Blame view

web/run.py 17.7 KB
9390ec89   Goutte   Initial experimen...
1
2
3
import random
import datetime
import StringIO
c42fea3a   Goutte   Rework the CSS wi...
4
from math import sqrt
9390ec89   Goutte   Initial experimen...
5

5ede388f   Goutte   Make sure failed ...
6
from os import listdir, environ, remove as removefile
9390ec89   Goutte   Initial experimen...
7
8
9
from os.path import isfile, join, abspath, dirname

import csv
8644387c   Goutte   Use real data.
10
11
12
import json
import gzip
import urllib
f75faf5f   Goutte   WIP
13
import logging
9390ec89   Goutte   Initial experimen...
14
15
16
17
from pprint import pprint
from csv import writer as csv_writer
from yaml import load as yaml_load
from flask import Flask
57f42bd7   Goutte   Log the abortions.
18
from flask import redirect, url_for, send_from_directory, abort as abort_flask
9390ec89   Goutte   Initial experimen...
19
20
21
22
from flask import request
from jinja2 import Environment, FileSystemLoader
from netCDF4 import Dataset

9390ec89   Goutte   Initial experimen...
23
24
25
26
27
28
29

# PATH RELATIVITY #############################################################

THIS_DIRECTORY = dirname(abspath(__file__))


def get_path(relative_path):
a4a9ef03   Goutte   Cache generated C...
30
    """Get an absolute path from the relative path to this script directory."""
9390ec89   Goutte   Initial experimen...
31
32
33
34
35
36
37
38
39
40
41
42
43
    return abspath(join(THIS_DIRECTORY, relative_path))


# COLLECT GLOBAL INFORMATION FROM SOURCES #####################################

# VERSION
with open(get_path('../VERSION'), 'r') as version_file:
    version = version_file.read().strip()

# CONFIG
with open(get_path('../config.yml'), 'r') as config_file:
    config = yaml_load(config_file.read())

c0df94bc   Goutte   Adding more logs.
44
45
FILE_DATE_FMT = "%Y-%m-%dT%H:%M:%S"

9390ec89   Goutte   Initial experimen...
46

f75faf5f   Goutte   WIP
47
48
49
# LOGGING #####################################################################

log = logging.getLogger("HelioPropa")
9bfa6c42   Goutte   More bug hunting.
50
log.setLevel(logging.DEBUG)
b2837a08   Goutte   Add three retries...
51
52
53
54
55
logHandler = logging.FileHandler(get_path('run.log'))
logHandler.setFormatter(logging.Formatter(
    "%(asctime)s - %(levelname)s - %(message)s"
))
log.addHandler(logHandler)
f75faf5f   Goutte   WIP
56
57


9390ec89   Goutte   Initial experimen...
58
59
60
61
# SETUP FLASK ENGINE ##########################################################

app = Flask(__name__, root_path=THIS_DIRECTORY)
app.debug = environ.get('DEBUG') == 'true'
b2837a08   Goutte   Add three retries...
62
63
64
65
if app.debug:
    log.info("Starting Flask app in debug mode...")
else:
    log.info("Starting Flask app...")
9390ec89   Goutte   Initial experimen...
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126


# 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.
    'tis a failure of jinja2 to not provide a shuffle filter by default.
    """
    try:
        result = list(seq)
        random.shuffle(result)
        return result
    except:
        return seq


def markdown_filter(value, nl2br=False, p=True):
    """
    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


tpl_engine = Environment(loader=FileSystemLoader([get_path('view')]),
                         trim_blocks=True,
                         lstrip_blocks=True)

tpl_engine.globals.update(
    url_for=url_for,
    static=static_global,
)

tpl_engine.filters['markdown'] = markdown_filter
tpl_engine.filters['md'] = markdown_filter
tpl_engine.filters['shuffle'] = shuffle_filter

tpl_global_vars = {
    'request': request,
    'version': version,
    'config': config,
    'now': datetime.datetime.now(),
}


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

57f42bd7   Goutte   Log the abortions.
127
128
129
130
131
def abort(code, message):
    log.error(message)
    abort_flask(code, message)


9390ec89   Goutte   Initial experimen...
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
def render_view(view, context=None):
    """
    A simple helper to render [view] template with [context] vars.
    It automatically adds the global template vars defined above, too.
    It returns a string, usually the HTML contents to display.
    """
    context = {} if context is None else context
    return tpl_engine.get_template(view).render(
        dict(tpl_global_vars.items() + context.items())
    )


