repo.py 15.9 KB
Newer Older
Markus Scheidgen's avatar
Markus Scheidgen committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
# 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.

"""
The repository API of the nomad@FAIRDI APIs. Currently allows to resolve repository
meta-data.
"""

20
from typing import List
Markus Scheidgen's avatar
Markus Scheidgen committed
21
from flask_restplus import Resource, abort, fields
22
from flask import request, g
23
from elasticsearch.exceptions import NotFoundError
Markus Scheidgen's avatar
Markus Scheidgen committed
24

25
from nomad import search, utils, datamodel
Markus Scheidgen's avatar
Markus Scheidgen committed
26
from nomad.app.utils import rfc3339DateTime
Markus Scheidgen's avatar
Markus Scheidgen committed
27

Markus Scheidgen's avatar
Markus Scheidgen committed
28
from .api import api
29
from .auth import login_if_available
Markus Scheidgen's avatar
Markus Scheidgen committed
30
31
from .common import pagination_model, pagination_request_parser, calc_route

32
ns = api.namespace('repo', description='Access repository metadata.')
Markus Scheidgen's avatar
Markus Scheidgen committed
33
34
35
36
37


@calc_route(ns)
class RepoCalcResource(Resource):
    @api.response(404, 'The upload or calculation does not exist')
38
    @api.response(401, 'Not authorized to access the calculation')
39
    @api.response(200, 'Metadata send', fields.Raw)
40
    @api.doc('get_repo_calc')
41
    @login_if_available
42
    def get(self, upload_id, calc_id):
Markus Scheidgen's avatar
Markus Scheidgen committed
43
44
45
        """
        Get calculation metadata in repository form.

46
        Repository metadata only entails the quantities shown in the repository.
47
        Calcs are references via *upload_id*, *calc_id* pairs.
Markus Scheidgen's avatar
Markus Scheidgen committed
48
49
        """
        try:
50
51
52
53
54
55
56
57
58
59
60
            calc = search.Entry.get(calc_id)
        except NotFoundError:
            abort(404, message='There is no calculation %s/%s' % (upload_id, calc_id))

        if calc.with_embargo or not calc.published:
            if g.user is None:
                abort(401, message='Not logged in to access %s/%s.' % (upload_id, calc_id))

            is_owner = g.user.user_id == 0
            if not is_owner:
                for owner in calc.owners:
61
62
63
                    # At somepoint ids will be emails (strings) anyways.
                    # Right now it is hard to make sure that both are either str or int.
                    if str(owner.user_id) == str(g.user.user_id):
64
65
66
67
68
69
                        is_owner = True
                        break
            if not is_owner:
                abort(401, message='Not authorized to access %s/%s.' % (upload_id, calc_id))

        return calc.to_dict(), 200
Markus Scheidgen's avatar
Markus Scheidgen committed
70
71
72


repo_calcs_model = api.model('RepoCalculations', {
Markus Scheidgen's avatar
Markus Scheidgen committed
73
    'pagination': fields.Nested(pagination_model, skip_none=True),
74
75
76
77
    'scroll': fields.Nested(allow_null=True, skip_none=True, model=api.model('Scroll', {
        'total': fields.Integer(description='The total amount of hits for the search.'),
        'scroll_id': fields.String(allow_null=True, description='The scroll_id that can be used to retrieve the next page.'),
        'size': fields.Integer(help='The size of the returned scroll page.')})),
78
79
80
    'results': fields.List(fields.Raw, description=(
        'A list of search results. Each result is a dict with quantitie names as key and '
        'values as values')),
81
82
83
84
    'statistics': fields.Raw(description=(
        'A dict with all statistics. Each statistic is dictionary with a metrics dict as '
        'value and quantity value as key. The possible metrics are code runs(calcs), %s. '
        'There is a pseudo quantity "total" with a single value "all" that contains the '
85
86
87
88
        ' metrics over all results. ' % ', '.join(datamodel.Domain.instance.metrics_names))),
    'datasets': fields.Raw(api.model('RepoDatasets', {
        'after': fields.String(description='The after value that can be used to retrieve the next datasets.'),
        'values': fields.Raw(description='A dict with names as key. The values are dicts with "total" and "examples" keys.')
Markus Scheidgen's avatar
Markus Scheidgen committed
89
    }), skip_none=True)
Markus Scheidgen's avatar
Markus Scheidgen committed
90
91
})

