test_api.py 43.7 KB
Newer Older
Markus Scheidgen's avatar
Markus Scheidgen committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
# 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.

15
from typing import Any
16
17
18
import pytest
import time
import json
19
import base64
20
21
import zipfile
import io
22
import inspect
23
from passlib.hash import bcrypt
Markus Scheidgen's avatar
Markus Scheidgen committed
24
import datetime
25
import os.path
26

Markus Scheidgen's avatar
Markus Scheidgen committed
27
from nomad.api.app import rfc3339DateTime
Markus Scheidgen's avatar
Markus Scheidgen committed
28
from nomad import coe_repo, search, parsing, files, config
29
30
from nomad.files import UploadFiles, PublicUploadFiles
from nomad.processing import Upload, Calc, SUCCESS
31
from nomad.datamodel import UploadWithMetadata, CalcWithMetadata
32

33
from tests.conftest import create_auth_headers, clear_elastic
34
from tests.test_files import example_file, example_file_mainfile, example_file_contents
35
from tests.test_files import create_staging_upload, create_public_upload, assert_upload_files
36
from tests.test_coe_repo import assert_coe_upload
37
from tests.test_search import assert_search_upload
38
39


40
41
42
43
44
def test_alive(client):
    rv = client.get('/alive')
    assert rv.status_code == 200


45
46
47
48
49
50
51
@pytest.fixture(scope='function')
def test_user_signature_token(client, test_user_auth):
    rv = client.get('/auth/token', headers=test_user_auth)
    assert rv.status_code == 200
    return json.loads(rv.data)['token']


52
53
54
55
56
57
58
59
def get_upload_with_metadata(upload: dict) -> UploadWithMetadata:
    """ Create a :class:`UploadWithMetadata` from a API upload json record. """
    return UploadWithMetadata(
        upload_id=upload['upload_id'], calcs=[
            CalcWithMetadata(calc_id=calc['calc_id'], mainfile=calc['mainfile'])
            for calc in upload['calcs']['results']])


60
61
62
63
64
class TestInfo:
    def test_info(self, client):
        rv = client.get('/info/')
        assert rv.status_code == 200

65

66
class TestAdmin:
Markus Scheidgen's avatar
Markus Scheidgen committed
67
    @pytest.mark.timeout(config.tests.default_timeout)
68
69
    def test_reset(self, client, admin_user_auth, expandable_postgres, monkeypatch):
        monkeypatch.setattr('nomad.config.services.disable_reset', False)
70
71
72
        rv = client.post('/admin/reset', headers=admin_user_auth)
        assert rv.status_code == 200

Markus Scheidgen's avatar
Markus Scheidgen committed
73
    @pytest.mark.timeout(config.tests.default_timeout)
74
75
    def test_remove(self, client, admin_user_auth, expandable_postgres, monkeypatch):
        monkeypatch.setattr('nomad.config.services.disable_reset', False)
76
77
        rv = client.post('/admin/remove', headers=admin_user_auth)
        assert rv.status_code == 200
78
79
80
81
82
83

    def test_doesnotexist(self, client, admin_user_auth):
        rv = client.post('/admin/doesnotexist', headers=admin_user_auth)
        assert rv.status_code == 404

    def test_only_admin(self, client, test_user_auth):
Markus Scheidgen's avatar
Markus Scheidgen committed
84
        rv = client.post('/admin/reset', headers=test_user_auth)
85
86
        assert rv.status_code == 401

87
88
    def test_disabled(self, client, admin_user_auth, expandable_postgres, monkeypatch):
        monkeypatch.setattr('nomad.config.services.disable_reset', True)
89
90
91
92
        rv = client.post('/admin/reset', headers=admin_user_auth)
        assert rv.status_code == 400


93
class TestAuth:
94
    def test_xtoken_auth(self, client, test_user: coe_repo.User, no_warn):
95
        rv = client.get('/uploads/', headers={
96
            'X-Token': test_user.first_name.lower()  # the test users have their firstname as tokens for convinience
97
        })
98

99
        assert rv.status_code == 200
Markus Scheidgen's avatar
Markus Scheidgen committed
100

101
    def test_xtoken_auth_denied(self, client, no_warn, postgres):
102
103
104
        rv = client.get('/uploads/', headers={
            'X-Token': 'invalid'
        })
Markus Scheidgen's avatar
Markus Scheidgen committed
105

106
        assert rv.status_code == 401
107

108
109
110
    def test_basic_auth(self, client, test_user_auth, no_warn):
        rv = client.get('/uploads/', headers=test_user_auth)
        assert rv.status_code == 200
111

112
113
114
115
116
117
118
    def test_basic_auth_denied(self, client, no_warn):
        basic_auth_base64 = base64.b64encode('invalid'.encode('utf-8')).decode('utf-8')
        rv = client.get('/uploads/', headers={
            'Authorization': 'Basic %s' % basic_auth_base64
        })
        assert rv.status_code == 401

119
    def test_get_user(self, client, test_user_auth, test_user: coe_repo.User, no_warn):
120
121
        rv = client.get('/auth/user', headers=test_user_auth)
        assert rv.status_code == 200
122
123
124
        self.assert_user(client, json.loads(rv.data))

    def assert_user(self, client, user):
125
126
127
128
129
130
131
        for key in ['first_name', 'last_name', 'email', 'token']:
            assert key in user

        rv = client.get('/uploads/', headers={
            'X-Token': user['token']
        })

132
133
        assert rv.status_code == 200

134
135
136
    def test_signature_token(self, test_user_signature_token, no_warn):
        assert test_user_signature_token is not None

