databases.py 25.4 KB
Newer Older
André Anjos's avatar
André Anjos committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :

###############################################################################
#                                                                             #
# Copyright (c) 2016 Idiap Research Institute, http://www.idiap.ch/           #
# Contact: beat.support@idiap.ch                                              #
#                                                                             #
# This file is part of the beat.cmdline module of the BEAT platform.          #
#                                                                             #
# Commercial License Usage                                                    #
# Licensees holding valid commercial BEAT licenses may use this file in       #
# accordance with the terms contained in a written agreement between you      #
# and Idiap. For further information contact tto@idiap.ch                     #
#                                                                             #
# Alternatively, this file may be used under the terms of the GNU Affero      #
# Public License version 3 as published by the Free Software and appearing    #
# in the file LICENSE.AGPL included in the packaging of this file.            #
# The BEAT platform is distributed in the hope that it will be useful, but    #
# WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY  #
# or FITNESS FOR A PARTICULAR PURPOSE.                                        #
#                                                                             #
# You should have received a copy of the GNU Affero Public License along      #
# with the BEAT platform. If not, see http://www.gnu.org/licenses/.           #
#                                                                             #
###############################################################################

import os
29
import sys
30
import click
André Anjos's avatar
André Anjos committed
31
import glob
32
import random
Samuel GAIST's avatar
Samuel GAIST committed
33
import zmq
34

André Anjos's avatar
André Anjos committed
35
import logging
Samuel GAIST's avatar
Samuel GAIST committed
36

André Anjos's avatar
André Anjos committed
37
38
39

import simplejson

40
from beat.cmdline.scripts.click_helper import AliasedGroup
Samuel GAIST's avatar
Samuel GAIST committed
41
42
from beat.core.hash import toPath
from beat.core.hash import hashDataset
André Anjos's avatar
André Anjos committed
43
44
from beat.core.utils import NumpyJSONEncoder
from beat.core.database import Database
45
from beat.core.data import load_data_index, RemoteDataSource
46
47
48
from beat.core import dock
from beat.core import inputs
from beat.core import utils
André Anjos's avatar
André Anjos committed
49
50
51

from . import common

Samuel GAIST's avatar
Samuel GAIST committed
52
logger = logging.getLogger(__name__)
André Anjos's avatar
André Anjos committed
53

54
55
56
57
CMD_DB_INDEX = 'index'
CMD_VIEW_OUTPUTS = 'databases_provider'


Samuel GAIST's avatar
Samuel GAIST committed
58
# ----------------------------------------------------------
59
60
61
62
63
64
65


def load_database_sets(configuration, database_name):
    # Process the name of the database
    parts = database_name.split('/')

    if len(parts) == 2:
Samuel GAIST's avatar
Samuel GAIST committed
66
67
68
        db_name = os.path.join(*parts[:2])
        protocol_filter = None
        set_filter = None
69
70

    elif len(parts) == 3:
Samuel GAIST's avatar
Samuel GAIST committed
71
72
73
        db_name = os.path.join(*parts[:2])
        protocol_filter = parts[2]
        set_filter = None
74
75

    elif len(parts) == 4:
Samuel GAIST's avatar
Samuel GAIST committed
76
77
78
        db_name = os.path.join(*parts[:2])
        protocol_filter = parts[2]
        set_filter = parts[3]
79
80

    else:
Samuel GAIST's avatar
Samuel GAIST committed
81
        logger.error("Database specification should have the format "
Samuel GAIST's avatar
Samuel GAIST committed
82
                     "`<database>/<version>/[<protocol>/[<set>]]', the value "
Samuel GAIST's avatar
Samuel GAIST committed
83
                     "you passed (%s) is not valid", database_name)
Samuel GAIST's avatar
Samuel GAIST committed
84
        return (None, None)
85
86
87

    # Load the dataformat
    dataformat_cache = {}
88
    database = Database(configuration.path,
Samuel GAIST's avatar
Samuel GAIST committed
89
                        db_name, dataformat_cache)
90
    if not database.valid:
Samuel GAIST's avatar
Samuel GAIST committed
91
92
93
94
        logger.error("Failed to load the database `%s':", db_name)
        for e in database.errors:
            logger.error('  * %s', e)
        return (None, None, None)
95
96
97
98
99

