Goutte   Cache clear (remo...
1373
    `started_at` and `stopped_at` are expected to be UTC.
bc18b96c   Goutte   Implement first (...
1374
1375
1376
1377

    targets: string list of targets' slugs, separated by `-`.
    params: string list of targets' parameters, separated by `-`.
    """
e18701b6   Goutte   Cache clear (remo...
1378
    separator = '-'  # /!\ this char should never be in target's slugs
bc18b96c   Goutte   Implement first (...
1379
    targets = targets.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1380
    targets.sorty()
bc18b96c   Goutte   Implement first (...
1381
1382
1383
1384
1385
1386
1387
    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...
1388

bc18b96c   Goutte   Implement first (...
1389
    params = params.split(separator)
d4b3d381   hitier   Tiny python3 synt...
1390
    params.sorty()
bc18b96c   Goutte   Implement first (...
1391
1392
1393
1394
1395
    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...
1396
    date_fmt = FILE_DATE_FMT
bc18b96c   Goutte   Implement first (...
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
    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...
1408
1409
1410
1411
1412
    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...
1413
    nc_path = join(CACHE_DIR, nc_filename)
bc18b96c   Goutte   Implement first (...
1414
1415

    if not isfile(nc_path):
89c56528   hitier   Rename heliopropa...
1416
        hp_logger.debug("Creating the NetCDF file '%s'..." % nc_filename)
bc18b96c   Goutte   Implement first (...
1417
1418
        nc_handle = Dataset(nc_path, "w", format="NETCDF4")
        try:
ea6c8d5d   Goutte   Add interval cons...
1419
            nc_handle.description = "Model and orbit data for targets"  # todo
bc18b96c   Goutte   Implement first (...
1420
            nc_handle.history = "Created " + time.ctime(time.time())
ea6c8d5d   Goutte   Add interval cons...
1421
            nc_handle.source = "Heliopropa (CDDP)"
bc18b96c   Goutte   Implement first (...
1422
1423
1424
            available_params = list(PROPERTIES)
            for target in targets_configs:
                target_slug = target['slug']
89c56528   hitier   Rename heliopropa...
1425
                hp_logger.debug("Adding group '%s' to the NetCDF..." % target_slug)
bc18b96c   Goutte   Implement first (...
1426
                nc_group = nc_handle.createGroup(target_slug)
297a7dfc   Goutte   Add support for i...
1427
1428
1429
1430
                data = get_data_for_target(
                    target_config=target, input_slug=input_slug,
                    started_at=started_at, stopped_at=stopped_at
                )
bc18b96c   Goutte   Implement first (...
1431
                dkeys = sorted(data)
34e94ae3   hitier   Code reformating
1432
                dimension = 'dim_' + target_slug
ceeb2f4a   Goutte   Add the target co...
1433
                nc_handle.createDimension(dimension, len(dkeys))
57493104   Goutte   Add the time to t...
1434
1435

                # TIME #
ceeb2f4a   Goutte   Add the target co...
1436
                nc_time = nc_group.createVariable('time', 'i8', (dimension,))
57493104   Goutte   Add the time to t...
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
                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 (...
1449
1450
1451
1452
                nc_vars = []
                indices = []
                for param in params:
                    indices.append(available_params.index(param))
ceeb2f4a   Goutte   Add the target co...
1453
                    nc_var = nc_group.createVariable(param, 'f8', (dimension,))
5a6d4498   Goutte   Add a title to ea...
1454
                    nc_var.units = PARAMETERS[param]['units']
bc18b96c   Goutte   Implement first (...
1455
1456
1457
1458
1459
1460
1461
1462
                    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...
1463
1464

