cheminee 0.0.14 → 0.0.15
Sign up to get free protection for your applications and to get access to all the features.
- checksums.yaml +4 -4
- data/Gemfile.lock +8 -8
- data/README.md +11 -33
- data/cheminee.gemspec +1 -2
- data/docs/DefaultApi.md +16 -475
- data/lib/cheminee/api/default_api.rb +17 -481
- data/lib/cheminee/api_client.rb +21 -23
- data/lib/cheminee/api_error.rb +1 -1
- data/lib/cheminee/configuration.rb +5 -6
- data/lib/cheminee/models/smile.rb +1 -1
- data/lib/cheminee/models/standardized_smile.rb +1 -1
- data/lib/cheminee/version.rb +2 -2
- data/lib/cheminee.rb +3 -18
- data/pkg/cheminee-0.0.15.gem +0 -0
- data/spec/api_client_spec.rb +1 -1
- data/spec/configuration_spec.rb +4 -4
- data/spec/spec_helper.rb +1 -1
- metadata +3 -75
- data/docs/BulkRequest.md +0 -18
- data/docs/BulkRequestDoc.md +0 -20
- data/docs/CreateIndexError.md +0 -18
- data/docs/GetIndexesResponseError.md +0 -18
- data/docs/IndexMeta.md +0 -20
- data/docs/IndexSchema.md +0 -20
- data/docs/ListIndexResponseErr.md +0 -18
- data/docs/PostIndexBulkResponseError.md +0 -18
- data/docs/PostIndexBulkResponseOk.md +0 -18
- data/docs/PostIndexBulkResponseOkStatus.md +0 -20
- data/docs/QueryResponseError.md +0 -18
- data/docs/QuerySearchHit.md +0 -22
- data/docs/Schema.md +0 -20
- data/docs/Smiles.md +0 -18
- data/docs/StandardizedSmiles.md +0 -20
- data/docs/StructureResponseError.md +0 -18
- data/docs/StructureSearchHit.md +0 -26
- data/docs/SubstructureSearchHit.md +0 -24
- data/lib/cheminee/models/bulk_request.rb +0 -223
- data/lib/cheminee/models/bulk_request_doc.rb +0 -232
- data/lib/cheminee/models/create_index_error.rb +0 -221
- data/lib/cheminee/models/get_indexes_response_error.rb +0 -221
- data/lib/cheminee/models/index_meta.rb +0 -237
- data/lib/cheminee/models/index_schema.rb +0 -233
- data/lib/cheminee/models/list_index_response_err.rb +0 -221
- data/lib/cheminee/models/post_index_bulk_response_error.rb +0 -221
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +0 -223
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +0 -223
- data/lib/cheminee/models/query_response_error.rb +0 -221
- data/lib/cheminee/models/query_search_hit.rb +0 -249
- data/lib/cheminee/models/schema.rb +0 -233
- data/lib/cheminee/models/smiles.rb +0 -221
- data/lib/cheminee/models/standardized_smiles.rb +0 -223
- data/lib/cheminee/models/structure_response_error.rb +0 -221
- data/lib/cheminee/models/structure_search_hit.rb +0 -281
- data/lib/cheminee/models/substructure_search_hit.rb +0 -265
- data/pkg/cheminee-0.0.14.gem +0 -0
- data/spec/models/bulk_request_doc_spec.rb +0 -42
- data/spec/models/bulk_request_spec.rb +0 -36
- data/spec/models/create_index_error_spec.rb +0 -36
- data/spec/models/get_indexes_response_error_spec.rb +0 -36
- data/spec/models/index_meta_spec.rb +0 -42
- data/spec/models/index_schema_spec.rb +0 -42
- data/spec/models/list_index_response_err_spec.rb +0 -36
- data/spec/models/post_index_bulk_response_error_spec.rb +0 -36
- data/spec/models/post_index_bulk_response_ok_spec.rb +0 -36
- data/spec/models/post_index_bulk_response_ok_status_spec.rb +0 -42
- data/spec/models/query_response_error_spec.rb +0 -36
- data/spec/models/query_search_hit_spec.rb +0 -48
- data/spec/models/schema_spec.rb +0 -42
- data/spec/models/smiles_spec.rb +0 -36
- data/spec/models/standardized_smiles_spec.rb +0 -42
- data/spec/models/structure_response_error_spec.rb +0 -36
- data/spec/models/structure_search_hit_spec.rb +0 -60
- data/spec/models/substructure_search_hit_spec.rb +0 -54
@@ -6,7 +6,7 @@
|
|
6
6
|
The version of the OpenAPI document: 1.0
|
7
7
|
|
8
8
|
Generated by: https://openapi-generator.tech
|
9
|
-
OpenAPI Generator version: 7.