137
138
139
140
141
142
143
144
145
146
147
    @pytest.mark.parametrize('token, affiliation', [
        ('test_token', dict(name='HU Berlin', address='Unter den Linden 6')),
        (None, None)])
    def test_put_user(self, client, postgres, admin_user_auth, token, affiliation):
        data = dict(
            email='test@email.com', last_name='Tester', first_name='Testi',
            token=token, affiliation=affiliation,
            password=bcrypt.encrypt('test_password', ident='2y'))

        data = {key: value for key, value in data.items() if value is not None}

148
149
        rv = client.put(
            '/auth/user', headers=admin_user_auth,
150
            content_type='application/json', data=json.dumps(data))
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187

        assert rv.status_code == 200
        self.assert_user(client, json.loads(rv.data))

    def test_put_user_admin_only(self, client, test_user_auth):
        rv = client.put(
            '/auth/user', headers=test_user_auth,
            content_type='application/json', data=json.dumps(dict(
                email='test@email.com', last_name='Tester', first_name='Testi',
                password=bcrypt.encrypt('test_password', ident='2y'))))
        assert rv.status_code == 401

    def test_put_user_required_field(self, client, admin_user_auth):
        rv = client.put(
            '/auth/user', headers=admin_user_auth,
            content_type='application/json', data=json.dumps(dict(
                email='test@email.com', password=bcrypt.encrypt('test_password', ident='2y'))))
        assert rv.status_code == 400

    def test_post_user(self, client, postgres, admin_user_auth):
        rv = client.put(
            '/auth/user', headers=admin_user_auth,
            content_type='application/json', data=json.dumps(dict(
                email='test@email.com', last_name='Tester', first_name='Testi',
                password=bcrypt.encrypt('test_password', ident='2y'))))

        assert rv.status_code == 200
        user = json.loads(rv.data)

        rv = client.post(
            '/auth/user', headers={'X-Token': user['token']},
            content_type='application/json', data=json.dumps(dict(
                last_name='Tester', first_name='Testi v.',
                password=bcrypt.encrypt('test_password_changed', ident='2y'))))
        assert rv.status_code == 200
        self.assert_user(client, json.loads(rv.data))

188
189
190
191
192

class TestUploads:

    def assert_uploads(self, upload_json_str, count=0, **kwargs):
        data = json.loads(upload_json_str)
193
194
195
196
        assert 'pagination' in data
        assert 'page' in data['pagination']

        data = data['results']
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
        assert isinstance(data, list)
        assert len(data) == count

        if count > 0:
            self.assert_upload(json.dumps(data[0]), **kwargs)

    def assert_upload(self, upload_json_str, id=None, **kwargs):
        data = json.loads(upload_json_str)
        assert 'upload_id' in data
        if id is not None:
            assert id == data['upload_id']
        assert 'create_time' in data

        for key, value in kwargs.items():
            assert data.get(key, None) == value

        return data

    def assert_processing(self, client, test_user_auth, upload_id):
        upload_endpoint = '/uploads/%s' % upload_id

        # poll until completed
219
        upload = self.block_until_completed(client, upload_id, test_user_auth)
220
221

        assert len(upload['tasks']) == 4
222
        assert upload['tasks_status'] == SUCCESS
223
        assert upload['current_task'] == 'cleanup'
224
        assert not upload['process_running']
225

226
227
        calcs = upload['calcs']['results']
        for calc in calcs:
228
            assert calc['tasks_status'] == SUCCESS
229
230
            assert calc['current_task'] == 'archiving'
            assert len(calc['tasks']) == 3
231
            assert client.get('/archive/logs/%s/%s' % (calc['upload_id'], calc['calc_id']), headers=test_user_auth).status_code == 200
232
233

        if upload['calcs']['pagination']['total'] > 1:
234
            rv = client.get('%s?page=2&per_page=1&order_by=tasks_status' % upload_endpoint, headers=test_user_auth)
235
236
237
238
            assert rv.status_code == 200
            upload = self.assert_upload(rv.data)
            assert len(upload['calcs']['results']) == 1

239
240
        upload_with_metadata = get_upload_with_metadata(upload)
        assert_upload_files(upload_with_metadata, files.StagingUploadFiles)
241
        assert_search_upload(upload_with_metadata, additional_keys=['atoms', 'system'])
242

243
    def assert_published(self, client, test_user_auth, upload_id, proc_infra, with_coe_repo=True, metadata={}, publish_with_metadata: bool = True):
244
245
        rv = client.get('/uploads/%s' % upload_id, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
246
247

        upload_with_metadata = get_upload_with_metadata(upload)
248

249
250
251
        rv = client.post(
            '/uploads/%s' % upload_id,
            headers=test_user_auth,
252
            data=json.dumps(dict(operation='publish', metadata=metadata if publish_with_metadata else {})),
253
            content_type='application/json')
254
        assert rv.status_code == 200
255
        upload = self.assert_upload(rv.data)
256
        assert upload['current_process'] == 'publish_upload'
257
        assert upload['process_running']
258

259
        additional_keys = ['with_embargo']
260
        if with_coe_repo:
261
            additional_keys.append('pid')
262

263
264
265
266
267
268
269
        self.block_until_completed(client, upload_id, test_user_auth)
        upload_proc = Upload.objects(upload_id=upload_id).first()
        assert upload_proc is not None
        assert upload_proc.published is True

        if with_coe_repo:
            assert_coe_upload(upload_with_metadata.upload_id, user_metadata=metadata)
270
        assert_upload_files(upload_with_metadata, files.PublicUploadFiles, published=True)
271
272
273
        assert_search_upload(upload_with_metadata, additional_keys=additional_keys, published=True)

    def block_until_completed(self, client, upload_id: str, test_user_auth):
274
275
276
277
278
        while True:
            time.sleep(0.1)
            rv = client.get('/uploads/%s' % upload_id, headers=test_user_auth)
            if rv.status_code == 200:
                upload = self.assert_upload(rv.data)
279
280
                if not upload['process_running'] and not upload['tasks_running']:
                    return upload
281
            elif rv.status_code == 404:
282
                return None
283
284
285
286
            else:
                raise Exception(
                    'unexpected status code while blocking for upload processing: %s' %
                    str(rv.status_code))
287
288
289

    def assert_upload_does_not_exist(self, client, upload_id: str, test_user_auth):
        self.block_until_completed(client, upload_id, test_user_auth)
290