    # Filter the protocols
    protocols = database.protocol_names

    if protocol_filter is not None:
Samuel GAIST's avatar
Samuel GAIST committed
100
101
102
103
        if protocol_filter not in protocols:
            logger.error("The database `%s' does not have the protocol `%s' - "
                         "choose one of `%s'", db_name, protocol_filter,
                         ', '.join(protocols))
104

Samuel GAIST's avatar
Samuel GAIST committed
105
            return (None, None, None)
106

Samuel GAIST's avatar
Samuel GAIST committed
107
        protocols = [protocol_filter]
108
109
110
111
112

    # Filter the sets
    loaded_sets = []

    for protocol_name in protocols:
Samuel GAIST's avatar
Samuel GAIST committed
113
        sets = database.set_names(protocol_name)
114

Samuel GAIST's avatar
Samuel GAIST committed
115
116
117
        if set_filter is not None:
            if set_filter not in sets:
                logger.error("The database/protocol `%s/%s' does not have the "
Samuel GAIST's avatar
Samuel GAIST committed
118
119
120
                             "set `%s' - choose one of `%s'",
                             db_name, protocol_name, set_filter,
                             ', '.join(sets))
Samuel GAIST's avatar
Samuel GAIST committed
121
                return (None, None, None)
122

Samuel GAIST's avatar
Samuel GAIST committed
123
            sets = [z for z in sets if z == set_filter]
124

Samuel GAIST's avatar
Samuel GAIST committed
125
126
        loaded_sets.extend([(protocol_name, set_name,
                             database.set(protocol_name, set_name))
Samuel GAIST's avatar
Samuel GAIST committed
127
                            for set_name in sets])
128
129
130
131

    return (db_name, database, loaded_sets)


Samuel GAIST's avatar
Samuel GAIST committed
132
# ----------------------------------------------------------
133
134


135
136
def start_db_container(configuration, cmd, host,
                       db_name, protocol_name, set_name, database, db_set,
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
                       excluded_outputs=None, uid=None, db_root=None):

    input_list = inputs.InputList()

    input_group = inputs.InputGroup(set_name, restricted_access=False)
    input_list.add(input_group)

    db_configuration = {
        'inputs': {},
        'channel': set_name,
    }

    if uid is not None:
        db_configuration['datasets_uid'] = uid

    if db_root is not None:
        db_configuration['datasets_root_path'] = db_root

    for output_name, dataformat_name in db_set['outputs'].items():
Samuel GAIST's avatar
Samuel GAIST committed
156
        if excluded_outputs is not None and output_name in excluded_outputs:
157
158
            continue

159
        dataset_hash = hashDataset(db_name, protocol_name, set_name)
160
        db_configuration['inputs'][output_name] = dict(
Samuel GAIST's avatar
Samuel GAIST committed
161
162
163
164
165
166
167
            database=db_name,
            protocol=protocol_name,
            set=set_name,
            output=output_name,
            channel=set_name,
            hash=dataset_hash,
            path=toPath(dataset_hash, '.db')
168
169
170
171
172
173
174
175
176
177
178
        )

    db_tempdir = utils.temporary_directory()

    with open(os.path.join(db_tempdir, 'configuration.json'), 'wb') as f:
        simplejson.dump(db_configuration, f, indent=4)

    tmp_prefix = os.path.join(db_tempdir, 'prefix')
    if not os.path.exists(tmp_prefix):
        os.makedirs(tmp_prefix)

179
    database.export(tmp_prefix)
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195

    if db_root is None:
        json_path = os.path.join(tmp_prefix, 'databases', db_name + '.json')

        with open(json_path, 'r') as f:
            db_data = simplejson.load(f)

        database_path = db_data['root_folder']
        db_data['root_folder'] = os.path.join('/databases', db_name)

        with open(json_path, 'w') as f:
            simplejson.dump(db_data, f, indent=4)

    try:
        db_envkey = host.db2docker([db_name])
    except:
Samuel GAIST's avatar
Samuel GAIST committed
196
        raise RuntimeError("No environment found for the database `%s' "
197
198
199
200
201
202
                           "- available environments are %s" % (
                               db_name,
                               ", ".join(host.db_environments.keys())))