                # ORBIT #
6491a1f1   Goutte   Fix up the bugs l...
1465
                nc_x = nc_group.createVariable('xhee', 'f8', (dimension,))
ceeb2f4a   Goutte   Add the target co...
1466
                nc_x.units = 'Au'
6491a1f1   Goutte   Fix up the bugs l...
1467
                nc_y = nc_group.createVariable('yhee', 'f8', (dimension,))
ceeb2f4a   Goutte   Add the target co...
1468
1469
1470
                nc_y.units = 'Au'
                values_x = []
                values_y = []
6491a1f1   Goutte   Fix up the bugs l...
1471
1472
                index_x = available_params.index('xhee')
                index_y = available_params.index('yhee')
ceeb2f4a   Goutte   Add the target co...
1473
1474
1475
1476
1477
1478
                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...
1479
            hp_logger.debug("Writing NetCDF '%s'..." % nc_filename)
ceeb2f4a   Goutte   Add the target co...
1480

d1c44c51   Goutte   Enable Earth
1481
        except Exception:
89c56528   hitier   Rename heliopropa...
1482
            hp_logger.error("Failed to generate NetCDF '%s'." % nc_filename)
d1c44c51   Goutte   Enable Earth
1483
            raise
bc18b96c   Goutte   Implement first (...
1484
1485
1486
1487
1488
1489
        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...
1490
    return send_from_directory(CACHE_DIR, nc_filename)
bc18b96c   Goutte   Implement first (...
1491
1492


297a7dfc   Goutte   Add support for i...
1493
1494
@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...
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
    """
    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...
1505
    targets.sorty()
aa7247d6   Goutte   Generate a CDF fi...
1506
1507
1508
1509
1510
1511
1512
1513
1514
    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...
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526

    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...
1527
1528
1529
1530
1531
    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...
1532
1533
1534
    cdf_path = join(CACHE_DIR, cdf_filename)

    if not isfile(cdf_path):
89c56528   hitier   Rename heliopropa...
1535
        hp_logger.debug("Creating the CDF file '%s'..." % cdf_filename)
604616e4   Goutte   Misc changes from...
1536
        try:
8a48d5fa   Goutte   Make sure spacepy...
1537
            from spacepy import pycdf
4aaf6874   Goutte   Try fixing the ge...
1538
1539
1540
1541
1542
1543
1544
        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...
1545
                hp_logger.error("Failed to import pycdf from spacepy : %s" % e)
4aaf6874   Goutte   Try fixing the ge...
1546
                raise
2fe06b17   Goutte   Move the ENV dire...
1547
        except Exception as e:
89c56528   hitier   Rename heliopropa...
1548
            hp_logger.error("Failed to import pycdf from spacepy : %s" % e)
2fe06b17   Goutte   Move the ENV dire...
1549
            raise
4aaf6874   Goutte   Try fixing the ge...
1550

8a48d5fa   Goutte   Make sure spacepy...
1551
        try:
952e3d8f   Goutte   Move to another s...
1552
            cdf_handle = pycdf.CDF(cdf_path, masterpath='')
54bb1311   Goutte   Bring back the CM...
1553
1554
            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...
1555
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            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...
1558

54bb1311   Goutte   Bring back the CM...
1559
1560
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1562
            # fixme: Try changing the name from 00 to something relevant
            cdf_handle.attrs['Title'] = "Heliopropa - %s" % targets_names
            #######

aa7247d6   Goutte   Generate a CDF fi...
1563
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            available_params = list(PROPERTIES)
            for target in targets_configs:
                target_slug = target['slug']
297a7dfc   Goutte   Add support for i...
1566
1567
1568
1569
                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...
1570
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1572
                dkeys = sorted(data)

                values = []
aa7247d6   Goutte   Generate a CDF fi...
1573
                for dkey in dkeys:
952e3d8f   Goutte   Move to another s...
1574
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1576
1577
                    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...
1578
                cdf_handle.new(kt, type=pycdf.const.CDF_EPOCH)
952e3d8f   Goutte   Move to another s...
1579
                cdf_handle[kt] = values
4aaf6874   Goutte   Try fixing the ge...
1580
                # cdf_handle[kt].attrs['FIELDNAM'] = "Time since 0 A.D"
aa7247d6   Goutte   Generate a CDF fi...
1581
1582
1583