291
292
293
294
295
296
        rv = client.get('/uploads/%s' % upload_id, headers=test_user_auth)
        assert rv.status_code == 404
        assert Upload.objects(upload_id=upload_id).first() is None
        assert Calc.objects(upload_id=upload_id).count() is 0
        upload_files = UploadFiles.get(upload_id)
        assert upload_files is None or isinstance(upload_files, PublicUploadFiles)
Markus Scheidgen's avatar
Markus Scheidgen committed
297

298
299
300
301
302
303
304
    def test_get_command(self, client, test_user_auth, no_warn):
        rv = client.get('/uploads/command', headers=test_user_auth)
        assert rv.status_code == 200
        data = json.loads(rv.data)
        assert 'upload_command' in data
        assert 'upload_url' in data

305
306
    def test_get_empty(self, client, test_user_auth, no_warn):
        rv = client.get('/uploads/', headers=test_user_auth)
Markus Scheidgen's avatar
Markus Scheidgen committed
307

308
309
        assert rv.status_code == 200
        self.assert_uploads(rv.data, count=0)
Markus Scheidgen's avatar
Markus Scheidgen committed
310

311
312
313
    def test_get_not_existing(self, client, test_user_auth, no_warn):
        rv = client.get('/uploads/123456789012123456789012', headers=test_user_auth)
        assert rv.status_code == 404
314

315
316
    @pytest.mark.parametrize('mode', ['multipart', 'stream', 'local_path'])
    @pytest.mark.parametrize('name', [None, 'test_name'])
Markus Scheidgen's avatar
Markus Scheidgen committed
317
    def test_put(self, client, test_user_auth, proc_infra, example_upload, mode, name, no_warn):
318
        file = example_upload
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
        if name:
            url = '/uploads/?name=%s' % name
        else:
            url = '/uploads/'

        if mode == 'multipart':
            rv = client.put(
                url, data=dict(file=(open(file, 'rb'), 'file')), headers=test_user_auth)
        elif mode == 'stream':
            with open(file, 'rb') as f:
                rv = client.put(url, data=f.read(), headers=test_user_auth)
        elif mode == 'local_path':
            url += '&' if name else '?'
            url += 'local_path=%s' % file
            rv = client.put(url, headers=test_user_auth)
        else:
            assert False
336

337
338
        assert rv.status_code == 200
        if mode == 'local_path':
339
            upload = self.assert_upload(rv.data, upload_path=file, name=name)
340
341
        else:
            upload = self.assert_upload(rv.data, name=name)
342
        assert upload['tasks_running']
343

344
        self.assert_processing(client, test_user_auth, upload['upload_id'])
345

346
347
348
349
350
351
352
353
    def test_upload_limit(self, client, mongo, test_user, test_user_auth, proc_infra):
        for _ in range(0, config.services.upload_limit):
            Upload.create(user=test_user)
        file = example_file
        rv = client.put('/uploads/?local_path=%s' % file, headers=test_user_auth)
        assert rv.status_code == 400
        assert Upload.user_uploads(test_user).count() == config.services.upload_limit

354
355
356
    def test_delete_not_existing(self, client, test_user_auth, no_warn):
        rv = client.delete('/uploads/123456789012123456789012', headers=test_user_auth)
        assert rv.status_code == 404
357

358
359
360
361
362
363
364
365
366
367
368
369
    @pytest.fixture(scope='function')
    def slow_processing(self, monkeypatch):
        old_cleanup = Upload.cleanup

        def slow_cleanup(self):
            time.sleep(0.5)
            old_cleanup(self)

        monkeypatch.setattr('nomad.processing.data.Upload.cleanup', slow_cleanup)
        yield True
        monkeypatch.setattr('nomad.processing.data.Upload.cleanup', old_cleanup)

370
    def test_delete_published(self, client, test_user_auth, proc_infra, no_warn, with_publish_to_coe_repo):
371
372
373
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
374
        self.assert_published(client, test_user_auth, upload['upload_id'], proc_infra, with_coe_repo=with_publish_to_coe_repo)
375
        rv = client.delete('/uploads/%s' % upload['upload_id'], headers=test_user_auth)
376
        assert rv.status_code == 400
377

Markus Scheidgen's avatar
Markus Scheidgen committed
378
    def test_delete(self, client, test_user_auth, proc_infra, no_warn):
379
380
381
382
383
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
        rv = client.delete('/uploads/%s' % upload['upload_id'], headers=test_user_auth)
        assert rv.status_code == 200
384
        self.assert_upload_does_not_exist(client, upload['upload_id'], test_user_auth)
385

386
387
388
389
390
391
392
393
394
395
396
397
398
399
    def test_post_empty(self, client, test_user_auth, empty_upload, proc_infra, no_warn):
        rv = client.put('/uploads/?local_path=%s' % empty_upload, headers=test_user_auth)
        assert rv.status_code == 200
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
        rv = client.post(
            '/uploads/%s' % upload['upload_id'], headers=test_user_auth,
            data=json.dumps(dict(operation='publish')),
            content_type='application/json')
        assert rv.status_code == 400

    def test_post(self, client, test_user_auth, non_empty_example_upload, proc_infra, no_warn, with_publish_to_coe_repo):
        rv = client.put('/uploads/?local_path=%s' % non_empty_example_upload, headers=test_user_auth)
        assert rv.status_code == 200
400
401
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
402
        self.assert_published(client, test_user_auth, upload['upload_id'], proc_infra, with_coe_repo=with_publish_to_coe_repo)
403