    # Creation of the container
    # Note: we only support one databases image loaded at the same time
203
204
205
206
207
    CONTAINER_PREFIX = '/beat/prefix'
    CONTAINER_CACHE = '/beat/cache'

    database_port = random.randint(51000, 60000)
    if cmd == CMD_VIEW_OUTPUTS:
Samuel GAIST's avatar
Samuel GAIST committed
208
209
210
211
212
213
        db_cmd = [
            cmd,
            '0.0.0.0:{}'.format(database_port),
            CONTAINER_PREFIX,
            CONTAINER_CACHE
        ]
214
    else:
Samuel GAIST's avatar
Samuel GAIST committed
215
216
217
218
219
220
221
222
        db_cmd = [
            cmd,
            CONTAINER_PREFIX,
            CONTAINER_CACHE,
            db_name,
            protocol_name,
            set_name
        ]
223
224

    databases_container = host.create_container(db_envkey, db_cmd)
225
    if cmd == CMD_VIEW_OUTPUTS:
Samuel GAIST's avatar
Samuel GAIST committed
226
227
        databases_container.add_port(
            database_port, database_port, host_address=host.ip)
228
229
    databases_container.add_volume(db_tempdir, '/beat/prefix')
    databases_container.add_volume(configuration.cache, '/beat/cache')
230
231

    # Specify the volumes to mount inside the container
Samuel GAIST's avatar
Samuel GAIST committed
232
    if 'datasets_root_path' not in db_configuration:
Samuel GAIST's avatar
Samuel GAIST committed
233
234
        databases_container.add_volume(
            database_path, os.path.join('/databases', db_name))
235
236
237
238
239
240
241
    else:
        databases_container.add_volume(db_configuration['datasets_root_path'],
                                       db_configuration['datasets_root_path'])

    # Start the container
    host.start(databases_container)

242
    if cmd == CMD_VIEW_OUTPUTS:
Samuel GAIST's avatar
Samuel GAIST committed
243
244
245
246
247
        # Communicate with container
        zmq_context = zmq.Context()
        db_socket = zmq_context.socket(zmq.PAIR)
        db_address = 'tcp://{}:{}'.format(host.ip, database_port)
        db_socket.connect(db_address)
248

Samuel GAIST's avatar
Samuel GAIST committed
249
        for output_name, dataformat_name in db_set['outputs'].items():
Samuel GAIST's avatar
Samuel GAIST committed
250
251
            if excluded_outputs is not None and \
               output_name in excluded_outputs:
Samuel GAIST's avatar
Samuel GAIST committed
252
                continue
253

Samuel GAIST's avatar
Samuel GAIST committed
254
255
256
            data_source = RemoteDataSource()
            data_source.setup(db_socket, output_name,
                              dataformat_name, configuration.path)
257

Samuel GAIST's avatar
Samuel GAIST committed
258
259
260
261
            input_ = inputs.Input(output_name,
                                  database.dataformats[dataformat_name],
                                  data_source)
            input_group.add(input_)
262

Samuel GAIST's avatar
Samuel GAIST committed
263
        return (databases_container, db_socket, zmq_context, input_list)
264
265

    return databases_container
266
267


Samuel GAIST's avatar
Samuel GAIST committed
268
# ----------------------------------------------------------
269
270


271
def pull_impl(webapi, prefix, names, force, indentation, format_cache):
Samuel GAIST's avatar
Samuel GAIST committed
272
    """Copies databases (and required dataformats) from the server.
André Anjos's avatar
André Anjos committed
273

Samuel GAIST's avatar
Samuel GAIST committed
274
    Parameters:
André Anjos's avatar
André Anjos committed
275

Samuel GAIST's avatar
Samuel GAIST committed
276
277
      webapi (object): An instance of our WebAPI class, prepared to access the
        BEAT server of interest
André Anjos's avatar
André Anjos committed
278

