|
1
|
|
|
import sys |
|
2
|
|
|
import os |
|
3
|
|
|
import argparse |
|
4
|
|
|
|
|
5
|
|
|
from skosprovider_rdf.providers import RDFProvider |
|
6
|
|
|
from rdflib import Graph |
|
7
|
|
|
from rdflib.util import SUFFIX_FORMAT_MAP, guess_format |
|
8
|
|
|
|
|
9
|
|
|
from skosprovider.providers import SimpleCsvProvider |
|
10
|
|
|
from skosprovider.uri import UriPatternGenerator |
|
11
|
|
|
import csv |
|
12
|
|
|
|
|
13
|
|
|
from skosprovider.providers import DictionaryProvider |
|
14
|
|
|
import json |
|
15
|
|
|
|
|
16
|
|
|
from skosprovider_sqlalchemy.utils import import_provider |
|
17
|
|
|
from skosprovider_sqlalchemy.models import ( |
|
18
|
|
|
ConceptScheme, |
|
19
|
|
|
Label, |
|
20
|
|
|
conceptscheme_label, |
|
21
|
|
|
Note, |
|
22
|
|
|
Source |
|
23
|
|
|
) |
|
24
|
|
|
|
|
25
|
|
|
from sqlalchemy import create_engine |
|
26
|
|
|
from sqlalchemy.orm import sessionmaker |
|
27
|
|
|
from sqlalchemy.engine import url |
|
28
|
|
|
|
|
29
|
|
|
|
|
30
|
|
|
def file_to_rdf_provider(**kwargs): |
|
31
|
|
|
""" |
|
32
|
|
|
Create RDF provider from the input file |
|
33
|
|
|
""" |
|
34
|
|
|
input_file = kwargs.get('input_file') |
|
35
|
|
|
input_name, input_ext = os.path.splitext(os.path.basename(input_file)) |
|
36
|
|
|
graph = Graph() |
|
37
|
|
|
graph.parse(input_file, format=guess_format(input_ext)) |
|
38
|
|
|
return RDFProvider( |
|
39
|
|
|
{'id': input_name.upper()}, |
|
40
|
|
|
graph |
|
41
|
|
|
) |
|
42
|
|
|
|
|
43
|
|
|
|
|
44
|
|
|
def file_to_csv_provider(**kwargs): |
|
45
|
|
|
""" |
|
46
|
|
|
Create CSV provider from the input file |
|
47
|
|
|
""" |
|
48
|
|
|
input_file = kwargs.get('input_file') |
|
49
|
|
|
input_name, input_ext = os.path.splitext(os.path.basename(input_file)) |
|
50
|
|
|
with open(input_file) as ifile: |
|
51
|
|
|
reader = csv.reader(ifile) |
|
52
|
|
|
uri_pattern = kwargs.get('uri_pattern') |
|
53
|
|
|
provider_kwargs = {'uri_generator': UriPatternGenerator(uri_pattern)} if uri_pattern else {} |
|
54
|
|
|
return SimpleCsvProvider( |
|
55
|
|
|
{'id': input_name.upper()}, |
|
56
|
|
|
reader, |
|
57
|
|
|
**provider_kwargs |
|
58
|
|
|
) |
|
59
|
|
|
|
|
60
|
|
|
|
|
61
|
|
|
def file_to_json_provider(**kwargs): |
|
62
|
|
|
""" |
|
63
|
|
|
Create Dictionary provider from the input file |
|
64
|
|
|
""" |
|
65
|
|
|
input_file = kwargs.get('input_file') |
|
66
|
|
|
input_name, input_ext = os.path.splitext(os.path.basename(input_file)) |
|
67
|
|
|
with open(input_file) as data_file: |
|
68
|
|
|
dictionary = json.load(data_file) |
|
69
|
|
|
uri_pattern = kwargs.get('uri_pattern') |
|
70
|
|
|
provider_kwargs = {'uri_generator': UriPatternGenerator(uri_pattern)} if uri_pattern else {} |
|
71
|
|
|
return DictionaryProvider( |
|
72
|
|
|
{'id': input_name.upper()}, |
|
73
|
|
|
dictionary, |
|
74
|
|
|
**provider_kwargs |
|
75
|
|
|
) |
|
76
|
|
|
|
|
77
|
|
|
|
|
78
|
|
|
supported_types = { |
|
79
|
|
|
'JSON': { |
|
80
|
|
|