|
9
|
+
OpenAPI Generator version: 7.0.0-SNAPSHOT
|
10
10
|
|
11
11
|
=end
|
12
12
|
|
@@ -19,491 +19,27 @@ module Cheminee
|
|
19
19
|
def initialize(api_client = ApiClient.default)
|
20
20
|
@api_client = api_client
|
21
21
|
end
|
22
|
-
#
|
22
|
+
# @param smile [Array<Smile>]
|
23
23
|
# @param [Hash] opts the optional parameters
|
24
|
-
# @return [Array<
|
25
|
-
def
|
26
|
-
data, _status_code, _headers =
|
24
|
+
# @return [Array<StandardizedSmile>]
|
25
|
+
def standardize_post(smile, opts = {})
|
26
|
+
data, _status_code, _headers = standardize_post_with_http_info(smile, opts)
|
27
27
|
data
|
28
28
|
end
|
29
29
|
|
30
|
-
#
|
30
|
+
# @param smile [Array<Smile>]
|
31
31
|
# @param [Hash] opts the optional parameters
|
32
|
-
# @return [Array<(Array<
|
33
|
-
def
|
32
|
+
# @return [Array<(Array<StandardizedSmile>, Integer, Hash)>] Array<StandardizedSmile> data, response status code and response headers
|
33
|
+
def standardize_post_with_http_info(smile, opts = {})
|
34
34
|
if @api_client.config.debugging
|
35
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.
|
35
|
+
@api_client.config.logger.debug 'Calling API: DefaultApi.standardize_post ...'
|
36
36
|
end
|
37
|
-
#
|
38
|
-
|
39
|
-
|
40
|
-
# query parameters
|
41
|
-
query_params = opts[:query_params] || {}
|
42
|
-
|
43
|
-
# header parameters
|
44
|
-
header_params = opts[:header_params] || {}
|
45
|
-
# HTTP header 'Accept' (if needed)
|
46
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
47
|
-
|
48
|
-
# form parameters
|
49
|
-
form_params = opts[:form_params] || {}
|
50
|
-
|
51
|
-
# http body (model)
|
52
|
-
post_body = opts[:debug_body]
|
53
|
-
|
54
|
-
# return_type
|
55
|
-
return_type = opts[:debug_return_type] || 'Array<IndexMeta>'
|
56
|
-
|
57
|
-
# auth_names
|
58
|
-
auth_names = opts[:debug_auth_names] || []
|
59
|
-
|
60
|
-
new_options = opts.merge(
|
61
|
-
:operation => :"DefaultApi.v1_indexes_get",
|
62
|
-
:header_params => header_params,
|
63
|
-
:query_params => query_params,
|
64
|
-
:form_params => form_params,
|
65
|
-
:body => post_body,
|
66
|
-
:auth_names => auth_names,
|
67
|
-
:return_type => return_type
|
68
|
-
)
|
69
|
-
|
70
|
-
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
71
|
-
if @api_client.config.debugging
|
72
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
73
|
-
end
|
74
|
-
return data, status_code, headers
|
75
|
-
end
|
76
|
-
|
77
|
-
# Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
|
78
|
-
# @param index [String]
|
79
|
-
# @param bulk_request [BulkRequest]
|
80
|
-
# @param [Hash] opts the optional parameters
|
81
|
-
# @return [PostIndexBulkResponseOk]
|
82
|
-
def v1_indexes_index_bulk_index_post(index, bulk_request, opts = {})
|
83
|
-
data, _status_code, _headers = v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, opts)
|
84
|
-
data
|
85
|
-
end
|
86
|
-
|
87
|
-
# Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
|
88
|
-
# @param index [String]
|
89
|
-
# @param bulk_request [BulkRequest]
|
90
|
-
# @param [Hash] opts the optional parameters
|
91
|
-
# @return [Array<(PostIndexBulkResponseOk, Integer, Hash)>] PostIndexBulkResponseOk data, response status code and response headers
|
92
|
-
def v1_indexes_index_bulk_index_post_with_http_info(index, bulk_request, opts = {})
|
93
|
-
if @api_client.config.debugging
|
94
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_bulk_index_post ...'
|
95
|
-
end
|
96
|
-
# verify the required parameter 'index' is set
|
97
|
-
if @api_client.config.client_side_validation && index.nil?