Samuel GAIST's avatar
Samuel GAIST committed
279
280
      prefix (str): A string representing the root of the path in which the
        user objects are stored
André Anjos's avatar
André Anjos committed
281

André Anjos's avatar
André Anjos committed
282
283
284
285
286
      names (:py:class:`list`): A list of strings, each representing the unique
        relative path of the objects to retrieve or a list of usernames from
        which to retrieve objects. If the list is empty, then we pull all
        available objects of a given type. If no user is set, then pull all
        public objects of a given type.
André Anjos's avatar
André Anjos committed
287

Samuel GAIST's avatar
Samuel GAIST committed
288
289
      force (bool): If set to ``True``, then overwrites local changes with the
        remotely retrieved copies.
André Anjos's avatar
André Anjos committed
290

Samuel GAIST's avatar
Samuel GAIST committed
291
292
293
      indentation (int): The indentation level, useful if this function is
        called recursively while downloading different object types. This is
        normally set to ``0`` (zero).
André Anjos's avatar
André Anjos committed
294

Samuel GAIST's avatar
Samuel GAIST committed
295
296
      format_cache (dict): A dictionary containing all dataformats already
        downloaded.
André Anjos's avatar
André Anjos committed
297
298


Samuel GAIST's avatar
Samuel GAIST committed
299
    Returns:
André Anjos's avatar
André Anjos committed
300

Samuel GAIST's avatar
Samuel GAIST committed
301
302
      int: Indicating the exit status of the command, to be reported back to
        the calling process. This value should be zero if everything works OK,
Samuel GAIST's avatar
Samuel GAIST committed
303
        otherwise, different than zero (POSIX compliance).
André Anjos's avatar
André Anjos committed
304

Samuel GAIST's avatar
Samuel GAIST committed
305
    """
André Anjos's avatar
André Anjos committed
306

307
    from .dataformats import pull_impl as dataformats_pull
André Anjos's avatar
André Anjos committed
308

Samuel GAIST's avatar
Samuel GAIST committed
309
    status, names = common.pull(webapi, prefix, 'database', names,
Samuel GAIST's avatar
Samuel GAIST committed
310
311
                                ['declaration', 'code', 'description'],
                                force, indentation)
André Anjos's avatar
André Anjos committed
312

Samuel GAIST's avatar
Samuel GAIST committed
313
314
315
316
317
    # see what dataformats one needs to pull
    dataformats = []
    for name in names:
        obj = Database(prefix, name)
        dataformats.extend(obj.dataformats.keys())
André Anjos's avatar
André Anjos committed
318

Samuel GAIST's avatar
Samuel GAIST committed
319
320
321
    # downloads any formats to which we depend on
    df_status = dataformats_pull(webapi, prefix, dataformats, force,
                                 indentation + 2, format_cache)
André Anjos's avatar
André Anjos committed
322

Samuel GAIST's avatar
Samuel GAIST committed
323
    return status + df_status
André Anjos's avatar
André Anjos committed
324
325


Samuel GAIST's avatar
Samuel GAIST committed
326
# ----------------------------------------------------------
André Anjos's avatar
André Anjos committed
327
328


329
def index_outputs(configuration, names, uid=None, db_root=None, docker=False):
André Anjos's avatar
André Anjos committed
330

331
332
    names = common.make_up_local_list(configuration.path, 'database', names)
    retcode = 0
André Anjos's avatar
André Anjos committed
333

Philip ABBET's avatar
Philip ABBET committed
334
    if docker:
Samuel GAIST's avatar
Samuel GAIST committed
335
        host = dock.Host(raise_on_errors=False)
André Anjos's avatar
André Anjos committed
336

337
    for database_name in names:
Samuel GAIST's avatar
Samuel GAIST committed
338
        logger.info("Indexing database %s...", database_name)
André Anjos's avatar
André Anjos committed
339

Samuel GAIST's avatar
Samuel GAIST committed
340
341
342
343
344
        (db_name, database, sets) = load_database_sets(
            configuration, database_name)
        if database is None:
            retcode += 1
            continue
André Anjos's avatar
André Anjos committed
345

