This repository was archived by the owner on Mar 25, 2022. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathopenapi.yaml
More file actions
435 lines (411 loc) · 12.9 KB
/
openapi.yaml
File metadata and controls
435 lines (411 loc) · 12.9 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
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
91
92
93
94
95
96
97
98
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
144
145
146
147
148
149
150
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
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
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
253
254
255
256
257
258
259
260
261
262
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
288
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
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
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
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
openapi: "3.0.0"
info:
description: Web services for the Softcite Knowledge Base
version: "0.1.0"
title: Softcite KB web service
contact:
name: Patrice Lopez
email: patrice.lopez@science-miner.com
url: https://science-miner.com
license:
name: Apache 2.0
url: https://www.apache.org/licenses/LICENSE-2.0.html
servers:
- url: http://localhost:5000/api
- url: http://work.local:5000/api
- url: /api
# Paths supported by the server application
paths:
/alive:
get:
operationId: generic.alive
tags:
- generic
summary: Return true if the API is up and running
description: Return true if the API is up and running
responses:
200:
description: API is up and running
400:
description: Bad request
/version:
get:
operationId: generic.version
tags:
- generic
summary: Return the version number of the current web API
description: Return the version number of the current web API
responses:
200:
description: API version number
400:
description: Bad request
/software/{id}:
get:
operationId: software.read_one
tags:
- software
summary: Access information for one software entity
description: Access information for one software entity
parameters:
- name: id
in: path
description: Identifier of the software entity
required: true
schema:
type: string
example: "Q8029"
responses:
200:
description: Successfully access the information for the software entity
400:
description: Bad request
/software/{id}/citations:
get:
operationId: software.read_citations
tags:
- software
summary: Access information to all citations of one software entity
description: Access information to all citations of one software entity
parameters:
- name: id
in: path
description: Identifier of the cited software entity
required: true
schema:
type: string
example: "Q8029"
responses:
200:
description: Successfully access the information for all the citations to the software entity
400:
description: Bad request
/software/disambiguate:
post:
operationId: software.disambiguate
tags:
- software
summary: Disambiguate a software mention against the database content
description: Disambiguate a software mention against the database content
requestBody:
description: The software mention JSON object
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/software'
responses:
200:
description: Successfully disambiguate the mention
400:
description: Bad request
/document/mentions:
get:
operationId: document.read_one_mentions
tags:
- document
summary: Access all mention information of one document
description: Access all mention information of one document
parameters:
- name: id
in: query
description: Identifier of the document
required: true
schema:
type: string
example: "10.1002/blabla"
responses:
200:
description: Successfully access the information for all the mentions to the document
400:
description: Bad request
/software/{id}/documents:
get:
operationId: software.nbest_documents
tags:
- software
summary: Provide the n-best citing documents for a software entity
description: Provide the n-best citing documents for a software entity
parameters:
- name: id
in: path
description: Identifier of the cited software entity
required: true
schema:
type: string
example: "Q8029"
- name: n
in: formData
description: Number of most relevant documents citing a software entity (default 1)
required: false
schema:
type: integer
default: 1
minimum: 1
responses:
200:
description: Successfully provide the n-best citing documents for a software entity
400:
description: Bad request
/software/{id}/related:
get:
operationId: software.nbest_software
tags:
- software
summary: Provide the n most related software entities for a given software entity
description: Provide the n most related software entities for a given software entity
parameters:
- name: id
in: path
description: Identifier of the cited software entity
required: true
schema:
type: string
example: "Q8029"
- name: n
in: formData
description: Number of most relevant software entities for a given software entity (default 1)
required: false
schema:
type: integer
default: 1
minimum: 1
responses:
200:
description: Successfully provide the n most related software entities for a given software entity
400:
description: Bad request
/person/{id}/software:
get:
operationId: person.software
tags:
- person
summary: Provide for a given person, all the software entities he has authored