92

93
94
95
96
97
repo_calc_id_model = api.model('RepoCalculationId', {
    'upload_id': fields.String(), 'calc_id': fields.String()
})


98
99
100
101
102
103
104
105
106
107
108
def add_common_parameters(request_parser):
    request_parser.add_argument(
        'owner', type=str,
        help='Specify which calcs to return: ``all``, ``public``, ``user``, ``staging``, default is ``all``')
    request_parser.add_argument(
        'from_time', type=lambda x: rfc3339DateTime.parse(x),
        help='A yyyy-MM-ddTHH:mm:ss (RFC3339) minimum entry time (e.g. upload time)')
    request_parser.add_argument(
        'until_time', type=lambda x: rfc3339DateTime.parse(x),
        help='A yyyy-MM-ddTHH:mm:ss (RFC3339) maximum entry time (e.g. upload time)')

109
    for quantity in search.quantities.values():
110
        request_parser.add_argument(
111
            quantity.name, help=quantity.description,
112
            action='append' if quantity.multi else None)
113
114


Markus Scheidgen's avatar
Markus Scheidgen committed
115
repo_request_parser = pagination_request_parser.copy()
116
add_common_parameters(repo_request_parser)
117
118
119
120
repo_request_parser.add_argument(
    'scroll', type=bool, help='Enable scrolling')
repo_request_parser.add_argument(
    'scroll_id', type=str, help='The id of the current scrolling window to use.')
121
122
repo_request_parser.add_argument(
    'date_histogram', type=bool, help='Add an additional aggregation over the upload time')
123
124
repo_request_parser.add_argument(
    'datasets_after', type=str, help='The last dataset id of the last scroll window for the dataset quantitiy')
Markus Scheidgen's avatar
Markus Scheidgen committed
125
repo_request_parser.add_argument(
126
    'metrics', type=str, action='append', help=(
127
        'Metrics to aggregate over all quantities and their values as comma separated list. '
128
        'Possible values are %s.' % ', '.join(datamodel.Domain.instance.metrics_names)))
Markus Scheidgen's avatar
Markus Scheidgen committed
129
130
131
132
repo_request_parser.add_argument(
    'datasets', type=bool, help=('Return dataset information.'))
repo_request_parser.add_argument(
    'statistics', type=bool, help=('Return statistics.'))
Markus Scheidgen's avatar
Markus Scheidgen committed
133

134

135
136
137
138
search_request_parser = api.parser()
add_common_parameters(search_request_parser)


139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
def add_query(search_request: search.SearchRequest):
    """
    Help that adds query relevant request parameters to the given SearchRequest.
    """
    # owner
    try:
        search_request.owner(
            request.args.get('owner', 'all'),
            g.user.user_id if g.user is not None else None)
    except ValueError as e:
        abort(401, getattr(e, 'message', 'Invalid owner parameter'))
    except Exception as e:
        abort(400, getattr(e, 'message', 'Invalid owner parameter'))

    # time range
154
155
156
157
    from_time_str = request.args.get('from_time', None)
    until_time_str = request.args.get('until_time', None)

    try:
158
159
160
        from_time = rfc3339DateTime.parse(from_time_str) if from_time_str is not None else None
        until_time = rfc3339DateTime.parse(until_time_str) if until_time_str is not None else None
        search_request.time_range(start=from_time, end=until_time)
161
162
163
    except Exception:
        abort(400, message='bad datetime format')

164
165
    # search parameter
    search_request.search_parameters(**{
166
        key: request.args.getlist(key) if search.quantities[key] else request.args.get(key)
167
        for key in request.args.keys()
168
        if key in search.quantities})
169
170


Markus Scheidgen's avatar
Markus Scheidgen committed
171
172
@ns.route('/')
class RepoCalcsResource(Resource):
173
    @api.doc('search')
174
    @api.response(400, 'Invalid requests, e.g. wrong owner type or bad search parameters')
Markus Scheidgen's avatar
Markus Scheidgen committed
175
    @api.expect(repo_request_parser, validate=True)
176
    @api.marshal_with(repo_calcs_model, skip_none=True, code=200, description='Search results send')
Markus Scheidgen's avatar
Markus Scheidgen committed
177
178
179
    @login_if_available
    def get(self):
        """
180
        Search for calculations in the repository form, paginated.
181
182

        The ``owner`` parameter determines the overall entries to search through.
183
184
185
186
        Possible values are: ``all`` (show all entries visible to the current user), ``public``
        (show all publically visible entries), ``user`` (show all user entries, requires login),
        ``staging`` (show all user entries in staging area, requires login).

