admin.py 20.2 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
# Copyright 2018 Markus Scheidgen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an"AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
Markus Scheidgen's avatar
Markus Scheidgen committed
14
import typing
15
import click
16
import datetime
Markus Scheidgen's avatar
Markus Scheidgen committed
17
18
import elasticsearch_dsl
import elasticsearch
19
import sys
20
21
22
23
import io
import re
import uuid
import json
24
import threading
25
26
27

import numpy as np
import requests
Markus Scheidgen's avatar
Markus Scheidgen committed
28
29
30
import ase
import bs4
import matid
31

32
from nomad import processing as proc, search, datamodel, infrastructure, utils, config
Markus Scheidgen's avatar
Markus Scheidgen committed
33
from nomad import normalizing
34
35
36
from nomad.cli.cli import cli


37
def __run_processing(
Markus Scheidgen's avatar
Markus Scheidgen committed
38
        uploads, parallel: int, process, label: str, reprocess_running: bool = False):
39
40
41
42
43
44
45
46
    if isinstance(uploads, (tuple, list)):
        uploads_count = len(uploads)

    else:
        uploads_count = uploads.count()
        uploads = list(uploads)  # copy the whole mongo query set to avoid cursor timeouts

    cv = threading.Condition()
Markus Scheidgen's avatar
Markus Scheidgen committed
47
    threads: typing.List[threading.Thread] = []
48
49
50
51
52
53
54
55
56
57
58
59
60
61

    state = dict(
        completed_count=0,
        skipped_count=0,
        available_threads_count=parallel)

    logger = utils.get_logger(__name__)

    print('%d uploads selected, %s ...' % (uploads_count, label))

    def process_upload(upload: proc.Upload):
        logger.info('%s started' % label, upload_id=upload.upload_id)

        completed = False
62
        if upload.process_running and not reprocess_running:
63
64
65
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
            logger.warn(
                'cannot trigger %s, since the upload is already/still processing' % label,
                current_process=upload.current_process,
                current_task=upload.current_task, upload_id=upload.upload_id)

        else:
            upload.reset()
            process(upload)
            upload.block_until_complete(interval=.5)

            if upload.tasks_status == proc.FAILURE:
                logger.info('%s with failure' % label, upload_id=upload.upload_id)

            completed = True

            logger.info('%s complete' % label, upload_id=upload.upload_id)

        with cv:
            state['completed_count'] += 1 if completed else 0
            state['skipped_count'] += 1 if not completed else 0
            state['available_threads_count'] += 1

            print(
                '   %s %s and skipped %s of %s uploads' %
                (label, state['completed_count'], state['skipped_count'], uploads_count))

            cv.notify()

    for upload in uploads:
        with cv:
            cv.wait_for(lambda: state['available_threads_count'] > 0)
            state['available_threads_count'] -= 1
            thread = threading.Thread(target=lambda: process_upload(upload))
            threads.append(thread)
            thread.start()

    for thread in threads:
        thread.join()


103
104
105
106
107
@cli.group(help='''The nomad admin commands to do nasty stuff directly on the databases.
                     Remember: With great power comes great responsibility!''')
@click.pass_context
def admin(ctx):
    pass
108
109


110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
@admin.command(help='Reset/remove all databases.')
@click.option('--remove', is_flag=True, help='Do not just reset all dbs, but also remove them.')
@click.option('--i-am-really-sure', is_flag=True, help='Must be set for the command to to anything.')
def reset(remove, i_am_really_sure):
    if not i_am_really_sure:
        print('You do not seem to be really sure about what you are doing.')
        sys.exit(1)

    infrastructure.setup_logging()
    infrastructure.setup_mongo()
    infrastructure.setup_elastic()

    infrastructure.reset(remove)