# def render_page(page, title="My Page", context=None):
#     """
#     A simple helper to render the md_page.html template with [context] vars &
#     the additional contents of `page/[page].md` in the `md_page` variable.
#     It automagically adds the global template vars defined above, too.
#     It returns a string, usually the HTML contents to display.
#     """
#     if context is None:
#         context = {}
#     context['title'] = title
#     context['md_page'] = ''
#     with file(get_path('page/%s.md' % page)) as f:
#         context['md_page'] = f.read()
#     return tpl_engine.get_template('md_page.html').render(
#         dict(tpl_global_vars.items() + context.items())
#     )

2d2af24b   Goutte   Add a basic orbit...
161
def datetime_from_list(time_list):
0b9821dd   Goutte   Clean up.
162
163
164
165
    """
    Datetimes in retrieved CDFs are stored in lists of numbers,
    with DayOfYear starting at 0. We want it starting at 1 for default parsers.
    """
2d2af24b   Goutte   Add a basic orbit...
166
167
168
169
170
171
    # Day Of Year starts at 0, but for our datetime parser it starts at 1
    doy = '{:03d}'.format(int(''.join(time_list[4:7])) + 1)
    return datetime.datetime.strptime(
        "%s%s%s" % (''.join(time_list[0:4]), doy, ''.join(time_list[7:])),
        "%Y%j%H%M%S%f"
    )
9390ec89   Goutte   Initial experimen...
172

ce8af118   Goutte   Fix the favicon.
173

8644387c   Goutte   Use real data.
174
def get_source_config(slug):
7d6dee0f   Goutte   Continue refacto ...
175
    for s in config['targets']:
8644387c   Goutte   Use real data.
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
        if s['slug'] == slug:
            return s
    raise Exception("No source found for slug '%s'." % slug)


def retrieve_data(orbiter, what, started_at, stopped_at):
    """
    Handles remote querying Myriam's API, downloading, extracting and caching
    the netCDF files.
    :param orbiter: key of the source in the YAML config
    :param what: either 'model' or 'orbit', a key in the config of the source
    :param started_at:
    :param stopped_at:
    :return: a list of local file paths to netCDF (.nc) files
    """

    url = config['amda'].format(
        dataSet=what,
        startTime=started_at.isoformat(),
        stopTime=stopped_at.isoformat()
    )
c50cc9d8   Goutte   Continue fixing.
197
    log.info("Fetching remote gzip files list at '%s'." % url)
b2837a08   Goutte   Add three retries...
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
    retries = 0
    success = False
    remote_gzip_files = []
    while not success and retries < 3:
        try:
            response = urllib.urlopen(url)
            remote_gzip_files = json.loads(response.read())
            if not remote_gzip_files:
                raise Exception("Failed to fetch data at '%s'." % url)
            if remote_gzip_files == 'NODATASET':
                raise Exception("No dataset at '%s'." % url)
            success = True
        except Exception as e:
            log.warn("Failed (%d/3) '%s' : %s" % (retries+1, url, e.message))
        finally:
            retries += 1
    if not remote_gzip_files:
8644387c   Goutte   Use real data.
215
        abort(400, "Failed to fetch data at '%s'." % url)
b2837a08   Goutte   Add three retries...
216
217
    if remote_gzip_files == 'NODATASET':
        abort(400, "No dataset at '%s'." % url)
9bfa6c42   Goutte   More bug hunting.
218
219
220
221
    # if remote_gzip_files == ['OUTOFTIME']:
    #     abort(400, "No data for time interval at '%s'." % url)

    log.debug("Fetched remote gzip files list : %s." % str(remote_gzip_files))
8644387c   Goutte   Use real data.
222
223
224
225