404
405
406
        # still visible
        assert client.get('/uploads/%s' % upload['upload_id'], headers=test_user_auth).status_code == 200
        # still listed with all=True
407
        rv = client.get('/uploads/?state=all', headers=test_user_auth)
408
        assert rv.status_code == 200
409
        data = json.loads(rv.data)['results']
410
411
412
413
414
        assert len(data) > 0
        assert any(item['upload_id'] == upload['upload_id'] for item in data)
        # not listed with all=False
        rv = client.get('/uploads/', headers=test_user_auth)
        assert rv.status_code == 200
415
        data = json.loads(rv.data)['results']
416
417
        assert not any(item['upload_id'] == upload['upload_id'] for item in data)

418
419
    def test_post_metadata(
            self, client, proc_infra, admin_user_auth, test_user_auth, test_user,
420
            other_test_user, no_warn, example_user_metadata):
421
422
423
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
424
        metadata = dict(**example_user_metadata)
Markus Scheidgen's avatar
Markus Scheidgen committed
425
        metadata['_upload_time'] = datetime.datetime.now().isoformat()
426
        self.assert_published(client, admin_user_auth, upload['upload_id'], proc_infra, metadata)
427

Markus Scheidgen's avatar
Markus Scheidgen committed
428
    def test_post_metadata_forbidden(self, client, proc_infra, test_user_auth, no_warn):
429
430
431
432
433
434
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
        rv = client.post(
            '/uploads/%s' % upload['upload_id'],
            headers=test_user_auth,
435
            data=json.dumps(dict(operation='publish', metadata=dict(_pid=256))),
436
437
438
            content_type='application/json')
        assert rv.status_code == 401

439
440
441
442
443
444
445
446
447
448
449
    def test_post_metadata_and_republish(
            self, client, proc_infra, admin_user_auth, test_user_auth, test_user,
            other_test_user, no_warn, example_user_metadata):
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
        upload = self.assert_upload(rv.data)
        self.assert_processing(client, test_user_auth, upload['upload_id'])
        metadata = dict(**example_user_metadata)
        metadata['_upload_time'] = datetime.datetime.now().isoformat()
        self.assert_published(client, admin_user_auth, upload['upload_id'], proc_infra, metadata)
        self.assert_published(client, admin_user_auth, upload['upload_id'], proc_infra, metadata, publish_with_metadata=False)

450
    # TODO validate metadata (or all input models in API for that matter)
451
    # def test_post_bad_metadata(self, client, proc_infra, test_user_auth, postgres):
452
453
454
455
456
457
    #     rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)
    #     upload = self.assert_upload(rv.data)
    #     self.assert_processing(client, test_user_auth, upload['upload_id'])
    #     rv = client.post(
    #         '/uploads/%s' % upload['upload_id'],
    #         headers=test_user_auth,
458
    #         data=json.dumps(dict(operation='publish', metadata=dict(doesnotexist='hi'))),
459
460
461
    #         content_type='application/json')
    #     assert rv.status_code == 400

462
    def test_potcar(self, client, proc_infra, test_user_auth):
463
        # only the owner, shared with people are supposed to download the original potcar file
464
465
466
467
468
469
470
471
472
473
474
475
476
477
        example_file = 'tests/data/proc/examples_potcar.zip'
        rv = client.put('/uploads/?local_path=%s' % example_file, headers=test_user_auth)

        upload = self.assert_upload(rv.data)
        upload_id = upload['upload_id']
        self.assert_processing(client, test_user_auth, upload_id)
        self.assert_published(client, test_user_auth, upload_id, proc_infra, with_coe_repo=True)
        rv = client.get('/raw/%s/examples_potcar/POTCAR' % upload_id)
        assert rv.status_code == 401
        rv = client.get('/raw/%s/examples_potcar/POTCAR' % upload_id, headers=test_user_auth)
        assert rv.status_code == 200
        rv = client.get('/raw/%s/examples_potcar/POTCAR.stripped' % upload_id)
        assert rv.status_code == 200

478

479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
class UploadFilesBasedTests:

    @staticmethod
    def fix_signature(func, wrapper):
        additional_args = list(inspect.signature(func).parameters.values())[4:]
        wrapper_sig = inspect.signature(wrapper)
        wrapper_args = list(wrapper_sig.parameters.values())[:3] + additional_args
        wrapper_sig = wrapper_sig.replace(parameters=tuple(wrapper_args))
        wrapper.__signature__ = wrapper_sig

    @staticmethod
    def check_authorizaton(func):
        @pytest.mark.parametrize('test_data', [
            [True, None, True],     # in staging for upload
            [True, None, False],    # in staging for different user
            [True, None, None],     # in staging for guest
            [False, True, True],    # in public, restricted for uploader
            [False, True, False],   # in public, restricted for different user
            [False, True, None],    # in public, restricted for guest
            [False, False, True],   # in public, public, for uploader
            [False, False, False],  # in public, public, for different user
            [False, False, None]    # in public, public, for guest
        ], indirect=True)
        def wrapper(self, client, test_data, *args, **kwargs):
            upload, authorized, auth_headers = test_data
            try:
                func(self, client, upload, auth_headers, *args, **kwargs)
            except AssertionError as assertion:
                assertion_str = str(assertion)
                if not authorized:
                    if '0 == 5' in assertion_str and 'ZipFile' in assertion_str:
                        # the user is not authorized an gets an empty zip as expected
                        return
                    if '401' in assertion_str:
                        # the user is not authorized and gets a 401 as expected
                        return
                raise assertion

            if not authorized:
                assert False
        UploadFilesBasedTests.fix_signature(func, wrapper)
        return wrapper

    @staticmethod
    def ignore_authorization(func):
        @pytest.mark.parametrize('test_data', [
            [True, None, True],      # in staging
            [False, False, None],    # in public
        ], indirect=True)
        def wrapper(self, client, test_data, *args, **kwargs):
            upload, _, auth_headers = test_data
            func(self, client, upload, auth_headers, *args, **kwargs)
        UploadFilesBasedTests.fix_signature(func, wrapper)
        return wrapper
533