125
126
127
128
129
130
131
132
133
@admin.command(help='Check and lift embargo of data with expired embargo period.')
@click.option('--dry', is_flag=True, help='Do not lift the embargo, just show what needs to be done.')
@click.option('--parallel', default=1, type=int, help='Use the given amount of parallel processes. Default is 1.')
def lift_embargo(dry, parallel):
    infrastructure.setup_logging()
    infrastructure.setup_mongo()
    infrastructure.setup_elastic()

    request = search.SearchRequest()
Markus Scheidgen's avatar
Markus Scheidgen committed
134
    request.q = elasticsearch_dsl.Q('term', with_embargo=True) & elasticsearch_dsl.Q('term', published=True)
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
    request.quantity('upload_id', 1000)
    result = request.execute()

    uploads_to_repack = []
    for upload_id in result['quantities']['upload_id']['values']:
        upload = proc.Upload.get(upload_id)
        embargo_length = upload.embargo_length
        if embargo_length is None:
            embargo_length = 36
            upload.embargo_length = 36

        if upload.upload_time + datetime.timedelta(days=int(embargo_length * 365 / 12)) < datetime.datetime.now():
            print('need to lift the embargo of %s (upload_time=%s, embargo=%d)' % (
                upload.upload_id, upload.upload_time, embargo_length))

            if not dry:
                proc.Calc._get_collection().update_many(
                    {'upload_id': upload_id},
                    {'$set': {'metadata.with_embargo': False}})
                uploads_to_repack.append(upload)
                upload.save()

157
158
                with upload.entries_metadata() as entries:
                    search.index_all(entries)
159
160
161
162
163

    if not dry:
        __run_processing(uploads_to_repack, parallel, lambda upload: upload.re_pack(), 're-packing')


164
@admin.command(help='(Re-)index all calcs.')
165
@click.option('--threads', type=int, default=1, help='Number of threads to use.')
166
167
@click.option('--dry', is_flag=True, help='Do not index, just compute entries.')
def index(threads, dry):
168
169
170
171
172
173
174
    infrastructure.setup_logging()
    infrastructure.setup_mongo()
    infrastructure.setup_elastic()

    all_calcs = proc.Calc.objects().count()
    print('indexing %d ...' % all_calcs)

175
    def elastic_updates():
176
177
178
        with utils.ETA(all_calcs, '   index %10d or %10d calcs, ETA %s') as eta:
            for calc in proc.Calc.objects():
                eta.add()
179
180
                entry_metadata = datamodel.EntryMetadata.m_from_dict(calc.metadata)
                entry = entry_metadata.a_elastic.create_index_entry().to_dict(include_meta=True)
181
182
                entry['_op_type'] = 'index'
                yield entry
Markus Scheidgen's avatar
Markus Scheidgen committed
183

184
185
186
    if dry:
        for _ in elastic_updates():
            pass
187
    if threads > 1:
188
        print('  use %d threads' % threads)
189
        for _ in elasticsearch.helpers.parallel_bulk(
190
                infrastructure.elastic_client, elastic_updates(), chunk_size=500,
191
192
                thread_count=threads):
            pass
193
    else:
194
195
196
        elasticsearch.helpers.bulk(
            infrastructure.elastic_client, elastic_updates())
    search.refresh()
197

198
    print('')
199
    print('indexing completed')
200
201


202
@admin.group(help='Generate scripts and commands for nomad operation.')
203
204
205
206
def ops():
    pass


207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
@ops.command(help=('Dump the mongo (calculation metadata) db.'))
@click.option('--restore', is_flag=True, help='Do not dump, but restore.')
def dump(restore: bool):
    date_str = datetime.datetime.utcnow().strftime('%Y_%m_%d')
    print('mongodump --host {} --port {} --db {} -o /backup/fairdi/mongo/{}'.format(
        config.mongo.host, config.mongo.port, config.mongo.db_name, date_str))


@ops.command(help=('Restore the mongo (calculation metadata) db.'))
@click.argument('PATH_TO_DUMP', type=str, nargs=1)
def restore(path_to_dump):
    print('mongorestore --host {} --port {} --db {} {}'.format(
        config.mongo.host, config.mongo.port, config.mongo.db_name, path_to_dump))


222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
@ops.command(help=('Generate an nginx.conf to serve the GUI and proxy pass to API container.'))
@click.option('--prefix', type=str, default='/example_nomad', help='Url path prefix. Default is /example_nomd, can be empty str.')
def nginx_conf(prefix):
    prefix = prefix.rstrip('/')
    prefix = '/%s' % prefix.lstrip('/')

    print('''\
server {{
    listen        80;
    server_name   www.example.com;

    location /{0} {{
        return 301 /example-nomad/gui;
    }}

    location {1}/gui {{
        root      /app/;
        rewrite ^{1}/gui/(.*)$ /nomad/$1 break;
        try_files $uri {1}/gui/index.html;
    }}

    location {1}/gui/service-worker.js {{
        add_header Last-Modified $date_gmt;
        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
        if_modified_since off;
        expires off;
        etag off;
        root      /app/;
        rewrite ^{1}/gui/service-worker.js /nomad/service-worker.js break;
    }}