description: Provide for a given person, all the software entities he has authored and for each software the citing documents supporting the authorship
parameters:
- name: id
in: path
description: Identifier of the person in the database
required: true
schema:
type: string
example: "Q93068"
responses:
200:
description: Successfully provide the software entities authored by one person
400:
description: Bad request
/person/disambiguate:
post:
operationId: person.disambiguate
tags:
- person
summary: Disambiguate a person name against the database content
description: Disambiguate a person name against the database content
requestBody:
description: The person JSON object information
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/person'
responses:
200:
description: Successfully disambiguate the person name
400:
description: Bad request
/organization/{id}/software:
get:
operationId: organization.software
tags:
- organization
summary: Provide for a given organization, all the software entities it is publishing
description: Provide for a given organization, all the software entities it is publishing and for each software the citing documents supporting the publication role
parameters:
- name: id
in: path
description: Identifier of the organization in the database
required: true
schema:
type: string
example: "Q93068"
responses:
200:
description: Successfully provide the software entities authored by one person
400:
description: Bad request
/organization/disambiguate:
post:
operationId: organization.disambiguate
tags:
- organization
summary: Disambiguate a organization name against the database content
description: Disambiguate a organization name and its additional metadata against the database content
requestBody:
description: The organization JSON object information
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/organization'
responses:
200:
description: Successfully disambiguate the organization name
400:
description: Bad request
/document:
post:
operationId: document.add
tags:
- document
summary: Add to the Knowledge Base a new annotated document
description: Add to the Knowledge Base a new document, its new annotations, try to disambiguate the software mention and creators, update the different KB object.
requestBody:
description: The annotation JSON object information
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/person'
responses:
200:
description: Successful addition of the document and its annotations into the knowledge base
400:
description: Bad request
/document/software:
get:
operationId: document.read_one_software
tags:
- document
summary: Access all software entities cited in one document
description: Access all software entities cited in one document
parameters:
- name: id
in: query
description: Identifier of the document
required: true
schema:
type: string
example: "10.1002/blabla"
responses:
200:
description: Successfully access the information for all the software entities cited in one document
400:
description: Bad request
/document:
delete:
operationId: document.delete
tags:
- document
summary: Delete a document from the Knowledge Base, this will also delete all its annotations/citations
description: Delete a document from the Knowledge Base, this will also delete all its annotations/citations at the software entity level
parameters:
- name: id
in: query
description: Identifier of the document that should be deleted from the KB
required: true
schema:
type: string
example: "10.1002/blabla"
responses:
200:
description: Successful deletion of the document into the knowledge base
400:
description: Bad request
/document/disambiguate:
post:
operationId: document.disambiguate
tags:
- document
summary: Disambiguate document metadata against the database content
description: Disambiguate document metadata against the database content
requestBody:
description: The metadata document JSON object information
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/document'
responses:
200:
description: Successfully disambiguate the document metadata
400:
description: Bad request
/document/software/related:
get:
operationId: document.nbest_software
tags:
- document
summary: Provide for a given document the n most relevant related software entities
description: Provide for a given document the n most relevant related software entities NOT mentioned in the document
parameters:
- name: id
in: query
description: Identifier of the document for which we want the most related software
required: true
schema:
type: string
example: "10.1002/blabla"
- name: n
in: query
description: Number of most relevant software entities for a given document (default 1)
required: false
schema:
type: integer
default: 1
minimum: 1
responses:
200:
description: Successfully provide the n most related software entities for a given document
400:
description: Bad request
components:
schemas:
software:
required:
- name
properties:
name:
type: string
creator:
type: string
version_number:
type: string
version_date:
type: string
url:
type: string
document:
properties:
doi:
type: string
pmc:
type: string
pmid:
type: string
arxiv_id:
type: string
person:
required:
- lastname
properties:
lastname:
type: string
firstname:
type: string
middlename:
type: string
orcid:
type: string
organization:
required:
- name
properties:
name:
type: string
acronym:
type: string
full_address:
type: string
country:
type: string