Samuel GAIST's avatar
Samuel GAIST committed
346
347
        for protocol_name, set_name, db_set in sets:
            if not docker:
348
349
350
351
352
353
354
                try:
                    view = database.view(protocol_name, set_name)
                except SyntaxError as error:
                    logger.error("Failed to load the database `%s':",
                                 database_name)
                    logger.error('  * Syntax error: %s', error)
                    view = None
André Anjos's avatar
André Anjos committed
355

Samuel GAIST's avatar
Samuel GAIST committed
356
357
358
                if view is None:
                    retcode += 1
                    continue
359

Samuel GAIST's avatar
Samuel GAIST committed
360
                dataset_hash = hashDataset(db_name, protocol_name, set_name)
361
362
363
364
365
366
367
368
369
                try:
                    view.index(os.path.join(configuration.cache,
                                            toPath(dataset_hash, '.db')))
                except RuntimeError as error:
                  logger.error("Failed to load the database `%s':",
                               database_name)
                  logger.error('  * Runtime error %s', error)
                  retcode += 1
                  continue
370

Samuel GAIST's avatar
Samuel GAIST committed
371
372
373
            else:
                databases_container = \
                    start_db_container(configuration, CMD_DB_INDEX,
Samuel GAIST's avatar
Samuel GAIST committed
374
375
                                       host, db_name, protocol_name, set_name,
                                       database, db_set,
Samuel GAIST's avatar
Samuel GAIST committed
376
377
378
379
380
                                       uid=uid, db_root=db_root
                                       )
                status = host.wait(databases_container)
                if status != 0:
                    retcode += 1
André Anjos's avatar
André Anjos committed
381

382
    return retcode
André Anjos's avatar
André Anjos committed
383
384


Samuel GAIST's avatar
Samuel GAIST committed
385
# ----------------------------------------------------------
André Anjos's avatar
André Anjos committed
386
387


388
def list_index_files(configuration, names):
389

390
    names = common.make_up_local_list(configuration.path, 'database', names)
391

392
    retcode = 0
393

394
395
    for database_name in names:
        logger.info("Listing database %s indexes...", database_name)
396

Samuel GAIST's avatar
Samuel GAIST committed
397
398
        (db_name, database, sets) = load_database_sets(
            configuration, database_name)
399
400
401
        if database is None:
            retcode += 1
            continue
André Anjos's avatar
André Anjos committed
402

403
        for protocol_name, set_name, db_set in sets:
404
405
406
407
408
            dataset_hash = hashDataset(db_name, protocol_name, set_name)
            index_filename = toPath(dataset_hash)
            basename = os.path.splitext(index_filename)[0]
            for g in glob.glob(basename + '.*'):
                logger.info(g)
409

410
    return retcode
411
412


Samuel GAIST's avatar
Samuel GAIST committed
413
# ----------------------------------------------------------
414
415


416
def delete_index_files(configuration, names):
417

418
    names = common.make_up_local_list(configuration.path, 'database', names)
419

420
    retcode = 0
421

422
423
    for database_name in names:
        logger.info("Deleting database %s indexes...", database_name)
424

Samuel GAIST's avatar
Samuel GAIST committed
425
426
        (db_name, database, sets) = load_database_sets(
            configuration, database_name)
427
428
429
        if database is None:
            retcode += 1
            continue
430

431
432
        for protocol_name, set_name, db_set in sets:
            for output_name in db_set['outputs'].keys():
433
434
435
436
                dataset_hash = hashDataset(db_name, protocol_name, set_name)
                index_filename = toPath(dataset_hash)
                basename = os.path.join(configuration.cache,
                                        os.path.splitext(index_filename)[0])
437

438
439
440
                for g in glob.glob(basename + '.*'):
                    logger.info("removing `%s'...", g)
                    os.unlink(g)
441

442
443
                common.recursive_rmdir_if_empty(os.path.dirname(basename),
                                                configuration.cache)
444

445
    return retcode
446
447


Samuel GAIST's avatar
Samuel GAIST committed
448
# ----------------------------------------------------------
449