|
98
|
-
fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_bulk_index_post"
|
99
|
-
end
|
100
|
-
# verify the required parameter 'bulk_request' is set
|
101
|
-
if @api_client.config.client_side_validation && bulk_request.nil?
|
102
|
-
fail ArgumentError, "Missing the required parameter 'bulk_request' when calling DefaultApi.v1_indexes_index_bulk_index_post"
|
103
|
-
end
|
104
|
-
# resource path
|
105
|
-
local_var_path = '/v1/indexes/{index}/bulk_index'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
106
|
-
|
107
|
-
# query parameters
|
108
|
-
query_params = opts[:query_params] || {}
|
109
|
-
|
110
|
-
# header parameters
|
111
|
-
header_params = opts[:header_params] || {}
|
112
|
-
# HTTP header 'Accept' (if needed)
|
113
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
114
|
-
# HTTP header 'Content-Type'
|
115
|
-
content_type = @api_client.select_header_content_type(['application/json; charset=utf-8'])
|
116
|
-
if !content_type.nil?
|
117
|
-
header_params['Content-Type'] = content_type
|
118
|
-
end
|
119
|
-
|
120
|
-
# form parameters
|
121
|
-
form_params = opts[:form_params] || {}
|
122
|
-
|
123
|
-
# http body (model)
|
124
|
-
post_body = opts[:debug_body] || @api_client.object_to_http_body(bulk_request)
|
125
|
-
|
126
|
-
# return_type
|
127
|
-
return_type = opts[:debug_return_type] || 'PostIndexBulkResponseOk'
|
128
|
-
|
129
|
-
# auth_names
|
130
|
-
auth_names = opts[:debug_auth_names] || []
|
131
|
-
|
132
|
-
new_options = opts.merge(
|
133
|
-
:operation => :"DefaultApi.v1_indexes_index_bulk_index_post",
|
134
|
-
:header_params => header_params,
|
135
|
-
:query_params => query_params,
|
136
|
-
:form_params => form_params,
|
137
|
-
:body => post_body,
|
138
|
-
:auth_names => auth_names,
|
139
|
-
:return_type => return_type
|
140
|
-
)
|
141
|
-
|
142
|
-
data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
|
143
|
-
if @api_client.config.debugging
|
144
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_bulk_index_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
145
|
-
end
|
146
|
-
return data, status_code, headers
|
147
|
-
end
|
148
|
-
|
149
|
-
# Get extended information about an index
|
150
|
-
# @param index [String]
|
151
|
-
# @param [Hash] opts the optional parameters
|
152
|
-
# @return [IndexSchema]
|
153
|
-
def v1_indexes_index_get(index, opts = {})
|
154
|
-
data, _status_code, _headers = v1_indexes_index_get_with_http_info(index, opts)
|
155
|
-
data
|
156
|
-
end
|
157
|
-
|
158
|
-
# Get extended information about an index
|
159
|
-
# @param index [String]
|
160
|
-
# @param [Hash] opts the optional parameters
|
161
|
-
# @return [Array<(IndexSchema, Integer, Hash)>] IndexSchema data, response status code and response headers
|
162
|
-
def v1_indexes_index_get_with_http_info(index, opts = {})
|
163
|
-
if @api_client.config.debugging
|
164
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_get ...'
|
165
|
-
end
|
166
|
-
# verify the required parameter 'index' is set
|
167
|
-
if @api_client.config.client_side_validation && index.nil?