'extensions': ['.json'], |
|
81
|
|
|
'file_to_provider': file_to_json_provider |
|
82
|
|
|
}, |
|
83
|
|
|
'RDF': { |
|
84
|
|
|
'extensions': ['.%s' % suffix for suffix in SUFFIX_FORMAT_MAP], |
|
85
|
|
|
'file_to_provider': file_to_rdf_provider |
|
86
|
|
|
}, |
|
87
|
|
|
'CSV': { |
|
88
|
|
|
'extensions': ['.csv'], |
|
89
|
|
|
'file_to_provider': file_to_csv_provider |
|
90
|
|
|
} |
|
91
|
|
|
} |
|
92
|
|
|
|
|
93
|
|
|
supported_ext = [item for sublist in [supported_types[filetype]['extensions'] for filetype in supported_types.keys()] |
|
94
|
|
|
for item in sublist] |
|
95
|
|
|
|
|
96
|
|
|
|
|
97
|
|
|
def parse_argv_for_import(argv): |
|
98
|
|
|
""" |
|
99
|
|
|
Parse parameters and validate |
|
100
|
|
|
""" |
|
101
|
|
|
cmd = os.path.basename(argv[0]) |
|
102
|
|
|
parser = argparse.ArgumentParser( |
|
103
|
|
|
description='Import file to a database', |
|
104
|
|
|
usage='{} [--from path_input_file] [--to conn_string] [--conceptscheme_label cs_label] [--conceptscheme_uri cs_uri] [--uri_pattern uri_pattern]\n ' |
|
105
|
|
|
'(example: "{} --from atramhasis/scripts/my_file --to sqlite:///atramhasis.sqlite --conceptscheme_label Labels --conceptscheme_uri urn:x-skosprovider:trees" --uri_pattern urn:x-skosprovider:trees:%s)'.format( |
|
106
|
|
|
cmd, cmd) |
|
107
|
|
|
) |
|
108
|
|
|
parser.add_argument('--from', |
|
109
|
|
|
dest='input_file', |
|
110
|
|
|
type=str, |
|
111
|
|
|
help='local path to the input file', |
|
112
|
|
|
required=True |
|
113
|
|
|
) |
|
114
|
|
|
parser.add_argument('--to', |
|
115
|
|
|
dest='to', |
|
116
|
|
|
type=str, |
|
117
|
|
|
help='Connection string of the output database', |
|
118
|
|
|
required=False, |
|
119
|
|
|
default='sqlite:///atramhasis.sqlite' |
|
120
|
|
|
) |
|
121
|
|
|
parser.add_argument('--conceptscheme_label', |
|
122
|
|
|
dest='cs_label', |
|
123
|
|
|
type=str, |
|
124
|
|
|
help='Label of the conceptscheme', |
|
125
|
|
|
required=False, |
|
126
|
|
|
default=None |
|
127
|
|
|
) |
|
128
|
|
|
parser.add_argument('--conceptscheme_uri', |
|
129
|
|
|
dest='cs_uri', |
|
130
|
|
|
type=str, |
|
131
|
|
|
help='URI of the conceptscheme', |
|
132
|
|
|
required=False, |
|
133
|
|
|
default=None |
|
134
|
|
|
) |
|
135
|
|
|
parser.add_argument('--uri_pattern', |
|
136
|
|
|
dest='uri_pattern', |
|
137
|
|
|
type=str, |
|
138
|
|
|
help='URI pattern input for the URIGenerator', |
|
139
|
|
|
required=False, |
|
140
|
|
|
default=None |
|
141
|
|
|
) |
|
142
|
|
|
args = parser.parse_args() |
|
143
|
|
|
if not validate_file(args.input_file) or not validate_connection_string(args.to): |
|
144
|
|
|
sys.exit(1) |
|
145
|
|
|
return args |
|
146
|
|
|
|
|
147
|
|
|
|
|
148
|
|
|
def validate_file(input_file): |
|
149
|
|
|
if not os.path.exists(input_file): |
|
150
|
|
|
print(f'The input file {input_file} does not exists') |
|
151
|
|
|
return False |
|
152
|
|
|
elif os.path.splitext(input_file)[1] not in supported_ext: |
|
153
|
|