534
    @pytest.fixture(scope='function')
535
    def test_data(self, request, postgres, mongo, raw_files, no_warn, test_user, other_test_user):
536
537
538
539
540
        # delete potential old test files
        for _ in [0, 1]:
            upload_files = UploadFiles.get('test_upload')
            if upload_files:
                upload_files.delete()
541

542
        in_staging, restricted, for_uploader = request.param
543

544
545
546
547
        if in_staging:
            authorized = for_uploader
        else:
            authorized = not restricted or for_uploader
548

549
550
551
552
553
554
        if for_uploader:
            auth_headers = create_auth_headers(test_user)
        elif for_uploader is False:
            auth_headers = create_auth_headers(other_test_user)
        else:
            auth_headers = None
555

556
557
        calc_specs = 'r' if restricted else 'p'
        if in_staging:
558
            Upload.create(user=test_user, upload_id='test_upload')
559
            _, upload_files = create_staging_upload('test_upload', calc_specs=calc_specs)
560
        else:
561
            _, upload_files = create_public_upload('test_upload', calc_specs=calc_specs)
562
            postgres.begin()
563
564
565
            coe_upload = coe_repo.Upload(
                upload_name='test_upload',
                user_id=test_user.user_id, is_processed=True)
566
567
            postgres.add(coe_upload)
            postgres.commit()
568

569
        yield 'test_upload', authorized, auth_headers
570

571
        upload_files.delete()
572
573


574
575
576
577
class TestArchive(UploadFilesBasedTests):
    @UploadFilesBasedTests.check_authorizaton
    def test_get(self, client, upload, auth_headers):
        rv = client.get('/archive/%s/0' % upload, headers=auth_headers)
578
        assert rv.status_code == 200
579
        assert json.loads(rv.data) is not None
580

581
582
583
584
585
586
    @UploadFilesBasedTests.ignore_authorization
    def test_get_signed(self, client, upload, _, test_user_signature_token):
        rv = client.get('/archive/%s/0?token=%s' % (upload, test_user_signature_token))
        assert rv.status_code == 200
        assert json.loads(rv.data) is not None

587
588
589
    @UploadFilesBasedTests.check_authorizaton
    def test_get_calc_proc_log(self, client, upload, auth_headers):
        rv = client.get('/archive/logs/%s/0' % upload, headers=auth_headers)
590
        assert rv.status_code == 200
591
        assert len(rv.data) > 0
592

593
594
595
596
597
598
    @UploadFilesBasedTests.ignore_authorization
    def test_get_calc_proc_log_signed(self, client, upload, _, test_user_signature_token):
        rv = client.get('/archive/logs/%s/0?token=%s' % (upload, test_user_signature_token))
        assert rv.status_code == 200
        assert len(rv.data) > 0

599
600
601
    @UploadFilesBasedTests.ignore_authorization
    def test_get_non_existing_archive(self, client, upload, auth_headers):
        rv = client.get('/archive/%s' % 'doesnt/exist', headers=auth_headers)
602
        assert rv.status_code == 404
Markus Scheidgen's avatar
Markus Scheidgen committed
603

604
605
606
607
608
609
610
    @pytest.mark.parametrize('info', [
        'all.nomadmetainfo.json',
        'all.experimental.nomadmetainfo.json',
        'vasp.nomadmetainfo.json',
        'mpes.nomadmetainfo.json'])
    def test_get_metainfo(self, client, info):
        rv = client.get('/archive/metainfo/%s' % info)
611
        assert rv.status_code == 200
612
613
        metainfo = json.loads((rv.data))
        assert len(metainfo) > 0
614

Markus Scheidgen's avatar
Markus Scheidgen committed
615

616
class TestRepo():
617
618
619
620
621
622
    @pytest.fixture(scope='class')
    def example_elastic_calcs(
            self, elastic_infra, normalized: parsing.LocalBackend,
            test_user: coe_repo.User, other_test_user: coe_repo.User):
        clear_elastic(elastic_infra)

Markus Scheidgen's avatar
Markus Scheidgen committed
623
        calc_with_metadata = CalcWithMetadata(upload_id=0, calc_id=0, upload_time=datetime.date.today())
624
        calc_with_metadata.files = ['test/mainfile.txt']
625
        calc_with_metadata.apply_domain_metadata(normalized)
626

Markus Scheidgen's avatar
Markus Scheidgen committed
627
628
        calc_with_metadata.update(
            calc_id='1', uploader=test_user.to_popo(), published=True, with_embargo=False)
629
630
        search.Entry.from_calc_with_metadata(calc_with_metadata).save(refresh=True)

Markus Scheidgen's avatar
Markus Scheidgen committed
631
632
633
634
635
        calc_with_metadata.update(
            calc_id='2', uploader=other_test_user.to_popo(), published=True, with_embargo=False,
            upload_time=datetime.date.today() - datetime.timedelta(days=5))
        calc_with_metadata.update(
            atoms=['Fe'], comment='this is a specific word', formula='AAA', basis_set='zzz')
636
637
        search.Entry.from_calc_with_metadata(calc_with_metadata).save(refresh=True)

Markus Scheidgen's avatar
Markus Scheidgen committed
638
639
        calc_with_metadata.update(
            calc_id='3', uploader=other_test_user.to_popo(), published=False, with_embargo=False)
640
641
        search.Entry.from_calc_with_metadata(calc_with_metadata).save(refresh=True)

Markus Scheidgen's avatar
Markus Scheidgen committed
642
643
        calc_with_metadata.update(
            calc_id='4', uploader=other_test_user.to_popo(), published=True, with_embargo=True)
644
645
        search.Entry.from_calc_with_metadata(calc_with_metadata).save(refresh=True)

646
647
648
649
650
651
652
653
654
655
656
    def assert_search(self, rv: Any, number_of_calcs: int) -> dict:
        assert rv.status_code == 200
        data = json.loads(rv.data)

        results = data.get('results', None)
        assert results is not None
        assert isinstance(results, list)
        assert len(results) == number_of_calcs

        return data

657
658
    def test_own_calc(self, client, example_elastic_calcs, no_warn, test_user_auth):
        rv = client.get('/repo/0/1', headers=test_user_auth)
659
660
        assert rv.status_code == 200