                for param in params:
                    k = "%s_%s" % (target_slug, param)
aa7247d6   Goutte   Generate a CDF fi...
1584
1585
                    values = []
                    i = available_params.index(param)
4aaf6874   Goutte   Try fixing the ge...
1586
                    has_nones = False
aa7247d6   Goutte   Generate a CDF fi...
1587
                    for dkey in dkeys:
4aaf6874   Goutte   Try fixing the ge...
1588
1589
1590
1591
1592
1593
1594
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1596
                        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...
1597
                    cdf_handle[k] = values
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1598
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1605
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1607
                    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...
1608
1609
1610
1611
1612
                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...
1613
1614
1615
                    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...
1616
                    # PyCDF does not digest Nones at all.
391d581c   Goutte   Make the CDF down...
1617
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1619
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1621
                    # 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...
1622
1623
                        values_xhee.append(0)
                        values_yhee.append(0)
89c56528   hitier   Rename heliopropa...
1624
                        hp_logger.warning("Orbit data for %s has NaNs." % target_slug)
952e3d8f   Goutte   Move to another s...
1625
1626
1627
1628
                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...
1629

89c56528   hitier   Rename heliopropa...
1630
            hp_logger.debug("Writing CDF '%s'..." % cdf_filename)
952e3d8f   Goutte   Move to another s...
1631
            cdf_handle.close()
89c56528   hitier   Rename heliopropa...
1632
            hp_logger.debug("Wrote CDF '%s'." % cdf_filename)
aa7247d6   Goutte   Generate a CDF fi...
1633
1634

        except Exception as e:
89c56528   hitier   Rename heliopropa...
1635
            hp_logger.error("Failed to generate CDF '%s'." % cdf_filename)
952e3d8f   Goutte   Move to another s...
1636
1637
            if isfile(cdf_path):
                removefile(cdf_path)
aa7247d6   Goutte   Generate a CDF fi...
1638
1639
            raise

aa7247d6   Goutte   Generate a CDF fi...
1640
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1644
1645
    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...
1646
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1648
@app.route("/<target>_auroral_catalog.csv")
def download_auroral_catalog_csv(target):
    tc = validate_tap_target_config(target)
89c56528   hitier   Rename heliopropa...
1649
    hp_logger.debug("Requesting auroral emissions CSV for %s..." % tc['name'])
11d86851   Goutte   Add support for s...
1650
1651
1652
1653

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

11d86851   Goutte   Add support for s...
1654
1655
1656
1657
1658
1659
1660
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1662
    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...
1663
1664
1665
1666
1667
1668
1669
        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...
1670
    si = StringIO()
11d86851   Goutte   Add support for s...
1671
1672
1673
    cw = csv_dict_writer(si, fieldnames=header)
    cw.writeheader()
    # 'time_min', 'time_max', 'thumbnail_url', 'external_link'
34e94ae3   hitier   Code reformating
1674
    # cw.writerow(head)
11d86851   Goutte   Add support for s...
1675

89c56528   hitier   Rename heliopropa...
1676
    hp_logger.debug("Writing auroral emissions CSV for %s..." % tc['name'])
11d86851   Goutte   Add support for s...
1677
1678
    cw.writerows(emissions)

89c56528   hitier   Rename heliopropa...
1679
    hp_logger.info("Generated auroral emissions CSV contents for %s." % tc['name'])
11d86851   Goutte   Add support for s...
1680
1681
1682
1683
1684
1685
1686
1687
    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...
1688
1689
1690
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1693
1694
1695
1696
@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...
1697
1698
# API #########################################################################

e18701b6   Goutte   Cache clear (remo...
1699
1700
1701
1702
1703
1704
1705
1706
1707
@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
1708
        % (count, 's' if count != 1 else '')
e18701b6   Goutte   Cache clear (remo...
1709
1710