|
print (f'the input file {input_file} is not supported. Allowed extensions are: {supported_ext}') |
|
154
|
|
|
return False |
|
155
|
|
|
else: |
|
156
|
|
|
return True |
|
157
|
|
|
|
|
158
|
|
|
|
|
159
|
|
|
def validate_connection_string(connection_string): |
|
160
|
|
|
""" |
|
161
|
|
|
Validate the connection string |
|
162
|
|
|
:param connection_string |
|
163
|
|
|
:return: Boolean True if correct connection string |
|
164
|
|
|
""" |
|
165
|
|
|
u = url.make_url(connection_string) |
|
166
|
|
|
if u.drivername == 'postgresql': |
|
167
|
|
|
if u.username and u.password and u.host and u.port and u.database: |
|
168
|
|
|
return True |
|
169
|
|
|
elif u.drivername == 'sqlite': |
|
170
|
|
|
if u.database: |
|
171
|
|
|
return True |
|
172
|
|
|
elif u.drivername: |
|
173
|
|
|
print('The database driver ' + u.drivername + ' is not supported.') |
|
174
|
|
|
print('Wrong structure of connection string "' + connection_string + '"') |
|
175
|
|
|
print('Structure: postgresql://username:password@host:port/db_name OR sqlite:///path/db_name.sqlite') |
|
176
|
|
|
return False |
|
177
|
|
|
|
|
178
|
|
|
|
|
179
|
|
|
def conn_str_to_session(conn_str): |
|
180
|
|
|
""" |
|
181
|
|
|
create session from database connection string |
|
182
|
|
|
""" |
|
183
|
|
|
connect_uri = conn_str |
|
184
|
|
|
engine = create_engine(connect_uri, echo=True) |
|
185
|
|
|
return sessionmaker( |
|
186
|
|
|
bind=engine, |
|
187
|
|
|
)() |
|
188
|
|
|
|
|
189
|
|
|
|
|
190
|
|
|
def create_conceptscheme(conceptscheme_label, conceptscheme_uri): |
|
191
|
|
|
""" |
|
192
|
|
|
Configure output conceptscheme based on arg values |
|
193
|
|
|
""" |
|
194
|
|
|
cs = ConceptScheme(uri=conceptscheme_uri) |
|
195
|
|
|
l = Label(conceptscheme_label, 'prefLabel', 'und') |
|
196
|
|
|
cs.labels.append(l) |
|
197
|
|
|
return cs |
|
198
|
|
|
|
|
199
|
|
|
def create_conceptscheme_from_skos(conceptscheme): |
|
200
|
|
|
""" |
|
201
|
|
|
Configure output conceptscheme based on a `skosprovider.skos.ConceptScheme` |
|
202
|
|
|
""" |
|
203
|
|
|
return ConceptScheme( |
|
204
|
|
|
uri=conceptscheme.uri, |
|
205
|
|
|
labels = [ |
|
206
|
|
|
Label(l.label, l.type, l.language) |
|
207
|
|
|
for l in conceptscheme.labels |
|
208
|
|
|
], |
|
209
|
|
|
notes = [ |
|
210
|
|
|
Note(n.note, n.type, n.language, n.markup) |
|
211
|
|
|
for n in conceptscheme.notes |
|
212
|
|
|
], |
|
213
|
|
|
sources = [ |
|
214
|
|
|
Source(s.citation, s.markup) |
|
215
|
|
|
for s in conceptscheme.sources |
|
216
|
|
|
], |
|
217
|
|
|
languages = [ |
|
218
|
|
|
l for l in conceptscheme.languages |
|
219
|
|
|
] |
|
220
|
|
|
) |
|
221
|
|
|
|
|
222
|
|
|
|
|
223
|
|
|
|
|
224
|
|
|
def provider_to_db(provider, conceptscheme, session): |
|
225
|
|
|
""" |
|
226
|
|
|
import provider data into the database |
|
227
|
|
|
""" |
|
228
|
|
|
session.add(conceptscheme) |
|
229
|
|
|
import_provider(provider, conceptscheme, session) |
|
230
|
|
|