|
168
|
-
fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_get"
|
169
|
-
end
|
170
|
-
# resource path
|
171
|
-
local_var_path = '/v1/indexes/{index}'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
172
|
-
|
173
|
-
# query parameters
|
174
|
-
query_params = opts[:query_params] || {}
|
175
|
-
|
176
|
-
# header parameters
|
177
|
-
header_params = opts[:header_params] || {}
|
178
|
-
# HTTP header 'Accept' (if needed)
|
179
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
180
|
-
|
181
|
-
# form parameters
|
182
|
-
form_params = opts[:form_params] || {}
|
183
|
-
|
184
|
-
# http body (model)
|
185
|
-
post_body = opts[:debug_body]
|
186
|
-
|
187
|
-
# return_type
|
188
|
-
return_type = opts[:debug_return_type] || 'IndexSchema'
|
189
|
-
|
190
|
-
# auth_names
|
191
|
-
auth_names = opts[:debug_auth_names] || []
|
192
|
-
|
193
|
-
new_options = opts.merge(
|
194
|
-
:operation => :"DefaultApi.v1_indexes_index_get",
|
195
|
-
:header_params => header_params,
|
196
|
-
:query_params => query_params,
|
197
|
-
:form_params => form_params,
|
198
|
-
:body => post_body,
|
199
|
-
:auth_names => auth_names,
|
200
|
-
:return_type => return_type
|
201
|
-
)
|
202
|
-
|
203
|
-
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
204
|
-
if @api_client.config.debugging
|
205
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
206
|
-
end
|
207
|
-
return data, status_code, headers
|
208
|
-
end
|
209
|
-
|
210
|
-
# Create an index
|
211
|
-
# @param index [String]
|
212
|
-
# @param schema [String]
|
213
|
-
# @param [Hash] opts the optional parameters
|
214
|
-
# @option opts [String] :sort_by
|
215
|
-
# @return [IndexMeta]
|
216
|
-
def v1_indexes_index_post(index, schema, opts = {})
|
217
|
-
data, _status_code, _headers = v1_indexes_index_post_with_http_info(index, schema, opts)
|
218
|
-
data
|
219
|
-
end
|
220
|
-
|
221
|
-
# Create an index
|
222
|
-
# @param index [String]
|
223
|
-
# @param schema [String]
|
224
|
-
# @param [Hash] opts the optional parameters
|
225
|
-
# @option opts [String] :sort_by
|
226
|
-
# @return [Array<(IndexMeta, Integer, Hash)>] IndexMeta data, response status code and response headers
|
227
|
-
def v1_indexes_index_post_with_http_info(index, schema, opts = {})
|
228
|
-
if @api_client.config.debugging
|
229
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_post ...'
|
230
|
-
end
|
231
|
-
# verify the required parameter 'index' is set
|
232
|
-
if @api_client.config.client_side_validation && index.nil?
|
233
|
-
fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_post"
|
234
|
-
end
|
235
|
-
# verify the required parameter 'schema' is set
|
236
|
-
if @api_client.config.client_side_validation && schema.nil?
|
237
|
-
fail ArgumentError, "Missing the required parameter 'schema' when calling DefaultApi.v1_indexes_index_post"
|
238
|
-
end
|
239
|
-
# resource path
|
240
|
-
local_var_path = '/v1/indexes/{index}'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
241
|
-
|
242
|
-
# query parameters
|
243
|
-
query_params = opts[:query_params] || {}
|
244
|
-
query_params[:'schema'] = schema
|
245
|
-
query_params[:'sort_by'] = opts[:'sort_by'] if !opts[:'sort_by'].nil?
|
246
|
-
|
247
|
-
# header parameters
|
248
|
-
header_params = opts[:header_params] || {}
|
249
|
-
# HTTP header 'Accept' (if needed)
|
250
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
251
|
-
|
252
|
-
# form parameters
|
253
|
-
form_params = opts[:form_params] || {}
|
254
|
-
|
255
|
-
# http body (model)
|
256
|
-
post_body = opts[:debug_body]
|
257
|
-
|
258
|
-
# return_type
|
259
|
-
return_type = opts[:debug_return_type] || 'IndexMeta'
|
260
|
-
|
261
|
-
# auth_names
|
262
|
-
auth_names = opts[:debug_auth_names] || []
|
263
|
-
|
264
|
-
new_options = opts.merge(
|
265
|
-
:operation => :"DefaultApi.v1_indexes_index_post",
|
266
|
-
:header_params => header_params,
|
267
|
-
:query_params => query_params,
|
268
|
-
:form_params => form_params,
|
269
|
-
:body => post_body,
|
270
|
-
:auth_names => auth_names,
|
271
|
-
:return_type => return_type
|
272
|
-
)
|
273
|
-
|
274
|
-
data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
|
275
|
-
if @api_client.config.debugging
|
276
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
277
|
-
end
|
278
|
-
return data, status_code, headers
|
279
|
-
end
|
280
|
-
|
281
|
-
# Perform basic query search against index
|
282
|
-
# @param index [String]
|
283
|
-
# @param query [String]
|
284
|
-
# @param [Hash] opts the optional parameters
|
285
|
-
# @option opts [Integer] :limit
|
286
|
-
# @return [Array<QuerySearchHit>]
|
287
|
-
def v1_indexes_index_search_basic_get(index, query, opts = {})
|
288
|
-
data, _status_code, _headers = v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
|
289
|
-
data
|
290
|
-
end
|
291
|
-
|
292
|
-
# Perform basic query search against index
|
293
|
-
# @param index [String]
|
294
|
-
# @param query [String]
|
295
|
-
# @param [Hash] opts the optional parameters
|
296
|
-
# @option opts [Integer] :limit
|
297
|
-
# @return [Array<(Array<QuerySearchHit>, Integer, Hash)>] Array<QuerySearchHit> data, response status code and response headers
|
298
|
-
def v1_indexes_index_search_basic_get_with_http_info(index, query, opts = {})
|
299
|
-
if @api_client.config.debugging
|
300
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_basic_get ...'