d9710a98   Goutte   Rename the cleanu...
1711
1712
@app.route("/cache/cleanup")
def cache_cleanup():
28bb4b28   Goutte   API for the cache...
1713
1714
    """
    Removes all files from the cache that are older than roughly one month.
e18701b6   Goutte   Cache clear (remo...
1715
    Note: It also removes the .gitkeep file. Maybe it should not, but hey.
28bb4b28   Goutte   API for the cache...
1716
1717
    """
    a_month_ago = datetime.datetime.now() - datetime.timedelta(days=32)
e18701b6   Goutte   Cache clear (remo...
1718
    removed_files = remove_files_created_before(a_month_ago, CACHE_DIR)
d9710a98   Goutte   Rename the cleanu...
1719
1720
    count = len(removed_files)
    return "Cache cleaned! Removed %d old file%s." \
95155804   hitier   Reformat code
1721
        % (count, 's' if count != 1 else '')
28bb4b28   Goutte   API for the cache...
1722
1723


b500e561   Goutte   Invert the orbits...
1724
1725
1726
1727
@app.route("/cache/warmup")
def cache_warmup():
    """
    Warms up the cache for the current day.
b500e561   Goutte   Invert the orbits...
1728
    """
390a3587   Goutte   Add a CRON config...
1729
    warmup_started_at = datetime.datetime.now()
284f4688   Goutte   Continue layers i...
1730
    sta, sto = get_interval_from_query()
b662fcc3   hitier   Change input name...
1731
    inp = config['defaults']['input_slug']  # default input, maybe warm them all up ?
fb383448   Goutte   Implement the cac...
1732
1733

    targets = get_active_targets()
fb383448   Goutte   Implement the cac...
1734
    targets_slugs = [target['slug'] for target in targets]
d4b3d381   hitier   Tiny python3 synt...
1735
    targets_slugs.sorty()
4aaf6874   Goutte   Try fixing the ge...
1736
1737
1738
1739

    update_spacepy()
    for target in targets:
        download_target_csv(target['slug'], inp, sta, sto)
297a7dfc   Goutte   Add support for i...
1740
    download_targets_cdf('-'.join(targets_slugs), inp, sta, sto)
fb383448   Goutte   Implement the cac...
1741

390a3587   Goutte   Add a CRON config...
1742
1743
1744
1745
    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...
1746
1747


1324cc91   Goutte   Make the footer i...
1748
@app.route("/log")
596da00d   Goutte   Add more exceptio...
1749
@app.route("/log.html")
1324cc91   Goutte   Make the footer i...
1750
1751
def log_show():
    with open(LOG_FILE, 'r') as f:
bde97e4d   Goutte   Add more changes ...
1752
        contents = f.read()
fb383448   Goutte   Implement the cac...
1753
    return "<pre>" + contents + "</pre>"
bde97e4d   Goutte   Add more changes ...
1754
1755


1324cc91   Goutte   Make the footer i...
1756
1757
1758
1759
1760
1761
1762
@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...
1763
1764
1765
1766
# DEV TOOLS ###################################################################

# @app.route("/inspect")
# def analyze_cdf():
a4a9ef03   Goutte   Cache generated C...
1767
#     """
1754789b   Goutte   Decorate and clea...
1768
#     For debug purposes.
a4a9ef03   Goutte   Cache generated C...
1769
#     """
1754789b   Goutte   Decorate and clea...
1770
1771
#     cdf_to_inspect = get_path("../res/dummy.nc")
#     cdf_to_inspect = get_path("../res/dummy_jupiter_coordinates.nc")
a4a9ef03   Goutte   Cache generated C...
1772
#
b33d5f62   hitier   Change StringIO i...
1773
#     si = StringIO()
1754789b   Goutte   Decorate and clea...
1774
1775
#     cw = csv.DictWriter(si, fieldnames=['Name', 'Shape', 'Length'])
#     cw.writeheader()
a4a9ef03   Goutte   Cache generated C...
1776
#
1754789b   Goutte   Decorate and clea...
1777
1778
1779
1780
1781
1782
1783
1784
1785
1786
#     # 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...
1787
1788
1789
1790
#
#     return si.getvalue()


9390ec89   Goutte   Initial experimen...
1791
1792
1793
# MAIN ########################################################################

if __name__ == "__main__":
952e3d8f   Goutte   Move to another s...
1794
    # Debug mode is on, as the production server does not use this but run.wsgi
9390ec89   Goutte   Initial experimen...
1795
1796
    extra_files = [get_path('../config.yml')]
    app.run(debug=True, extra_files=extra_files)