253
254
255
256
257
258
259
260
261
262
    location {1}/gui/meta.json {{
        add_header Last-Modified $date_gmt;
        add_header Cache-Control 'no-store, no-cache, must-revalidate, proxy-revalidate, max-age=0';
        if_modified_since off;
        expires off;
        etag off;
        root      /app/;
        rewrite ^{1}/gui/meta.json /nomad/meta.json break;
    }}

263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
    location {1}/api {{
        proxy_set_header Host $host;
        proxy_pass_request_headers on;
        proxy_pass http://api:8000;
    }}

    location {1}/api/uploads {{
        client_max_body_size 35g;
        proxy_request_buffering off;
        proxy_set_header Host $host;
        proxy_pass_request_headers on;
        proxy_pass http://api:8000;
    }}

    location {1}/api/raw {{
        proxy_buffering off;
        proxy_set_header Host $host;
        proxy_pass_request_headers on;
        proxy_pass http://api:8000;
    }}
}}
    '''.format(prefix.lstrip('/'), prefix))


@ops.command(help=('Generate a proxy pass config for apache2 reverse proxy servers.'))
288
@click.option('--prefix', type=str, default='app', help='The path prefix under which everything is proxy passed.')
289
290
@click.option('--host', type=str, default='130.183.207.104', help='The host to proxy to.')
@click.option('--port', type=str, default='30001', help='The port to proxy to.')
291
292
def apache_conf(prefix, host, port):
    print('''\
293
294
295
296
ProxyPass "/{0}" "http://{1}:{2}/{0}"
ProxyPassReverse "/{0}" "http://{1}:{2}/{0}"
<Proxy http://{1}:{2}/{0}>
    ProxyPreserveHost On
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
    <IfModule !mod_access_compat.c>
         Require all granted
     </IfModule>
     <IfModule mod_access_compat.c>
         Order allow,deny
         Allow from all
     </IfModule>
</Proxy>

RequestHeader set "X-Forwarded-Proto" expr=%{{REQUEST_SCHEME}}
RequestHeader set "X-Forwarded-SSL" expr=%{{HTTPS}}

ProxyPass /fairdi/keycloak http://{1}:8002/fairdi/keycloak
ProxyPassReverse /fairdi/keycloak http://{1}:8002/fairdi/keycloak
<Proxy http://{1}:8002/app>
     ProxyPreserveHost On
     <IfModule !mod_access_compat.c>
         Require all granted
     </IfModule>
     <IfModule mod_access_compat.c>
         Order allow,deny
         Allow from all
     </IfModule>
</Proxy>

RewriteEngine on
RewriteCond %{QUERY_STRING} ^pid=([^&]+)$
RewriteRule ^/NomadRepository-1.1/views/calculation.zul$ /{0}/gui/entry/pid/%1? [R=301]

AllowEncodedSlashes On
327
'''.format(prefix, host, port))  # type: ignore
328
329
330


def write_prototype_data_file(aflow_prototypes: dict, filepath) -> None:
331
    '''Writes the prototype data file in a compressed format to a python
332
333
334
335
    module.

    Args:
        aflow_prototypes
336
    '''
337
338
339
340
341
    class NoIndent(object):
        def __init__(self, value):
            self.value = value

    class NoIndentEncoder(json.JSONEncoder):
342
        '''A custom JSON encoder that can pretty-print objects wrapped in the
343
        NoIndent class.
344
        '''
345
346
347
348
349
350
351
352
353
354
355
356
357
358
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
405
406
407
408
409
        def __init__(self, *args, **kwargs):
            super(NoIndentEncoder, self).__init__(*args, **kwargs)
            self.kwargs = dict(kwargs)
            del self.kwargs['indent']
            self._replacement_map = {}

        def default(self, o):  # pylint: disable=E0202
            if isinstance(o, NoIndent):
                key = uuid.uuid4().hex
                self._replacement_map[key] = json.dumps(o.value, **self.kwargs)
                return "@@%s@@" % (key,)
            else:
                return super(NoIndentEncoder, self).default(o)

        def encode(self, o):
            result = super(NoIndentEncoder, self).encode(o)
            for k, v in self._replacement_map.items():
                result = result.replace('"@@%s@@"' % (k,), v)
            return result

    prototype_dict = aflow_prototypes["prototypes_by_spacegroup"]
    for prototypes in prototype_dict.values():
        for prototype in prototypes:
            # Save the information back in a prettified form
            prototype["atom_positions"] = NoIndent(prototype["atom_positions"])
            prototype["atom_labels"] = NoIndent(prototype["atom_labels"])
            prototype["lattice_vectors"] = NoIndent(prototype["lattice_vectors"])
            try:
                prototype["normalized_wyckoff_matid"] = NoIndent(prototype["normalized_wyckoff_matid"])
            except KeyError:
                pass