|
301
|
-
end
|
302
|
-
# verify the required parameter 'index' is set
|
303
|
-
if @api_client.config.client_side_validation && index.nil?
|
304
|
-
fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_basic_get"
|
305
|
-
end
|
306
|
-
# verify the required parameter 'query' is set
|
307
|
-
if @api_client.config.client_side_validation && query.nil?
|
308
|
-
fail ArgumentError, "Missing the required parameter 'query' when calling DefaultApi.v1_indexes_index_search_basic_get"
|
309
|
-
end
|
310
|
-
# resource path
|
311
|
-
local_var_path = '/v1/indexes/{index}/search/basic'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
312
|
-
|
313
|
-
# query parameters
|
314
|
-
query_params = opts[:query_params] || {}
|
315
|
-
query_params[:'query'] = query
|
316
|
-
query_params[:'limit'] = opts[:'limit'] if !opts[:'limit'].nil?
|
317
|
-
|
318
|
-
# header parameters
|
319
|
-
header_params = opts[:header_params] || {}
|
320
|
-
# HTTP header 'Accept' (if needed)
|
321
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
322
|
-
|
323
|
-
# form parameters
|
324
|
-
form_params = opts[:form_params] || {}
|
325
|
-
|
326
|
-
# http body (model)
|
327
|
-
post_body = opts[:debug_body]
|
328
|
-
|
329
|
-
# return_type
|
330
|
-
return_type = opts[:debug_return_type] || 'Array<QuerySearchHit>'
|
331
|
-
|
332
|
-
# auth_names
|
333
|
-
auth_names = opts[:debug_auth_names] || []
|
334
|
-
|
335
|
-
new_options = opts.merge(
|
336
|
-
:operation => :"DefaultApi.v1_indexes_index_search_basic_get",
|
337
|
-
:header_params => header_params,
|
338
|
-
:query_params => query_params,
|
339
|
-
:form_params => form_params,
|
340
|
-
:body => post_body,
|
341
|
-
:auth_names => auth_names,
|
342
|
-
:return_type => return_type
|
343
|
-
)
|
344
|
-
|
345
|
-
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
346
|
-
if @api_client.config.debugging
|
347
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_basic_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
348
|
-
end
|
349
|
-
return data, status_code, headers
|
350
|
-
end
|
351
|
-
|
352
|
-
# Perform substructure search against index
|
353
|
-
# @param index [String]
|
354
|
-
# @param smiles [String]
|
355
|
-
# @param [Hash] opts the optional parameters
|
356
|
-
# @option opts [Integer] :result_limit
|
357
|
-
# @option opts [Integer] :tautomer_limit
|
358
|
-
# @option opts [String] :extra_query
|
359
|
-
# @return [Array<StructureSearchHit>]
|
360
|
-
def v1_indexes_index_search_substructure_get(index, smiles, opts = {})
|
361
|
-
data, _status_code, _headers = v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
|
362
|
-
data
|
363
|
-
end
|
364
|
-
|
365
|
-
# Perform substructure search against index
|
366
|
-
# @param index [String]
|
367
|
-
# @param smiles [String]
|
368
|
-
# @param [Hash] opts the optional parameters
|
369
|
-
# @option opts [Integer] :result_limit
|
370
|
-
# @option opts [Integer] :tautomer_limit
|
371
|
-
# @option opts [String] :extra_query
|
372
|
-
# @return [Array<(Array<StructureSearchHit>, Integer, Hash)>] Array<StructureSearchHit> data, response status code and response headers
|
373
|
-
def v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts = {})
|
374
|
-
if @api_client.config.debugging
|
375
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_indexes_index_search_substructure_get ...'
|
376
|
-
end
|
377
|
-
# verify the required parameter 'index' is set
|
378
|
-
if @api_client.config.client_side_validation && index.nil?