187
188
189
190
191
        You can use the various quantities to search/filter for. For some of the
        indexed quantities this endpoint returns aggregation information. This means
        you will be given a list of all possible values and the number of entries
        that have the certain value. You can also use these aggregations on an empty
        search to determine the possible values.
192
193
194

        The pagination parameters allows determine which page to return via the
        ``page`` and ``per_page`` parameters. Pagination however, is limited to the first
Markus Scheidgen's avatar
Markus Scheidgen committed
195
196
197
198
199
200
201
202
        100k (depending on ES configuration) hits.

        An alternative to pagination is to use ``scroll`` and ``scroll_id``. With ``scroll``
        you will get a ``scroll_id`` on the first request. Each call with ``scroll`` and
        the respective ``scroll_id`` will return the next ``per_page`` (here the default is 1000)
        results. Scroll however, ignores ordering and does not return aggregations.
        The scroll view used in the background will stay alive for 1 minute between requests.
        If the given ``scroll_id`` is not available anymore, a HTTP 400 is raised.
203
204
205
206
207

        The search will return aggregations on a predefined set of quantities. Aggregations
        will tell you what quantity values exist and how many entries match those values.

        Ordering is determined by ``order_by`` and ``order`` parameters.
208
        """
209

210
211
212
        search_request = search.SearchRequest()
        add_query(search_request)

213
        try:
214
215
            scroll = bool(request.args.get('scroll', False))
            scroll_id = request.args.get('scroll_id', None)
216
            page = int(request.args.get('page', 1))
217
            per_page = int(request.args.get('per_page', 10 if not scroll else 1000))
218
            order = int(request.args.get('order', -1))
219
220
221
222
            order_by = request.args.get('order_by', 'formula')

            if bool(request.args.get('date_histogram', False)):
                search_request.date_histogram()
223
            metrics: List[str] = request.args.getlist('metrics')
Markus Scheidgen's avatar
Markus Scheidgen committed
224
225
226

            with_datasets = request.args.get('datasets', False)
            with_statistics = request.args.get('statistics', False)
227
228
229
        except Exception:
            abort(400, message='bad parameter types')

230
        try:
231
            assert page >= 1
232
233
234
235
            assert per_page > 0
        except AssertionError:
            abort(400, message='invalid pagination')

236
237
238
        if order not in [-1, 1]:
            abort(400, message='invalid pagination')

239
240
        for metric in metrics:
            if metric not in search.metrics_names:
241
242
                abort(400, message='there is no metric %s' % metric)

Markus Scheidgen's avatar
Markus Scheidgen committed
243
244
245
246
247
248
249
250
        if with_statistics:
            search_request.default_statistics(metrics_to_use=metrics)
            if 'datasets' not in metrics:
                total_metrics = metrics + ['datasets']
            else:
                total_metrics = metrics
            search_request.totals(metrics_to_use=total_metrics)
            search_request.statistic('authors', 1000)
251

252
        try:
253
            if scroll:
254
                results = search_request.execute_scrolled(scroll_id=scroll_id, size=per_page)
255

256
            else:
Markus Scheidgen's avatar
Markus Scheidgen committed
257
258
259
260
261
                if with_datasets:
                    search_request.quantity(
                        'dataset_id', size=per_page, examples=1,
                        after=request.args.get('datasets_after', None))

262
263
                results = search_request.execute_paginated(
                    per_page=per_page, page=page, order=order, order_by=order_by)
264
265