    # Save the updated data
    with io.open(filepath, "w", encoding="utf8") as f:
        json_dump = json.dumps(aflow_prototypes, ensure_ascii=False, indent=4, sort_keys=True, cls=NoIndentEncoder)
        json_dump = re.sub(r"\"(-?\d+(?:[\.,]\d+)?)\"", r'\1', json_dump)  # Removes quotes around numbers
        f.write("# -*- coding: utf-8 -*-\naflow_prototypes = {}\n".format(json_dump))


@ops.command(help='Updates the AFLOW prototype information using the latest online version and writes the results to a python module in the given FILEPATH.')
@click.argument('FILEPATH', nargs=1, type=str)
@click.option('--matches-only', is_flag=True, help='Only update the match information that depends on the symmetry analysis settings. Will not perform and online update.')
@click.pass_context
def prototypes_update(ctx, filepath, matches_only):

    if matches_only:
        from nomad.normalizing.data.aflow_prototypes import aflow_prototypes
    else:
        # The basic AFLOW prototype data is available in a Javascript file. Here we
        # retrieve it and read only the prototype list from it.
        prototypes_file_url = 'http://aflowlib.org/CrystalDatabase/js/table_sort.js'
        r = requests.get(prototypes_file_url, allow_redirects=True)
        datastring = r.content.decode("utf-8")
        datastring = datastring.split('];')[0]
        datastring = datastring.split('= [')[1]
        data = json.loads('[' + datastring + ']')

        newdictarray = []
        n_prototypes = 0
        n_missing = 0
        for protodict in data:
            n_prototypes += 1
            newdict = {}

            # Make prototype plaintext
Markus Scheidgen's avatar
Markus Scheidgen committed
410
            prototype = bs4.BeautifulSoup(protodict["Prototype"], "html5lib").getText()
411
412
413
414
415
416
417
418
419
420
421

            # Add to new dictionary
            newdict['Notes'] = protodict['Notes']
            newdict['Prototype'] = prototype
            newdict['Space Group Symbol'] = protodict['Space Group Symbol']
            newdict['Space Group Number'] = protodict['Space Group Number']
            newdict['Pearsons Symbol'] = protodict['Pearson Symbol']
            newdict['Strukturbericht Designation'] = protodict['Strukturbericht Designation']
            newdict['aflow_prototype_id'] = protodict['AFLOW Prototype']
            newdict['aflow_prototype_url'] = 'http://www.aflowlib.org/CrystalDatabase/' + protodict['href'][2:]

Markus Scheidgen's avatar
Markus Scheidgen committed
422
            # Download cif or poscar if possible make ASE ase.Atoms object if possible
423
424
425
426
            # to obtain labels, positions, cell
            cifurl = 'http://www.aflowlib.org/CrystalDatabase/CIF/' + protodict['href'][2:-5] + '.cif'
            r = requests.get(cifurl, allow_redirects=True)
            cif_str = r.content.decode("utf-8")
Markus Scheidgen's avatar
Markus Scheidgen committed
427
            cif_file = io.StringIO()
428
429
430
431
432
433
434
435
436
437
438
            cif_file.write(cif_str)
            cif_file.seek(0)
            try:
                atoms = ase.io.read(cif_file, format='cif')
            except Exception:
                print("Error in getting prototype structure from CIF: {}", format(cifurl))
                # Then try to get structure from POSCAR
                try:
                    poscarurl = 'http://www.aflowlib.org/CrystalDatabase/POSCAR/' + protodict['href'][2:-5] + '.poscar'
                    r = requests.get(poscarurl, allow_redirects=True)
                    poscar_str = r.content.decode("utf-8")
Markus Scheidgen's avatar
Markus Scheidgen committed
439
                    poscar_file = io.StringIO()
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
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
                    poscar_file.write(poscar_str)
                    poscar_file.seek(0)
                    atoms = ase.io.read(poscar_file, format='vasp')
                except Exception:
                    print("Error in getting prototype structure from POSCAR: {}".format(poscarurl))
                    print("Could not read prototype structure from CIF or POSCAR file for prototype: {}, {}, ".format(prototype, newdict['aflow_prototype_url']))
                    n_missing += 1
                    continue

