test_parsing.py 6.8 KB
Newer Older
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
import os
16
17
18
from io import StringIO
import json
import pytest
19
20
21

from nomadcore.local_meta_info import loadJsonFile

22
from nomad.parsing import JSONStreamWriter, parser_dict
23
from nomad.parsing import LocalBackend, BadContextURI
24

25
parser_examples = [
26
    ('parsers/template', 'tests/data/parsers/template.json'),
27
28
29
30
31
32
    ('parsers/exciting', '.dependencies/parsers/exciting/test/examples/Ag/INFO.OUT'),
    ('parsers/exciting', '.dependencies/parsers/exciting/test/examples/GW/INFO.OUT'),
    ('parsers/vasp', '.dependencies/parsers/vasp/test/examples/xml/perovskite.xml'),
    ('parsers/fhi-aims', 'tests/data/parsers/aims.out')
]

33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
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

class TestLocalBackend(object):

    @pytest.fixture(scope='session')
    def meta_info(self):
        path = '.dependencies/nomad-meta-info/meta_info/nomad_meta_info/all.nomadmetainfo.json'
        meta_info, _ = loadJsonFile(path)
        return meta_info

    @pytest.fixture(scope='function')
    def backend(self, meta_info):
        return LocalBackend(meta_info, debug=True)

    def test_meta_info(self, meta_info):
        assert 'section_topology' in meta_info

    def test_section(self, backend):
        g_index = backend.openSection('section_run')
        assert g_index == 0
        backend.addValue('program_name', 't0')
        backend.closeSection('section_run', 0)

        g_index = backend.openSection('section_run')
        assert g_index == 1

        g_index = backend.openSection('section_run')
        assert g_index == 2

        backend.addValue('program_name', 't1', 1)
        backend.addValue('program_name', 't2', 2)

        backend.closeSection('section_run', 1)
        backend.closeSection('section_run', 2)

        assert backend.get_sections('section_run') == [0, 1, 2]
        for i in range(0, 3):
            assert backend.get_value('program_name', i) == 't%d' % i

    def test_subsection(self, backend: LocalBackend):
        backend.openSection('section_run')
        backend.openSection('section_method')
        backend.closeSection('section_method', -1)

        backend.openSection('section_method')
        backend.closeSection('section_method', -1)

        backend.openSection('section_run')
        backend.closeSection('section_run', 0)
        backend.closeSection('section_run', 1)

        backend.openSection('section_method')
        backend.closeSection('section_method', -1)

        runs = backend.data['section_run']
        assert len(runs) == 2
        assert len(runs[0]['section_method']) == 2
        assert len(runs[1]['section_method']) == 1

91
92
93
94
95
96
    def test_context(self, backend: LocalBackend):
        backend.openSection('section_run')
        backend.openSection('section_method')
        backend.closeSection('section_method', -1)
        backend.closeSection('section_run', -1)

97
98
        backend.openSection('section_run')
        backend.closeSection('section_run', -1)
99

100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
        backend.openContext('/section_run/0')
        backend.addValue('program_name', 't1')
        backend.closeContext('/section_run/0')

        backend.openContext('/section_run/1')
        backend.addValue('program_name', 't2')
        backend.closeContext('/section_run/1')

        backend.openContext('/section_run/0/section_method/0')
        backend.closeContext('/section_run/0/section_method/0')

        runs = backend.data['section_run']
        assert runs[0]['program_name'] == 't1'
        assert runs[1]['program_name'] == 't2'

    def test_multi_context(self, backend: LocalBackend):
        backend.openSection('section_run')
        backend.closeSection('section_run', -1)

        backend.openContext('/section_run/0')
        backend.openSection('section_method')
        backend.closeSection('section_method', -1)
        backend.closeContext('/section_run/0')

        backend.openContext('/section_run/0')
        backend.openSection('section_method')
        backend.closeSection('section_method', -1)
        backend.closeContext('/section_run/0')

        assert len(backend.data['section_method']) == 1

    def test_bad_context(self, backend: LocalBackend):
        try:
            backend.openContext('section_run/0')
            assert False
        except BadContextURI:
            pass

        try:
            backend.openContext('dsfds')
            assert False
        except BadContextURI:
            pass

144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166

def create_reference(data, pretty):
    if (pretty):
        return json.dumps(data, indent=2)
    else:
        return json.dumps(data, separators=(',', ':'))


@pytest.mark.parametrize("pretty", [False, True])
def test_stream_generator(pretty):
    example_data = [
        {
            'key1': 'value',
            'key2': 1
        },
        {
            'key': {
                'key': 'value'
            }
        }
    ]

    out = StringIO()
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
    writer = JSONStreamWriter(out, pretty=pretty)
    writer.open_array()
    writer.open_object()
    writer.key('key1')
    writer.value('value')
    writer.key('key2')
    writer.value(1)
    writer.close_object()
    writer.open_object()
    writer.key('key')
    writer.open_object()
    writer.key('key')
    writer.value('value')
    writer.close_object()
    writer.close_object()
    writer.close_array()
    writer.close()
184
185
186

    assert create_reference(example_data, pretty) == out.getvalue()

187

188
189
def assert_parser_result(backend):
    status, errors = backend.status
190
191
    assert status == 'ParseSuccess'
    assert errors is None or len(errors) == 0
192
193


194
195
196
def run_parser(parser_name, mainfile):
    parser = parser_dict[parser_name]
    return parser.run(mainfile)
Markus Scheidgen's avatar
Markus Scheidgen committed
197
198


199
200
201
202
@pytest.fixture
def parsed_vasp_example() -> LocalBackend:
    return run_parser(
        'parsers/vasp', '.dependencies/parsers/vasp/test/examples/xml/perovskite.xml')
Markus Scheidgen's avatar
Markus Scheidgen committed
203
204


205
206
207
208
209
210
211
212
@pytest.fixture(params=parser_examples, ids=lambda spec: '%s-%s' % spec)
def parsed_example(request) -> LocalBackend:
    parser_name, mainfile = request.param
    return run_parser(parser_name, mainfile)


def test_parser(parsed_example):
    assert_parser_result(parsed_example)
Markus Scheidgen's avatar
Markus Scheidgen committed
213
214


215
def test_match():
Markus Scheidgen's avatar
Markus Scheidgen committed
216
    directory = 'tests/data/proc/match'
217
218
219
220
221

    count = 0
    for dirpath, _, filenames in os.walk(directory):
        for filename in filenames:
            fullname = os.path.join(dirpath, filename)
Markus Scheidgen's avatar
Markus Scheidgen committed
222
223
224
            for parser in parser_dict.values():
                if parser.is_mainfile(fullname, lambda fn: open(fn)):
                    count += 1
225

Markus Scheidgen's avatar
Markus Scheidgen committed
226
    assert count == 6