|
379
|
-
fail ArgumentError, "Missing the required parameter 'index' when calling DefaultApi.v1_indexes_index_search_substructure_get"
|
380
|
-
end
|
381
|
-
# verify the required parameter 'smiles' is set
|
382
|
-
if @api_client.config.client_side_validation && smiles.nil?
|
383
|
-
fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_indexes_index_search_substructure_get"
|
384
|
-
end
|
385
|
-
# resource path
|
386
|
-
local_var_path = '/v1/indexes/{index}/search/substructure'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
387
|
-
|
388
|
-
# query parameters
|
389
|
-
query_params = opts[:query_params] || {}
|
390
|
-
query_params[:'smiles'] = smiles
|
391
|
-
query_params[:'result_limit'] = opts[:'result_limit'] if !opts[:'result_limit'].nil?
|
392
|
-
query_params[:'tautomer_limit'] = opts[:'tautomer_limit'] if !opts[:'tautomer_limit'].nil?
|
393
|
-
query_params[:'extra_query'] = opts[:'extra_query'] if !opts[:'extra_query'].nil?
|
394
|
-
|
395
|
-
# header parameters
|
396
|
-
header_params = opts[:header_params] || {}
|
397
|
-
# HTTP header 'Accept' (if needed)
|
398
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
399
|
-
|
400
|
-
# form parameters
|
401
|
-
form_params = opts[:form_params] || {}
|
402
|
-
|
403
|
-
# http body (model)
|
404
|
-
post_body = opts[:debug_body]
|
405
|
-
|
406
|
-
# return_type
|
407
|
-
return_type = opts[:debug_return_type] || 'Array<StructureSearchHit>'
|
408
|
-
|
409
|
-
# auth_names
|
410
|
-
auth_names = opts[:debug_auth_names] || []
|
411
|
-
|
412
|
-
new_options = opts.merge(
|
413
|
-
:operation => :"DefaultApi.v1_indexes_index_search_substructure_get",
|
414
|
-
:header_params => header_params,
|
415
|
-
:query_params => query_params,
|
416
|
-
:form_params => form_params,
|
417
|
-
:body => post_body,
|
418
|
-
:auth_names => auth_names,
|
419
|
-
:return_type => return_type
|
420
|
-
)
|
421
|
-
|
422
|
-
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
423
|
-
if @api_client.config.debugging
|
424
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_substructure_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
425
|
-
end
|
426
|
-
return data, status_code, headers
|
427
|
-
end
|
428
|
-
|
429
|
-
# List schemas available for creating indexes
|
430
|
-
# @param [Hash] opts the optional parameters
|
431
|
-
# @return [Array<Schema>]
|
432
|
-
def v1_schemas_get(opts = {})
|
433
|
-
data, _status_code, _headers = v1_schemas_get_with_http_info(opts)
|
434
|
-
data
|
435
|
-
end
|
436
|
-
|
437
|
-
# List schemas available for creating indexes
|
438
|
-
# @param [Hash] opts the optional parameters
|
439
|
-
# @return [Array<(Array<Schema>, Integer, Hash)>] Array<Schema> data, response status code and response headers
|
440
|
-
def v1_schemas_get_with_http_info(opts = {})
|
441
|
-
if @api_client.config.debugging
|
442
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_schemas_get ...'