    # retriever = urllib.URLopener()  # would we need to do this every time ?
    local_gzip_files = []
    for remote_gzip_file in remote_gzip_files:
9bfa6c42   Goutte   More bug hunting.
226
227
        if remote_gzip_file == 'OUTOFTIME':
            continue
4cf497e0   Goutte   Make the targets ...
228
        # hotfix removeme @Myriam
8644387c   Goutte   Use real data.
229
230
231
232
233
234
235
236
        if remote_gzip_file.endswith('/.gz'):
            continue
        remote_gzip_file = remote_gzip_file.replace('cdpp1', 'cdpp', 1)
        #########################
        filename = "%s_%s" % (orbiter, str(remote_gzip_file).split('/')[-1])
        local_gzip_file = get_path("../cache/%s" % filename)
        local_gzip_files.append(local_gzip_file)
        if not isfile(local_gzip_file):
9bfa6c42   Goutte   More bug hunting.
237
            log.debug("Retrieving '%s'..." % local_gzip_file)
8644387c   Goutte   Use real data.
238
            urllib.urlretrieve(remote_gzip_file, local_gzip_file)
9bfa6c42   Goutte   More bug hunting.
239
            log.debug("Retrieved '%s'." % local_gzip_file)
8644387c   Goutte   Use real data.
240
241
242
243
244

    local_netc_files = []
    for local_gzip_file in local_gzip_files:
        local_netc_file = local_gzip_file[0:-3]
        local_netc_files.append(local_netc_file)
9bfa6c42   Goutte   More bug hunting.
245
        log.debug("Unzipping '%s'..." % local_gzip_file)
3c064b17   Goutte   Ignore failures w...
246
247
248
249
250
251
252
253
254
255
256
257
        success = True
        try:
            with gzip.open(local_gzip_file, 'rb') as f:
                file_content = f.read()
                with open(local_netc_file, 'w+b') as g:
                    g.write(file_content)
        except Exception as e:
            success = False
            log.warning("Cannot process gz file '%s' from '%s' : %s" %
                        (local_gzip_file, url, e))
        if success:
            log.debug("Unzipped '%s'." % local_gzip_file)
8644387c   Goutte   Use real data.
258
259
260
261

    return local_netc_files


a4a9ef03   Goutte   Cache generated C...
262
def generate_csv_contents(source_config, started_at, stopped_at):
b2837a08   Goutte   Add three retries...
263
    # @todo iterate on models when there are many
8644387c   Goutte   Use real data.
264
265
266
    try:
        model_slug = source_config['models'][0]['slug']
    except:
a4a9ef03   Goutte   Cache generated C...
267
        abort(500, "Invalid model configuration for '%s'." % source_config['slug'])
28ef3790   Goutte   Clean up.
268
269
270
271

    # Grab the list of netCDF files from Myriam's API
    # http://cdpp.irap.omp.eu/BASE/DDService/getDataUrl.php?dataSet=jupiter_orb_all&StartTime=2014-02-23T10:00:10&StopTime=2017-02-24T23:59:00
    # http://cdpp.irap.omp.eu/BASE/DATA/TAO/JUPITER/SW/sw_2014.nc.gz
9bfa6c42   Goutte   More bug hunting.
272
    log.info("Generating CSV for '%s'..." % source_config['slug'])
a4a9ef03   Goutte   Cache generated C...
273
274
    model_files = retrieve_data(source_config['slug'], model_slug, started_at, stopped_at)
    orbits_files = retrieve_data(source_config['slug'], source_config['orbit']['model'], started_at, stopped_at)
61179cdc   Goutte   Initial work on t...
275

a7ef1487   Goutte   More logs !
276
    log.debug("Crunching CSV contents for '%s'..." % source_config['name'])
61179cdc   Goutte   Initial work on t...
277
278
    si = StringIO.StringIO()
    cw = csv_writer(si)
8644387c   Goutte   Use real data.
279
    cw.writerow((  # the order matters !
61179cdc   Goutte   Initial work on t...
280
281
        'time',
        'vrad', 'vtan', 'vlen',
8644387c   Goutte   Use real data.
282
283
        'magn', 'temp', 'pdyn', 'dens', 'angl',
        'xhci', 'yhci'
61179cdc   Goutte   Initial work on t...
284
    ))
9390ec89   Goutte   Initial experimen...
285