session.commit() |
|
231
|
|
|
|
|
232
|
|
|
|
|
233
|
|
|
def main(argv=sys.argv): |
|
234
|
|
|
""" |
|
235
|
|
|
Documentation: import -h |
|
236
|
|
|
Run: import --from <path_input_file> --to <conn_string> --conceptscheme_label <cs_label> --conceptscheme_uri <cs_uri> --uri_pattern <uri_pattern> |
|
237
|
|
|
|
|
238
|
|
|
example path_input_file: |
|
239
|
|
|
atramhasis/scripts/my_file |
|
240
|
|
|
|
|
241
|
|
|
structure conn_string: |
|
242
|
|
|
postgresql://username:password@host:port/db_name |
|
243
|
|
|
sqlite:///path/db_name.sqlite |
|
244
|
|
|
default conn_string: |
|
245
|
|
|
sqlite:///atramhasis.sqlite |
|
246
|
|
|
|
|
247
|
|
|
example conceptscheme_label |
|
248
|
|
|
My Conceptscheme |
|
249
|
|
|
default conceptscheme_label is the name of the file if a URI is specified. |
|
250
|
|
|
If no URI is specified, a conceptscheme will be imported from the input |
|
251
|
|
|
file. This only works for RDf files. For other file types (JSON and CSV) |
|
252
|
|
|
conceptscheme_uri is mandatory and conceptscheme_label is recommended. |
|
253
|
|
|
""" |
|
254
|
|
|
|
|
255
|
|
|
# Import the data |
|
256
|
|
|
args = parse_argv_for_import(argv) |
|
257
|
|
|
input_name, input_ext = os.path.splitext(os.path.basename(args.input_file)) |
|
258
|
|
|
session = conn_str_to_session(args.to) |
|
259
|
|
|
file_to_provider_function = [supported_types[filetype]['file_to_provider'] for filetype in supported_types.keys() |
|
260
|
|
|
if input_ext in supported_types[filetype]['extensions']][0] |
|
261
|
|
|
provider = file_to_provider_function(**vars(args)) |
|
262
|
|
|
if args.cs_uri: |
|
263
|
|
|
cs_uri = args.cs_uri |
|
264
|
|
|
cs_label = args.cs_label if args.cs_label else input_name.capitalize() |
|
265
|
|
|
cs = create_conceptscheme(cs_label, cs_uri) |
|
266
|
|
|
else: |
|
267
|
|
|
cs = create_conceptscheme_from_skos(provider.concept_scheme) |
|
268
|
|
|
provider_to_db(provider, cs, session) |
|
269
|
|
|
|
|
270
|
|
|
# Get info to return to the user |
|
271
|
|
|
prov_id = input_name.upper() |
|
272
|
|
|
scheme_id = cs.id |
|
273
|
|
|
print("\n\n*** The import of conceptscheme {0} from the {1} file to {2} was succesful. ***\ |
|
274
|
|
|
\n\nTo use the data in Atramhasis, you must edit the file my_thesaurus/skos/__init__.py.\ |
|
275
|
|
|
\nAdd a configuration similar to:\ |
|
276
|
|
|
\n\ndef create_registry(request):\ |
|
277
|
|
|
\n\t# create the SKOS registry\ |
|
278
|
|
|
\n\tregistry = Registry(instance_scope='threaded_thread')\ |
|
279
|
|
|
\n\t{3} = SQLAlchemyProvider(\ |
|
280
|
|
|
\n\t\t{{'id': '{4}', 'conceptscheme_id': {5}}},\ |
|
281
|
|
|
\n\t\trequest.db\ |
|
282
|
|
|
\n\t)\ |
|
283
|
|
|
\n\tregistry.register_provider({6})\ |
|
284
|
|
|
\n\treturn registry\ |
|
285
|
|
|
\n\n". |
|
286
|
|
|
format(prov_id, args.input_file, args.to, |
|
287
|
|
|
prov_id.replace(' ', '_'), prov_id, scheme_id, prov_id.replace(' ', '_'))) |
|
288
|
|
|
|
OnroerendErfgoed /
atramhasis