|
443
|
-
end
|
444
|
-
# resource path
|
445
|
-
local_var_path = '/v1/schemas'
|
446
|
-
|
447
|
-
# query parameters
|
448
|
-
query_params = opts[:query_params] || {}
|
449
|
-
|
450
|
-
# header parameters
|
451
|
-
header_params = opts[:header_params] || {}
|
452
|
-
# HTTP header 'Accept' (if needed)
|
453
|
-
header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
|
454
|
-
|
455
|
-
# form parameters
|
456
|
-
form_params = opts[:form_params] || {}
|
457
|
-
|
458
|
-
# http body (model)
|
459
|
-
post_body = opts[:debug_body]
|
460
|
-
|
461
|
-
# return_type
|
462
|
-
return_type = opts[:debug_return_type] || 'Array<Schema>'
|
463
|
-
|
464
|
-
# auth_names
|
465
|
-
auth_names = opts[:debug_auth_names] || []
|
466
|
-
|
467
|
-
new_options = opts.merge(
|
468
|
-
:operation => :"DefaultApi.v1_schemas_get",
|
469
|
-
:header_params => header_params,
|
470
|
-
:query_params => query_params,
|
471
|
-
:form_params => form_params,
|
472
|
-
:body => post_body,
|
473
|
-
:auth_names => auth_names,
|
474
|
-
:return_type => return_type
|
475
|
-
)
|
476
|
-
|
477
|
-
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
478
|
-
if @api_client.config.debugging
|
479
|
-
@api_client.config.logger.debug "API called: DefaultApi#v1_schemas_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
480
|
-
end
|
481
|
-
return data, status_code, headers
|
482
|
-
end
|
483
|
-
|
484
|
-
# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
|
485
|
-
# @param smiles [Array<Smiles>]
|
486
|
-
# @param [Hash] opts the optional parameters
|
487
|
-
# @return [Array<StandardizedSmiles>]
|
488
|
-
def v1_standardize_post(smiles, opts = {})
|
489
|
-
data, _status_code, _headers = v1_standardize_post_with_http_info(smiles, opts)
|
490
|
-
data
|
491
|
-
end
|
492
|
-
|
493
|
-
# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
|
494
|
-
# @param smiles [Array<Smiles>]
|
495
|
-
# @param [Hash] opts the optional parameters
|
496
|
-
# @return [Array<(Array<StandardizedSmiles>, Integer, Hash)>] Array<StandardizedSmiles> data, response status code and response headers
|
497
|
-
def v1_standardize_post_with_http_info(smiles, opts = {})
|
498
|
-
if @api_client.config.debugging
|
499
|
-
@api_client.config.logger.debug 'Calling API: DefaultApi.v1_standardize_post ...'
|
500
|
-
end
|
501
|
-
# verify the required parameter 'smiles' is set
|
502
|
-
if @api_client.config.client_side_validation && smiles.nil?
|
503
|
-
fail ArgumentError, "Missing the required parameter 'smiles' when calling DefaultApi.v1_standardize_post"
|
37
|
+
# verify the required parameter 'smile' is set
|
38
|
+
if @api_client.config.client_side_validation && smile.nil?
|
39
|
+
fail ArgumentError, "Missing the required parameter 'smile' when calling DefaultApi.standardize_post"
|
504
40
|
end
|
505
41
|
# resource path
|
506
|
-
local_var_path = '/
|
42
|
+
local_var_path = '/standardize'
|
507
43
|
|
508
44
|
# query parameters
|
509
45
|
query_params = opts[:query_params] || {}
|
@@ -522,16 +58,16 @@ module Cheminee
|
|
522
58
|
form_params = opts[:form_params] || {}
|
523
59
|
|
524
60
|
# http body (model)
|
525
|
-
post_body = opts[:debug_body] || @api_client.object_to_http_body(
|
61
|
+
post_body = opts[:debug_body] || @api_client.object_to_http_body(smile)
|
526
62
|
|
527
63
|
# return_type
|
528
|
-
return_type = opts[:debug_return_type] || 'Array<
|
64
|
+
return_type = opts[:debug_return_type] || 'Array<StandardizedSmile>'
|
529
65
|
|
530
66
|
# auth_names
|
531
67
|
auth_names = opts[:debug_auth_names] || []
|
532
68
|
|
533
69
|
new_options = opts.merge(
|
534
|
-
:operation => :"DefaultApi.
|
70
|
+
:operation => :"DefaultApi.standardize_post",
|
535
71
|
:header_params => header_params,
|
536
72
|
:query_params => query_params,
|
537
73
|
:form_params => form_params,
|
@@ -542,7 +78,7 @@ module Cheminee
|
|
542
78
|
|
543
79
|
data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
|
544
80
|
if @api_client.config.debugging
|
545
|
-
@api_client.config.logger.debug "API called: DefaultApi#
|
81
|
+
@api_client.config.logger.debug "API called: DefaultApi#standardize_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
546
82
|
end
|
547
83
|
return data, status_code, headers
|
548
84
|
end
|
data/lib/cheminee/api_client.rb
CHANGED
@@ -6,7 +6,7 @@
|
|
6
6
|
The version of the OpenAPI document: 1.0
|
7
7
|
|
8
8
|
Generated by: https://openapi-generator.tech
|
9
|
-
OpenAPI Generator version: 7.