661
662
663
664
665
666
667
668
    def test_public_calc(self, client, example_elastic_calcs, no_warn, other_test_user_auth):
        rv = client.get('/repo/0/1', headers=other_test_user_auth)
        assert rv.status_code == 200

    def test_embargo_calc(self, client, example_elastic_calcs, no_warn, test_user_auth):
        rv = client.get('/repo/0/4', headers=test_user_auth)
        assert rv.status_code == 401

669
670
671
672
    def test_own_embargo_calc(self, client, example_elastic_calcs, no_warn, other_test_user_auth):
        rv = client.get('/repo/0/4', headers=other_test_user_auth)
        assert rv.status_code == 200

673
674
675
676
    def test_staging_calc(self, client, example_elastic_calcs, no_warn, test_user_auth):
        rv = client.get('/repo/0/3', headers=test_user_auth)
        assert rv.status_code == 401

677
678
679
680
    def test_own_staging_calc(self, client, example_elastic_calcs, no_warn, other_test_user_auth):
        rv = client.get('/repo/0/3', headers=other_test_user_auth)
        assert rv.status_code == 200

681
682
    def test_non_existing_calcs(self, client, example_elastic_calcs, test_user_auth):
        rv = client.get('/repo/0/10', headers=test_user_auth)
683
684
        assert rv.status_code == 404

685
686
687
    @pytest.mark.parametrize('calcs, owner, auth', [
        (2, 'all', 'none'),
        (2, 'all', 'test_user'),
688
        (4, 'all', 'other_test_user'),
689
        (1, 'user', 'test_user'),
690
        (3, 'user', 'other_test_user'),
691
        (0, 'staging', 'test_user'),
692
        (1, 'staging', 'other_test_user')
693
    ])
694
    def test_search_owner(self, client, example_elastic_calcs, no_warn, test_user_auth, other_test_user_auth, calcs, owner, auth):
695
696
        auth = dict(none=None, test_user=test_user_auth, other_test_user=other_test_user_auth).get(auth)
        rv = client.get('/repo/?owner=%s' % owner, headers=auth)
697
        data = self.assert_search(rv, calcs)
698
699
700
701
702
        results = data.get('results', None)
        if calcs > 0:
            for key in ['uploader', 'calc_id', 'formula', 'upload_id']:
                assert key in results[0]

Markus Scheidgen's avatar
Markus Scheidgen committed
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
    @pytest.mark.parametrize('calcs, start, end', [
        (2, datetime.date.today() - datetime.timedelta(days=6), datetime.date.today()),
        (2, datetime.date.today() - datetime.timedelta(days=5), datetime.date.today()),
        (1, datetime.date.today() - datetime.timedelta(days=4), datetime.date.today()),
        (1, datetime.date.today(), datetime.date.today()),
        (1, datetime.date.today() - datetime.timedelta(days=6), datetime.date.today() - datetime.timedelta(days=5)),
        (0, datetime.date.today() - datetime.timedelta(days=7), datetime.date.today() - datetime.timedelta(days=6)),
        (2, None, None),
        (1, datetime.date.today(), None),
        (2, None, datetime.date.today())
    ])
    def test_search_time(self, client, example_elastic_calcs, no_warn, calcs, start, end):
        query_string = ''
        if start is not None:
            query_string = 'from_time=%s' % rfc3339DateTime.format(start)
        if end is not None:
            if query_string != '':
                query_string += '&'
            query_string += 'until_time=%s' % rfc3339DateTime.format(end)
        if query_string != '':
            query_string = '?%s' % query_string

        rv = client.get('/repo/%s' % query_string)
726
        self.assert_search(rv, calcs)
Markus Scheidgen's avatar
Markus Scheidgen committed
727

728
    @pytest.mark.parametrize('calcs, quantity, value', [
729
730
        (2, 'system', 'bulk'),
        (0, 'system', 'atom'),
731
732
733
734
735
736
737
738
739
740
741
742
        (1, 'atoms', 'Br'),
        (1, 'atoms', 'Fe'),
        (0, 'atoms', ['Fe', 'Br']),
        (1, 'comment', 'specific'),
        (1, 'authors', 'Hofstadter, Leonard'),
        (2, 'files', 'test/mainfile.txt'),
        (2, 'paths', 'mainfile.txt'),
        (2, 'paths', 'test'),
        (2, 'quantities', ['wyckoff_letters_primitive', 'hall_number']),
        (0, 'quantities', 'dos')
    ])
    def test_search_quantities(self, client, example_elastic_calcs, no_warn, test_user_auth, calcs, quantity, value):
743
        query_string = '%s=%s' % (quantity, ','.join(value) if isinstance(value, list) else value)
744

745
746
        rv = client.get('/repo/?%s' % query_string, headers=test_user_auth)
        data = self.assert_search(rv, calcs)
747

748
749
        quantities = data.get('quantities', None)
        assert quantities is not None
750
        if quantity == 'system' and calcs != 0:
751
752
753
754
            # for simplicity we only assert on quantities for this case
            assert 'system' in quantities
            assert len(quantities['system']) == 1
            assert value in quantities['system']
755

756
757
    metrics_permutations = [[], search.metrics_names] + [[metric] for metric in search.metrics_names]