            atom_positions = atoms.get_positions()
            atom_labels = atoms.get_chemical_symbols()
            cell = atoms.get_cell()

            newdict['lattice_vectors'] = cell.tolist()
            newdict['atom_positions'] = atom_positions.tolist()
            newdict['atom_labels'] = atom_labels
            newdictarray.append(newdict)

            print("Processed: {}".format(len(newdictarray)))

        # Sort prototype dictionaries by spacegroup and make dictionary
        structure_types_by_spacegroup = {}
        for i_sg in range(1, 231):
            protos_sg = []
            for newdict in newdictarray:
                if newdict['Space Group Number'] == i_sg:
                    protos_sg.append(newdict)
            structure_types_by_spacegroup[i_sg] = protos_sg

        # Wrap in a dictionary that can hold other data, e.g. the symmemtry tolerance parameter.
        aflow_prototypes = {
            "prototypes_by_spacegroup": structure_types_by_spacegroup
        }
        print(
            "Extracted latest AFLOW prototypes online. Total number of "
            "successfully fetched prototypes: {}, missing: {}"
            .format(n_prototypes, n_missing)
        )

    # Update matches
    n_prototypes = 0
    n_failed = 0
    n_unmatched = 0
    prototype_dict = aflow_prototypes["prototypes_by_spacegroup"]

    for aflow_spg_number, prototypes in prototype_dict.items():
        n_prototypes += len(prototypes)
        for prototype in prototypes:

            # Read prototype structure
            pos = np.array(prototype["atom_positions"])
            labels = prototype["atom_labels"]
            cell = np.array(prototype["lattice_vectors"])
Markus Scheidgen's avatar
Markus Scheidgen committed
493
            atoms = ase.Atoms(
494
495
496
497
498
499
500
501
502
                symbols=labels,
                positions=pos,
                cell=cell,
                pbc=True
            )

            # Try to first see if the space group can be matched with the one in AFLOW
            tolerance = config.normalize.symmetry_tolerance
            try:
Markus Scheidgen's avatar
Markus Scheidgen committed
503
                symm = matid.SymmetryAnalyzer(atoms, tolerance)
504
505
506
507
508
509
510
511
512
513
                spg_number = symm.get_space_group_number()
                wyckoff_matid = symm.get_wyckoff_letters_conventional()
                norm_system = symm.get_conventional_system()
            except Exception:
                n_failed += 1
            else:
                # If the space group is matched, add the MatID normalized Wyckoff
                # letters to the data.
                if spg_number == aflow_spg_number:
                    atomic_numbers = norm_system.get_atomic_numbers()
Markus Scheidgen's avatar
Markus Scheidgen committed
514
                    normalized_wyckoff_matid = normalizing.aflow_prototypes.get_normalized_wyckoff(atomic_numbers, wyckoff_matid)
515
516
517
518
519
520
521
522
523
524
525
526
527
                    prototype["normalized_wyckoff_matid"] = normalized_wyckoff_matid
                else:
                    n_unmatched += 1
    print(
        "Updated matches in AFLOW prototype library. Total number of "
        "prototypes: {}, unmatched: {}, failed: {}"
        .format(n_prototypes, n_unmatched, n_failed)
    )

    aflow_prototypes["matid_symmetry_tolerance"] = tolerance

    # Write data file to the specified path
    write_prototype_data_file(aflow_prototypes, filepath)
528
529
530
531
532
533


@admin.command(help='Updates the springer database in nomad.config.springer_msg_db_path.')
@click.option('--max-n-query', default=10, type=int, help='Number of unsuccessful springer request before returning an error. Default is 10.')
@click.option('--retry-time', default=120, type=int, help='Time in seconds to retry after unsuccessful request. Default is 120.')
def springer_update(max_n_query, retry_time):
Markus Scheidgen's avatar
Markus Scheidgen committed
534
    normalizing.springer.update_springer_data(max_n_query, retry_time)