André Anjos's avatar
André Anjos committed
450

451
452
def view_outputs(configuration, dataset_name, excluded_outputs=None, uid=None,
                 db_root=None, docker=False):
André Anjos's avatar
André Anjos committed
453

454
455
    def data_to_json(data, indent):
        value = common.stringify(data.as_dict())
André Anjos's avatar
André Anjos committed
456

457
458
459
460
461
462
        value = simplejson.dumps(value, indent=4, cls=NumpyJSONEncoder) \
            .replace('"BEAT_LIST_DELIMITER[', '[') \
            .replace(']BEAT_LIST_DELIMITER"', ']') \
            .replace('"...",', '...') \
            .replace('"BEAT_LIST_SIZE(', '(') \
            .replace(')BEAT_LIST_SIZE"', ')')
André Anjos's avatar
André Anjos committed
463

464
        return ('\n' + ' ' * indent).join(value.split('\n'))
André Anjos's avatar
André Anjos committed
465

466
467
468
    # Load the infos about the database set
    (db_name, database, sets) = load_database_sets(configuration, dataset_name)
    if (database is None) or (len(sets) != 1):
469
        sys.exit(1)
470
        return 1
André Anjos's avatar
André Anjos committed
471

472
473
474
    (protocol_name, set_name, db_set) = sets[0]

    if excluded_outputs is not None:
Samuel GAIST's avatar
Samuel GAIST committed
475
476
        excluded_outputs = map(lambda x: x.strip(),
                               excluded_outputs.split(','))
André Anjos's avatar
André Anjos committed
477

478
479
    # Setup the view so the outputs can be used
    if not docker:
Samuel GAIST's avatar
Samuel GAIST committed
480
        view = database.view(protocol_name, set_name)
481

482
        if view is None:
483
            sys.exit(1)
484
            return 1
485
486
487
488
489
490
491

        dataset_hash = hashDataset(db_name, protocol_name, set_name)
        view.setup(os.path.join(configuration.cache,
                                toPath(dataset_hash, '.db')), pack=False)
        input_group = inputs.InputGroup(set_name, restricted_access=False)

        for output_name, dataformat_name in db_set['outputs'].items():
Samuel GAIST's avatar
Samuel GAIST committed
492
493
            if excluded_outputs is not None and \
               output_name in excluded_outputs:
494
495
                continue

Samuel GAIST's avatar
Samuel GAIST committed
496
497
498
            input = inputs.Input(output_name,
                                 database.dataformats[dataformat_name],
                                 view.data_sources[output_name])
499
500
            input_group.add(input)

501
502
503
504
    else:
        host = dock.Host(raise_on_errors=False)

        (databases_container, db_socket, zmq_context, input_list) = \
505
            start_db_container(configuration, CMD_VIEW_OUTPUTS,
Samuel GAIST's avatar
Samuel GAIST committed
506
507
508
509
                               host, db_name, protocol_name,
                               set_name, database, db_set,
                               excluded_outputs=excluded_outputs,
                               uid=uid, db_root=db_root)
510

511
        input_group = input_list.group(set_name)
André Anjos's avatar
André Anjos committed
512

513
514
515
    # Display the data
    try:
        previous_start = -1
André Anjos's avatar
André Anjos committed
516

517
518
        while input_group.hasMoreData():
            input_group.next()
André Anjos's avatar
André Anjos committed
519

520
521
            start = input_group.data_index
            end = input_group.data_index_end
André Anjos's avatar
André Anjos committed
522

523
524
            if start != previous_start:
                print(80 * '-')
André Anjos's avatar
André Anjos committed
525

526
                print('FROM %d TO %d' % (start, end))
André Anjos's avatar
André Anjos committed
527

Samuel GAIST's avatar
Samuel GAIST committed
528
529
530
                whole_inputs = [input_ for input_ in input_group
                                if input_.data_index == start and
                                input_.data_index_end == end]
André Anjos's avatar
André Anjos committed
531