758
759
760
761
762
763
764
765
766
767
768
    def test_search_admin(self, client, example_elastic_calcs, no_warn, admin_user_auth):
        rv = client.get('/repo/?owner=admin', headers=admin_user_auth)
        self.assert_search(rv, 4)

    def test_search_admin_auth(self, client, example_elastic_calcs, no_warn, test_user_auth):
        rv = client.get('/repo/?owner=admin', headers=test_user_auth)
        assert rv.status_code == 401

        rv = client.get('/repo/?owner=admin')
        assert rv.status_code == 401

769
    @pytest.mark.parametrize('metrics', metrics_permutations)
Markus Scheidgen's avatar
Markus Scheidgen committed
770
    def test_search_total_metrics(self, client, example_elastic_calcs, no_warn, metrics):
771
        rv = client.get('/repo/?metrics=%s' % ','.join(metrics))
Markus Scheidgen's avatar
Markus Scheidgen committed
772
773
        assert rv.status_code == 200
        data = json.loads(rv.data)
774
775
776
        total_metrics = data.get('quantities', {}).get('total', {}).get('all', None)
        assert total_metrics is not None
        assert 'code_runs' in total_metrics
Markus Scheidgen's avatar
Markus Scheidgen committed
777
        for metric in metrics:
778
            assert metric in total_metrics
Markus Scheidgen's avatar
Markus Scheidgen committed
779

780
    @pytest.mark.parametrize('metrics', metrics_permutations)
Markus Scheidgen's avatar
Markus Scheidgen committed
781
    def test_search_aggregation_metrics(self, client, example_elastic_calcs, no_warn, metrics):
782
        rv = client.get('/repo/?metrics=%s' % ','.join(metrics))
Markus Scheidgen's avatar
Markus Scheidgen committed
783
784
        assert rv.status_code == 200
        data = json.loads(rv.data)
785
786
        for quantities in data.get('quantities').values():
            for metrics_result in quantities.values():
Markus Scheidgen's avatar
Markus Scheidgen committed
787
788
789
790
                assert 'code_runs' in metrics_result
                for metric in metrics:
                    assert metric in metrics_result

791
792
793
    @pytest.mark.parametrize('n_results, page, per_page', [(2, 1, 5), (1, 1, 1), (0, 2, 3)])
    def test_search_pagination(self, client, example_elastic_calcs, no_warn, n_results, page, per_page):
        rv = client.get('/repo/?page=%d&per_page=%d' % (page, per_page))
794
795
796
        assert rv.status_code == 200
        data = json.loads(rv.data)
        results = data.get('results', None)
797
        assert data['pagination']['total'] == 2
798
        assert results is not None
799
        assert len(results) == n_results
800

801
802
    @pytest.mark.parametrize('first, order_by, order', [
        ('1', 'formula', -1), ('2', 'formula', 1),
803
804
        ('2', 'basis_set', -1), ('1', 'basis_set', 1),
        (None, 'authors', -1)])
805
806
807
808
809
810
811
    def test_search_order(self, client, example_elastic_calcs, no_warn, first, order_by, order):
        rv = client.get('/repo/?order_by=%s&order=%d' % (order_by, order))
        assert rv.status_code == 200
        data = json.loads(rv.data)
        results = data.get('results', None)
        assert data['pagination']['total'] == 2
        assert len(results) == 2
812
813
        if first is not None:
            assert results[0]['calc_id'] == first
814

815
816
817
818
819
820
821
822
823
824
    @pytest.mark.parametrize('n_results, size', [(2, None), (2, 5), (1, 1)])
    def test_search_scroll(self, client, example_elastic_calcs, no_warn, n_results, size):
        if size is not None:
            rv = client.get('/repo/?scroll=1,&per_page=%d' % size)
        else:
            rv = client.get('/repo/?scroll=1')

        assert rv.status_code == 200
        data = json.loads(rv.data)
        results = data.get('results', None)
825
        assert data.get('scroll', {}).get('size', -1) > 0
826
827
        assert results is not None
        assert len(results) == n_results
828
        scroll_id = data.get('scroll', {}).get('scroll_id', None)
829
830
831
832
833
834
        assert scroll_id is not None

        has_another_page = False
        while scroll_id is not None:
            rv = client.get('/repo/?scroll=1&scroll_id=%s' % scroll_id)
            data = json.loads(rv.data)
835
            scroll_id = data.get('scroll', {}).get('scroll_id', None)
836
837
838
839
840
            has_another_page |= len(data.get('results')) > 0

        if n_results < 2:
            assert has_another_page

841
842
843
    def test_search_user_authrequired(self, client, example_elastic_calcs, no_warn):
        rv = client.get('/repo/?owner=user')
        assert rv.status_code == 401
844
845


846
class TestRaw(UploadFilesBasedTests):
Markus Scheidgen's avatar
Markus Scheidgen committed
847

848
849
850
851
852
853
854
855
856
857
858
859
860
861
    def test_raw_file_from_calc(self, client, non_empty_processed, test_user_auth):
        calc = list(non_empty_processed.calcs)[0]
        url = '/raw/calc/%s/%s/%s' % (
            non_empty_processed.upload_id, calc.calc_id, os.path.basename(calc.mainfile))
        rv = client.get(url, headers=test_user_auth)
        assert rv.status_code == 200
        assert len(rv.data) > 0

        url = '/raw/calc/%s/%s/' % (non_empty_processed.upload_id, calc.calc_id)
        rv = client.get(url, headers=test_user_auth)
        assert rv.status_code == 200
        result = json.loads(rv.data)
        assert len(result['contents']) > 0

862
863
    @UploadFilesBasedTests.check_authorizaton
    def test_raw_file(self, client, upload, auth_headers):
864
        url = '/raw/%s/%s' % (upload, example_file_mainfile)
865
        rv = client.get(url, headers=auth_headers)
866
867
868
        assert rv.status_code == 200
        assert len(rv.data) > 0

869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
    @UploadFilesBasedTests.check_authorizaton
    def test_raw_file_partial(self, client, upload, auth_headers):
        url = '/raw/%s/%s?offset=0&length=20' % (upload, example_file_mainfile)
        rv = client.get(url, headers=auth_headers)
        assert rv.status_code == 200
        start_data = rv.data
        assert len(start_data) == 20

        url = '/raw/%s/%s?offset=10&length=10' % (upload, example_file_mainfile)
        rv = client.get(url, headers=auth_headers)
        assert rv.status_code == 200
        next_data = rv.data
        assert len(rv.data) == 10
        assert start_data[10:] == next_data