                # TODO just a work around to make things prettier
Markus Scheidgen's avatar
Markus Scheidgen committed
266
267
268
269
270
271
272
273
                if with_statistics:
                    statistics = results['statistics']
                    if 'code_name' in statistics and 'currupted mainfile' in statistics['code_name']:
                        del(statistics['code_name']['currupted mainfile'])

                if with_datasets:
                    datasets = results.pop('quantities')['dataset_id']
                    results['datasets'] = datasets
274

275
            return results, 200
Markus Scheidgen's avatar
Markus Scheidgen committed
276
277
        except search.ScrollIdNotFound:
            abort(400, 'The given scroll_id does not exist.')
278
        except KeyError as e:
279
280
            import traceback
            traceback.print_exc()
281
            abort(400, str(e))
282
283
284


repo_quantity_values_model = api.model('RepoQuantityValues', {
285
286
    'quantity': fields.Nested(api.model('RepoQuantity', {
        'after': fields.String(description='The after value that can be used to retrieve the next set of values.'),
287
        'values': fields.Raw(description='A dict with values as key. Values are dicts with "total" and "examples" keys.')
288
    }), allow_null=True)
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
})

repo_quantity_search_request_parser = api.parser()
add_common_parameters(repo_quantity_search_request_parser)
repo_quantity_search_request_parser.add_argument(
    'after', type=str, help='The after value to use for "scrolling".')
repo_request_parser.add_argument(
    'size', type=int, help='The max size of the returned values.')


@ns.route('/<string:quantity>')
class RepoQuantityResource(Resource):
    @api.doc('quantity_search')
    @api.response(400, 'Invalid requests, e.g. wrong owner type, bad quantity, bad search parameters')
    @api.expect(repo_quantity_search_request_parser, validate=True)
    @api.marshal_with(repo_quantity_values_model, skip_none=True, code=200, description='Search results send')
    @login_if_available
    def get(self, quantity: str):
        """
        Retrieve quantity values from entries matching the search.

        You can use the various quantities to search/filter for. For some of the
        indexed quantities this endpoint returns aggregation information. This means
        you will be given a list of all possible values and the number of entries
        that have the certain value. You can also use these aggregations on an empty
        search to determine the possible values.

        There is no ordering and no pagination. Instead there is an 'after' key based
        scrolling. The result will contain an 'after' value, that can be specified
        for the next request. You can use the 'size' and 'after' parameters accordingly.

320
321
322
        The result will contain a 'quantity' key with quantity values and the "after"
        value. There will be upto 'size' many values. For the rest of the values use the
        "after" parameter in another request.
323
324
        """

325
326
327
        search_request = search.SearchRequest()
        add_query(search_request)

328
329
330
331
332
333
334
335
336
337
338
        try:
            after = request.args.get('after', None)
            size = int(request.args.get('size', 100))
        except Exception:
            abort(400, message='bad parameter types')

        try:
            assert size >= 0
        except AssertionError:
            abort(400, message='invalid size')

339
        search_request.quantity(quantity, size=size, after=after)
340
341

        try:
342
343
344
            results = search_request.execute()
            quantities = results.pop('quantities')
            results['quantity'] = quantities[quantity]
345
346
347
348
349
350

            return results, 200
        except KeyError as e:
            import traceback
            traceback.print_exc()
            abort(400, 'Given quantity does not exist: %s' % str(e))
351
352
353
354
355
356
357
358
359


@ns.route('/pid/<int:pid>')
class RepoPidResource(Resource):
    @api.doc('resolve_pid')
    @api.response(404, 'Entry with PID does not exist')
    @api.marshal_with(repo_calc_id_model, skip_none=True, code=200, description='Entry resolved')
    @login_if_available
    def get(self, pid: int):
360
361
362
363
        search_request = search.SearchRequest()

        if g.user is not None:
            search_request.owner('all', user_id=g.user.user_id)
364
        else:
365
366
367
368
369
370
371
372
373
374
375
            search_request.owner('all')

        search_request.search_parameter('pid', pid)

        results = list(search_request.execute_scan())
        total = len(results)

        if total == 0:
            abort(404, 'Entry with PID %d does not exist' % pid)

        if total > 1:
376
            utils.get_logger(__name__).error('Two entries for the same pid', pid=pid)
377
378
379
380
381

        result = results[0]
        return dict(
            upload_id=result['upload_id'],
            calc_id=result['calc_id'])