8644387c   Goutte   Use real data.
286
287
288
    precision = "%Y-%m-%dT%H"  # model and orbits times are equal-ish
    orbits_data = {}  # keys are datetime as str, values arrays of XY
    for orbits_file in orbits_files:
a7ef1487   Goutte   More logs !
289
        log.debug("%s: opening orbit NETCDF4 '%s'..." % (source_config['name'], orbits_file))
8644387c   Goutte   Use real data.
290
291
292
293
294
295
296
297
        cdf_handle = Dataset(orbits_file, "r", format="NETCDF4")
        times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
        data_hci = cdf_handle.variables['HCI']
        for time, datum_hci in zip(times, data_hci):
            dtime = datetime_from_list(time)
            if started_at <= dtime <= stopped_at:
                dkey = dtime.strftime(precision)
                orbits_data[dkey] = datum_hci
a7ef1487   Goutte   More logs !
298
        cdf_handle.close()
8644387c   Goutte   Use real data.
299
300
301
    all_data = {}  # keys are datetime as str, values tuples of data
    for model_file in model_files:
        # Time, StartTime, StopTime, V, B, N, T, Delta_angle, P_dyn
a7ef1487   Goutte   More logs !
302
303
        log.debug("%s: opening model NETCDF4 '%s'..." %
                  (source_config['name'], model_file))
8644387c   Goutte   Use real data.
304
305
306
307
308
309
310
311
        cdf_handle = Dataset(model_file, "r", format="NETCDF4")
        times = cdf_handle.variables['Time']  # YYYY DOY HH MM SS .ms
        data_v = cdf_handle.variables['V']
        data_b = cdf_handle.variables['B']
        data_t = cdf_handle.variables['T']
        data_n = cdf_handle.variables['N']
        data_p = cdf_handle.variables['P_dyn']
        data_d = cdf_handle.variables['Delta_angle']
8380e043   Goutte   Fix an awful bug ...
312
        for time, datum_v, datum_b, datum_t, datum_n, datum_p, datum_d \
8644387c   Goutte   Use real data.
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
                in zip(times, data_v, data_b, data_t, data_n, data_p, data_d):
            vrad = datum_v[0]
            vtan = datum_v[1]
            dtime = datetime_from_list(time)
            if started_at <= dtime <= stopped_at:
                dkey = dtime.strftime(precision)
                x_hci = None
                y_hci = None
                if dkey in orbits_data:
                    x_hci = orbits_data[dkey][0]
                    y_hci = orbits_data[dkey][1]
                all_data[dkey] = (
                    dtime.strftime("%Y-%m-%dT%H:%M:%S+00:00"),
                    vrad, vtan, sqrt(vrad * vrad + vtan * vtan),
                    datum_b, datum_t, datum_n, datum_p, datum_d,
                    x_hci, y_hci
                )
        cdf_handle.close()

9bfa6c42   Goutte   More bug hunting.
332
    log.debug("Sorting CSV contents for '%s'..." % source_config['slug'])
8644387c   Goutte   Use real data.
333
334
    for dkey in sorted(all_data):
        cw.writerow(all_data[dkey])
2d2af24b   Goutte   Add a basic orbit...
335

9bfa6c42   Goutte   More bug hunting.
336
    log.info("Done CSV generation for '%s'." % source_config['slug'])
2d2af24b   Goutte   Add a basic orbit...
337
338
    return si.getvalue()

8644387c   Goutte   Use real data.
339

c0df94bc   Goutte   Adding more logs.
340
def generate_csv_file_if_needed(target_config, started_at, stopped_at):
9bfa6c42   Goutte   More bug hunting.
341
    filename = "%s_%s_%s.csv" % (target_config['slug'],
c0df94bc   Goutte   Adding more logs.
342
343
344
345
346
347
348
349
350
351
352
353
                                 started_at.strftime(FILE_DATE_FMT),
                                 stopped_at.strftime(FILE_DATE_FMT))
    local_csv_file = get_path("../cache/%s" % filename)
    if not isfile(local_csv_file):
        log.info("Generating CSV '%s'..." % local_csv_file)
        try:
            with open(local_csv_file, mode="w+") as f:
                f.write(generate_csv_contents(target_config,
                                              started_at=started_at,
                                              stopped_at=stopped_at))
            log.info("Generation of '%s' done." % filename)
        except Exception as e:
5ede388f   Goutte   Make sure failed ...
354
355
            if isfile(local_csv_file):
                removefile(local_csv_file)
9bfa6c42   Goutte   More bug hunting.
356
            abort(500, "Failed creating CSV '%s' : %s" % (filename, e))
c0df94bc   Goutte   Adding more logs.
357
358


a4a9ef03   Goutte   Cache generated C...
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
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


# ROUTING #####################################################################

@app.route('/favicon.ico')
def favicon():
    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():
    return render_view('home.html.jinja2', {
        'targets': config['targets'],
        'planets': [s for s in config['targets'] if s['type'] == 'planet'],
        'probes':  [s for s in config['targets'] if s['type'] == 'probe'],
        'comets':  [s for s in config['targets'] if s['type'] == 'comet'],
        'visits':  increment_hit_counter(),
    })