884
885
886
887
888
889
890
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_file_signed(self, client, upload, _, test_user_signature_token):
        url = '/raw/%s/%s?token=%s' % (upload, example_file_mainfile, test_user_signature_token)
        rv = client.get(url)
        assert rv.status_code == 200
        assert len(rv.data) > 0

891
892
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_file_missing_file(self, client, upload, auth_headers):
893
        url = '/raw/%s/does/not/exist' % upload
894
        rv = client.get(url, headers=auth_headers)
895
        assert rv.status_code == 404
896
897
898
        data = json.loads(rv.data)
        assert 'files' not in data

899
    @pytest.mark.parametrize('compress', [True, False])
900
901
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_file_wildcard(self, client, upload, auth_headers, compress):
902
        url = '/raw/%s/examples*' % upload
903
904
        if compress:
            url = '%s?compress=1' % url
905
        rv = client.get(url, headers=auth_headers)
906
907
908
909
910
911
912

        assert rv.status_code == 200
        assert len(rv.data) > 0
        with zipfile.ZipFile(io.BytesIO(rv.data)) as zip_file:
            assert zip_file.testzip() is None
            assert len(zip_file.namelist()) == len(example_file_contents)

913
914
915
916
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_file_wildcard_missing(self, client, upload, auth_headers):
        url = '/raw/%s/does/not/exist*' % upload
        rv = client.get(url, headers=auth_headers)
917
        assert rv.status_code == 404
918

919
920
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_file_missing_upload(self, client, upload, auth_headers):
921
        url = '/raw/doesnotexist/%s' % example_file_mainfile
922
        rv = client.get(url, headers=auth_headers)
923
924
        assert rv.status_code == 404

925
    @pytest.mark.parametrize('compress', [True, False])
926
927
    @UploadFilesBasedTests.check_authorizaton
    def test_raw_files(self, client, upload, auth_headers, compress):
928
        url = '/raw/%s?files=%s' % (
929
            upload, ','.join(example_file_contents))
930
931
        if compress:
            url = '%s&compress=1' % url
932
        rv = client.get(url, headers=auth_headers)
Markus Scheidgen's avatar
Markus Scheidgen committed
933

934
935
936
937
        assert rv.status_code == 200
        assert len(rv.data) > 0
        with zipfile.ZipFile(io.BytesIO(rv.data)) as zip_file:
            assert zip_file.testzip() is None
938
            assert len(zip_file.namelist()) == len(example_file_contents)
Markus Scheidgen's avatar
Markus Scheidgen committed
939

940
941
942
943
944
945
946
947
948
949
950
951
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_files_signed(self, client, upload, _, test_user_signature_token):
        url = '/raw/%s?files=%s&token=%s' % (
            upload, ','.join(example_file_contents), test_user_signature_token)
        rv = client.get(url)

        assert rv.status_code == 200
        assert len(rv.data) > 0
        with zipfile.ZipFile(io.BytesIO(rv.data)) as zip_file:
            assert zip_file.testzip() is None
            assert len(zip_file.namelist()) == len(example_file_contents)

952
    @pytest.mark.parametrize('compress', [True, False, None])
953
954
955
    @UploadFilesBasedTests.check_authorizaton
    def test_raw_files_post(self, client, upload, auth_headers, compress):
        url = '/raw/%s' % upload
956
        data = dict(files=example_file_contents)
957
958
        if compress is not None:
            data.update(compress=compress)
959
        rv = client.post(url, data=json.dumps(data), content_type='application/json', headers=auth_headers)
960
961
962
963
964

        assert rv.status_code == 200
        assert len(rv.data) > 0
        with zipfile.ZipFile(io.BytesIO(rv.data)) as zip_file:
            assert zip_file.testzip() is None
965
            assert len(zip_file.namelist()) == len(example_file_contents)
966

967
    @pytest.mark.parametrize('compress', [True, False])
968
969
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_files_missing_file(self, client, upload, auth_headers, compress):
970
        url = '/raw/%s?files=%s,missing/file.txt' % (upload, example_file_mainfile)
971
972
        if compress:
            url = '%s&compress=1' % url
973
        rv = client.get(url, headers=auth_headers)
Markus Scheidgen's avatar
Markus Scheidgen committed
974

975
976
977
978
979
        assert rv.status_code == 200
        assert len(rv.data) > 0
        with zipfile.ZipFile(io.BytesIO(rv.data)) as zip_file:
            assert zip_file.testzip() is None
            assert len(zip_file.namelist()) == 1
980

981
982
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_files_missing_upload(self, client, upload, auth_headers):
983
        url = '/raw/doesnotexist?files=shoud/not/matter.txt'
984
        rv = client.get(url, headers=auth_headers)
985

986
        assert rv.status_code == 404
987

988
989
    @UploadFilesBasedTests.ignore_authorization
    def test_raw_files_list(self, client, upload, auth_headers):
990
        url = '/raw/%s/examples_template' % upload
991
992
993
994
995
996
997
998
        rv = client.get(url, headers=auth_headers)
        assert rv.status_code == 200
        data = json.loads(rv.data)

        assert len(data['contents']) == 5
        assert data['upload_id'] == upload
        assert data['directory'] == 'examples_template'
        for content in data['contents']:
999
            assert content['name'] is not None
1000
1001
1002
1003
            assert content['size'] >= 0

    @UploadFilesBasedTests.ignore_authorization
    def test_raw_files_list_missing(self, client, upload, auth_headers):
1004
        url = '/raw/%s/examples_' % upload
1005
1006
1007
        rv = client.get(url, headers=auth_headers)
        assert rv.status_code == 404

1008
1009
1010
1011
1012

def test_docs(client):
    rv = client.get('/docs/index.html')
    rv = client.get('/docs/introduction.html')
    assert rv.status_code == 200