532
533
                for input in whole_inputs:
                    label = ' - ' + str(input.name) + ': '
534
                    print(label + data_to_json(input.data, len(label)))
André Anjos's avatar
André Anjos committed
535

536
                previous_start = start
André Anjos's avatar
André Anjos committed
537

Samuel GAIST's avatar
Samuel GAIST committed
538
539
540
541
542
            selected_inputs = \
                [input_ for input_ in input_group
                 if input_.data_index == input_group.first_data_index and
                 (input_.data_index != start or
                  input_.data_index_end != end)]
André Anjos's avatar
André Anjos committed
543

544
            grouped_inputs = {}
Samuel GAIST's avatar
Samuel GAIST committed
545
546
547
            for input_ in selected_inputs:
                key = (input_.data_index, input_.data_index_end)
                if key not in grouped_inputs:
548
549
                    grouped_inputs[key] = []
                grouped_inputs[key].append(input)
André Anjos's avatar
André Anjos committed
550

551
            sorted_keys = sorted(grouped_inputs.keys())
552
553
554

            for key in sorted_keys:
                print
555
                print('  FROM %d TO %d' % key)
556
557
558

                for input in grouped_inputs[key]:
                    label = '   - ' + str(input.name) + ': '
559
                    print(label + data_to_json(input.data, len(label)))
André Anjos's avatar
André Anjos committed
560
561

    except Exception as e:
562
        logger.error("Failed to retrieve the next data: %s", e)
563
        sys.exit(1)
564
565
        return 1

566
    sys.exit(0)
567
    return 0
André Anjos's avatar
André Anjos committed
568

569

Samuel GAIST's avatar
Samuel GAIST committed
570
# ----------------------------------------------------------
André Anjos's avatar
André Anjos committed
571
572


573
@click.group(cls=AliasedGroup)
574
@click.pass_context
575
def databases(ctx):
576
577
    """Database commands"""
    pass
578

Samuel GAIST's avatar
Samuel GAIST committed
579

580
@databases.command()
581
582
583
584
585
@click.option('--remote', help='Only acts on the remote copy of the database.',
              is_flag=True)
@click.pass_context
def list(ctx, remote):
    '''Lists all the databases available on the platform.
586

587
    To list all existing databases on your local prefix:
588

589
        $ beat databases list
590
591
592
    '''
    configuration = ctx.meta['config']
    if remote:
593
        with common.make_webapi(configuration) as webapi:
594
595
596
597
598
            return common.display_remote_list(webapi, 'database')
    else:
        return common.display_local_list(configuration.path, 'database')


599
@databases.command()
600
601
602
603
604
@click.argument('db_names', nargs=-1)
@click.pass_context
def check(ctx, db_names):
    '''Checks a local database for validity.

605
    $ beat databases check [<name>]...
606
607
608
609
610
611
612

    <name>:
        Database name formatted as "<database>/<version>"
    '''
    return common.check(ctx.meta['config'].path, 'database', db_names)


613
@databases.command()
614
@click.argument('db_names', nargs=-1)
615
@click.option('--force', help='Performs operation regardless of conflicts',
616
617
618
619
620
              is_flag=True)
@click.pass_context
def pull(ctx, db_names, force):
    '''Downloads the specified databases from the server.

621
       $ beat databases pull [<name>]...
622
623
624
625
626
627
628
629
630

    <name>:
        Database name formatted as "<database>/<version>"
    '''
    configuration = ctx.meta['config']
    with common.make_webapi(configuration) as webapi:
        return pull_impl(webapi, configuration.path, db_names, force, 0, {})


631
@databases.command()
632
@click.argument('db_names', nargs=-1)
633
@click.option('--force', help='Performs operation regardless of conflicts',
634
635
636
637
638
639
640
              is_flag=True)
@click.option('--dry-run', help='Dry run',
              is_flag=True)
@click.pass_context
def push(ctx, db_names, force, dry_run):
    '''Uploads databases to the server (must provide a valid admin token).