@app.route("/<source>_<started_at>_<stopped_at>.csv")
def get_target_csv(source, started_at, stopped_at):
    """
    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.
    """
a4a9ef03   Goutte   Cache generated C...
405
    source_config = get_source_config(source)
a4a9ef03   Goutte   Cache generated C...
406
    try:
c0df94bc   Goutte   Adding more logs.
407
        started_at = datetime.datetime.strptime(started_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
408
409
410
    except:
        abort(400, "Invalid started_at parameter : '%s'." % started_at)
    try:
c0df94bc   Goutte   Adding more logs.
411
        stopped_at = datetime.datetime.strptime(stopped_at, FILE_DATE_FMT)
a4a9ef03   Goutte   Cache generated C...
412
413
414
    except:
        abort(400, "Invalid stopped_at parameter : '%s'." % stopped_at)

a4a9ef03   Goutte   Cache generated C...
415
    filename = "%s_%s_%s.csv" % (source,
c0df94bc   Goutte   Adding more logs.
416
417
                                 started_at.strftime(FILE_DATE_FMT),
                                 stopped_at.strftime(FILE_DATE_FMT))
a4a9ef03   Goutte   Cache generated C...
418
    local_csv_file = get_path("../cache/%s" % filename)
c0df94bc   Goutte   Adding more logs.
419
    generate_csv_file_if_needed(source_config, started_at, stopped_at)
a4a9ef03   Goutte   Cache generated C...
420
421
422
423
424
425
    if not isfile(local_csv_file):
        abort(500, "Could not cache CSV file at '%s'." % local_csv_file)

    return send_from_directory(get_path("../cache/"), filename)


b2837a08   Goutte   Add three retries...
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
@app.route("/<targets>_<started_at>_<stopped_at>.zip")
def download_targets_zip(targets, started_at, stopped_at):
    """
    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.

    targets: string list of targets' slugs, separated by `:`.


    fixme


    """

    targets_confs = []
    for target in targets.split(':').sort():
        if not target:
            abort(400, "Invalid targets format : `%s`." % targets)
        targets_confs.append(get_source_config(target))
    if 0 == len(targets_confs):
        abort(400, "No valid targets specified. What are you doing?")

    date_fmt = "%Y-%m-%dT%H:%M:%S"
    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)


    filename = "%s_%s_%s.csv" % (source,
                                 started_at.strftime(date_fmt),
                                 stopped_at.strftime(date_fmt))

    local_csv_file = get_path("../cache/%s" % filename)
    if not isfile(local_csv_file):
        with open(local_csv_file, mode="w+") as f:
            f.write(generate_csv_contents(source_config,
                                          started_at=started_at,
                                          stopped_at=stopped_at))

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

    return send_from_directory(get_path("../cache/"), filename)

1754789b   Goutte   Decorate and clea...
476
477
478
479
# DEV TOOLS ###################################################################

# @app.route("/inspect")
# def analyze_cdf():
a4a9ef03   Goutte   Cache generated C...
480
#     """
1754789b   Goutte   Decorate and clea...
481
#     For debug purposes.
a4a9ef03   Goutte   Cache generated C...
482
#     """
1754789b   Goutte   Decorate and clea...
483
484
#     cdf_to_inspect = get_path("../res/dummy.nc")
#     cdf_to_inspect = get_path("../res/dummy_jupiter_coordinates.nc")
a4a9ef03   Goutte   Cache generated C...
485
486
#
#     si = StringIO.StringIO()
1754789b   Goutte   Decorate and clea...
487
488
#     cw = csv.DictWriter(si, fieldnames=['Name', 'Shape', 'Length'])
#     cw.writeheader()
a4a9ef03   Goutte   Cache generated C...
489
#
1754789b   Goutte   Decorate and clea...
490
491
492
493
494
495
496
497
498
499
#     # 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...
500
501
502
503
#
#     return si.getvalue()


9390ec89   Goutte   Initial experimen...
504
505
506
507
508
509
# MAIN ########################################################################

if __name__ == "__main__":
    # Debug mode on, as the production server does not use this.
    extra_files = [get_path('../config.yml')]
    app.run(debug=True, extra_files=extra_files)