|
9
|
+
OpenAPI Generator version: 7.0.0-SNAPSHOT
|
10
10
|
|
11
11
|
=end
|
12
12
|
|
@@ -17,7 +17,6 @@ require 'tempfile'
|
|
17
17
|
require 'time'
|
18
18
|
require 'typhoeus'
|
19
19
|
|
20
|
-
|
21
20
|
module Cheminee
|
22
21
|
class ApiClient
|
23
22
|
# The Configuration object holding settings to be used in the API client.
|
@@ -46,10 +45,9 @@ module Cheminee
|
|
46
45
|
# Call an API with given options.
|
47
46
|
#
|
48
47
|
# @return [Array<(Object, Integer, Hash)>] an array of 3 elements:
|
49
|
-
# the data deserialized from response body (
|
48
|
+
# the data deserialized from response body (could be nil), response status code and response headers.
|
50
49
|
def call_api(http_method, path, opts = {})
|
51
50
|
request = build_request(http_method, path, opts)
|
52
|
-
tempfile = download_file(request) if opts[:return_type] == 'File'
|
53
51
|
response = request.run
|
54
52
|
|
55
53
|
if @config.debugging
|
@@ -71,9 +69,7 @@ module Cheminee
|
|
71
69
|
end
|
72
70
|
end
|
73
71
|
|
74
|
-
if opts[:return_type]
|
75
|
-
data = tempfile
|
76
|
-
elsif opts[:return_type]
|
72
|
+
if opts[:return_type]
|
77
73
|
data = deserialize(response, opts[:return_type])
|
78
74
|
else
|
79
75
|
data = nil
|
@@ -128,7 +124,9 @@ module Cheminee
|
|
128
124
|
end
|
129
125
|
end
|
130
126
|
|
131
|
-
Typhoeus::Request.new(url, req_opts)
|
127
|
+
request = Typhoeus::Request.new(url, req_opts)
|
128
|
+
download_file(request) if opts[:return_type] == 'File'
|
129
|
+
request
|
132
130
|
end
|
133
131
|
|
134
132
|
# Builds the HTTP request body
|
@@ -166,8 +164,6 @@ module Cheminee
|
|
166
164
|
# process can use.
|
167
165
|
#
|
168
166
|
# @see Configuration#temp_folder_path
|
169
|
-
#
|
170
|
-
# @return [Tempfile] the tempfile generated
|
171
167
|
def download_file(request)
|
172
168
|
tempfile = nil
|
173
169
|
encoding = nil
|
@@ -182,24 +178,21 @@ module Cheminee
|
|
182
178
|
prefix = prefix + '-' unless prefix.end_with?('-')
|
183
179
|
encoding = response.body.encoding
|
184
180
|
tempfile = Tempfile.open(prefix, @config.temp_folder_path, encoding: encoding)
|
181
|
+
@tempfile = tempfile
|
185
182
|
end
|
186
183
|
request.on_body do |chunk|
|
187
184
|
chunk.force_encoding(encoding)
|
188
185
|
tempfile.write(chunk)
|
189
186
|
end
|
190
|
-
|
191
|
-
|
192
|
-
|
193
|
-
|
194
|
-
|
195
|
-
|
196
|
-
|
197
|
-
|
198
|
-
else
|
199
|
-
fail ApiError.new("Failed to create the tempfile based on the HTTP response from the server: #{request.inspect}")
|
187
|
+
request.on_complete do |response|
|
188
|
+
if tempfile
|
189
|
+
tempfile.close
|
190
|
+
@config.logger.info "Temp file written to #{tempfile.path}, please copy the file to a proper folder "\
|
191
|
+
"with e.g. `FileUtils.cp(tempfile.path, '/new/file/path')` otherwise the temp file "\
|
192
|
+
"will be deleted automatically with GC. It's also recommended to delete the temp file "\
|
193
|
+
"explicitly with `tempfile.delete`"
|
194
|
+
end
|
200
195
|
end
|
201
|
-
|
202
|
-
tempfile
|
203
196
|
end
|
204
197
|
|
205
198
|
# Check if the given MIME is a JSON MIME.
|
@@ -220,10 +213,15 @@ module Cheminee
|
|
220
213
|
# @param [String] return_type some examples: "User", "Array<User>", "Hash<String, Integer>"
|
221
214
|
def deserialize(response, return_type)
|
222
215
|
body = response.body
|
216
|
+
|
217
|
+
# handle file downloading - return the File instance processed in request callbacks
|
218
|
+
# note that response body is empty when the file is written in chunks in request on_body callback
|
219
|
+
return @tempfile if return_type == 'File'
|
220
|
+
|
223
221
|
return nil if body.nil? || body.empty?
|
224
222
|
|
225
223
|
# return response body directly for String return type
|
226
|
-
return body
|
224
|
+
return body if return_type == 'String'
|
227
225
|
|
228
226
|
# ensuring a default content type
|
229
227
|
content_type = response.headers['Content-Type'] || 'application/json'
|