641
    $ beat databases push [<name>]...
642
643
644
645
646
647
648
649
650
651
652
653
654

    <name>:
        Database name formatted as "<database>/<version>"

    '''
    configuration = ctx.meta['config']
    with common.make_webapi(configuration) as webapi:
        return common.push(webapi, configuration.path, 'database',
                           db_names, ['name', 'declaration',
                                      'code', 'description'],
                           {}, force, dry_run, 0)


655
@databases.command()
656
657
658
659
660
@click.argument('db_names', nargs=-1)
@click.pass_context
def diff(ctx, db_names):
    '''Shows changes between the local database and the remote version.

661
    $ beat databases diff [<name>]...
662
663
664
665
666
667
668
669
670
671
672
673
674

    <name>:
        Database name formatted as "<database>/<version>"
    '''
    configuration = ctx.meta['config']
    if len(db_names) < 1:
        raise click.ClickException("Requires at least one database name")
    with common.make_webapi(configuration) as webapi:
        return common.diff(webapi, configuration.path, 'database',
                           db_names[0],
                           ['declaration', 'code', 'description'])


675
@databases.command()
676
677
678
679
680
681
682
683
@click.pass_context
def status(ctx):
    '''Shows (editing) status for all available databases'''
    configuration = ctx.meta['config']
    with common.make_webapi(configuration) as webapi:
        return common.status(webapi, configuration.path, 'database')[0]


684
@databases.command()
685
686
687
688
689
@click.argument('db_names', nargs=-1)
@click.pass_context
def version(ctx, db_names):
    '''Creates a new version of an existing database.

690
    $ beat databases version [<name>]...
691
692
693
694
695
696
697
698
699
700
701

    <name>:
        Database name formatted as "<database>/<version>"

    '''
    configuration = ctx.meta['config']
    if len(db_names) < 1:
        raise click.ClickException("Requires at least one database name")
    return common.new_version(configuration.path, 'database', db_names[0])


702
@databases.command()
703
704
705
706
707
708
@click.argument('db_names', nargs=-1)
@click.option('--list', help='List index files matching output if they exist',
              is_flag=True)
@click.option('--delete', help='Delete index files matching output if they '
              'exist (also, recursively deletes empty directories)',
              is_flag=True)
709
710
@click.option('--checksum', help='Checksums index files', is_flag=True,
              default=True)
711
712
713
714
715
716
717
718
719
@click.option('--uid', type=click.INT, default=None)
@click.option('--db-root', help="Database root")
@click.option('--docker', is_flag=True)
@click.pass_context
def index(ctx, db_names, list, delete, checksum, uid, db_root, docker):
    '''Indexes all outputs (of all sets) of a database.

    To index the contents of a database

720
        $ beat databases index simple/1
721
722
723

    To index the contents of a protocol on a database

724
        $ beat databases index simple/1/double
725
726
727

    To index the contents of a set in a protocol on a database

728
        $ beat databases index simple/1/double/double
729
730
    '''
    configuration = ctx.meta['config']
731
    code = 1
732
    if list:
733
        code = list_index_files(configuration, db_names)
734
    elif delete:
735
        code = delete_index_files(configuration, db_names)
736
    elif checksum:
737
738
739
740
        code = index_outputs(configuration, db_names, uid=uid,
                             db_root=db_root, docker=docker)
    sys.exit(code)
    return code
Samuel GAIST's avatar
Samuel GAIST committed
741

742
743
@databases.command()
@click.argument('set_name', nargs=1)
744
745
746
747
748
749
750
751
752
753
754
@click.option('--exclude', help='When viewing, excludes this output',
              default=None)
@click.option('--uid', type=click.INT, default=None)
@click.option('--db-root', help="Database root")
@click.option('--docker', is_flag=True)
@click.pass_context
def view(ctx, set_name, exclude, uid, db_root, docker):
    '''View the data of the specified dataset.

    To view the contents of a specific set

755
    $ beat databases view simple/1/protocol/set
756
757
758
759
760
761
762
763
764
    '''
    configuration = ctx.meta['config']
    if exclude is not None:
        return view_outputs(
            configuration, set_name, exclude, uid=uid, db_root=db_root,
            docker=docker)
    return view_outputs(
        configuration, set_name, uid=uid, db_root=db_root, docker=docker
    )