NCBI C++ ToolKit
entrez2_client.cpp
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1 /* $Id: entrez2_client.cpp 89906 2020-04-30 12:37:23Z grichenk $
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
9  * the author's official duties as a United States Government employee and
10  * thus cannot be copyrighted. This software/database is freely available
11  * to the public for use. The National Library of Medicine and the U.S.
12  * Government have not placed any restriction on its use or reproduction.
13  *
14  * Although all reasonable efforts have been taken to ensure the accuracy
15  * and reliability of the software and data, the NLM and the U.S.
16  * Government do not and cannot warrant the performance or results that
17  * may be obtained by using this software or data. The NLM and the U.S.
18  * Government disclaim all warranties, express or implied, including
19  * warranties of performance, merchantability or fitness for any particular
20  * purpose.
21  *
22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Author: Josh Cherry
27  *
28  * File Description:
29  * Entrez2 network client
30  *
31  * Remark:
32  * This code was originally generated by application DATATOOL
33  * using specifications from the data definition file
34  * 'entrez2.asn'.
35  */
36 
37 // standard includes
38 
39 // generated includes
40 
41 #include <ncbi_pch.hpp>
56 
57 #include <algorithm>
58 
59 // generated classes
60 
62 
63 BEGIN_objects_SCOPE // namespace ncbi::objects::
64 
65 // destructor
67 {
68 }
69 
70 
71 /// A simplified interface for getting neighbors (links)
72 
73 /// This form just yields a vector of UIDs
75  const string& db,
76  const string& link_type,
77  vector<TUid>& neighbor_uids)
78 {
79  vector<TUid> uids;
80  uids.push_back(query_uid);
81  GetNeighbors(uids, db, link_type, neighbor_uids);
82 }
83 
84 
85 /// This form just yields a vector of UIDs
86 void CEntrez2Client::GetNeighbors(const vector<TUid>& query_uids,
87  const string& db,
88  const string& link_type,
89  vector<TUid>& neighbor_uids)
90 {
91  // first retrieve the link_set
92  CRef<CEntrez2_link_set> link_set;
93  link_set = GetNeighbors(query_uids, db, link_type);
94 
95  // then extract the UIDs
97  = link_set->GetIds().GetConstUidIterator();
98  if (link_set->GetIds().IsSetNum()) {
99  neighbor_uids.reserve(link_set->GetIds().GetNum());
100  }
101  for ( ; !it.AtEnd(); ++it) {
102  neighbor_uids.push_back(*it);
103  }
104 }
105 
106 
107 /// This form returns the entire CEntrez2_link_set object,
108 /// which includes scores.
110  const string& db,
111  const string& link_type)
112 {
113  vector<TUid> uids;
114  uids.push_back(query_uid);
115  return GetNeighbors(uids, db, link_type);
116 }
117 
118 
119 /// This form returns the entire CEntrez2_link_set object,
120 /// which includes scores.
122 CEntrez2Client::GetNeighbors(const vector<TUid>& query_uids,
123  const string& db,
124  const string& link_type)
125 {
126  CEntrez2_id_list uids;
127  uids.SetDb() = CEntrez2_db_id(db);
128  uids.AssignUids(query_uids);
129 
131  gl.SetUids(uids);
132  gl.SetLinktype().Set(db + "_" + link_type);
133 
134  CRef<CEntrez2_link_set> link_set = AskGet_links(gl);
135  return link_set;
136 }
137 
138 
139 /// Retrieve counts of the various types of neighbors available
142  const string& db)
143 {
144  CEntrez2_id uid;
145  uid.SetDb() = CEntrez2_db_id(db);
146  uid.SetUid(ENTREZ_ID_FROM(TIntId, query_uid));
147  return AskGet_link_counts(uid);
148 }
149 
150 
151 /// Query a db with a string, returning uids as integers
152 void CEntrez2Client::Query(const string& query,
153  const string& db,
154  vector<TUid>& result_uids,
155  size_t start,
156  size_t count,
157  TReply* reply)
158 {
160  bel->SetStr(query);
161 
163  bexp.SetDb().Set(db);
164  bexp.SetExp().push_back(bel);
165 
166  // set some limits
167  if (start > 0) {
168  bexp.SetLimits().SetOffset_UIDs(start);
169  }
170  if (count > 0) {
171  bexp.SetLimits().SetMax_UIDs(count);
172  }
173 
175  req.SetReturn_UIDs(true);
176  req.SetQuery(bexp);
177 
178  CRef<CEntrez2_boolean_reply> bool_reply = AskEval_boolean(req, reply);
179 
180  // now extract the UIDs
181  if (!bool_reply->GetUids().CanGetUids()) {
182  // this happens when no matches were found
183  return;
184  }
186  = bool_reply->GetUids().GetConstUidIterator();
187  !it.AtEnd(); ++it) {
188  result_uids.push_back(*it);
189  }
190 }
191 
192 
193 /// Given some uids, a database, and an entrez query string,
194 /// determine which of these uids match the query string.
195 ///
196 /// Note: If a uid appears more than once in query_uids and
197 /// matches the query string, it may or may not appear more
198 /// more than once in the result.
199 void CEntrez2Client::FilterIds(const vector<TUid>& query_uids,
200  const string& db,
201  const string& query_string,
202  vector<TUid>& result_uids)
203 {
204  const unsigned int kMaxIdsInQueryString = 2500;
205 
206  if (query_uids.empty()) {
207  return;
208  }
209 
210  if (query_uids.size() <= kMaxIdsInQueryString) {
211  // Query with a big query string that includes
212  // all the query_uids OR'd together
213  string uids;
214  ITERATE (vector<TUid>, uid, query_uids) {
215  if ( !uids.empty() ) {
216  uids += " OR ";
217  }
218  uids += NStr::NumericToString(*uid) + "[UID]";
219  }
220 
221  string whole_query = "(" + query_string + ") AND (" + uids + ")";
222  Query(whole_query, db, result_uids);
223  } else {
224  // Break query_uids into chunks <= kMaxIdsInQueryString
225  vector<TUid> subset_query_uids;
226  subset_query_uids.reserve(kMaxIdsInQueryString);
227  for (size_t start = 0; start < query_uids.size();
228  start += kMaxIdsInQueryString) {
229  subset_query_uids.clear();
230  // end is one past the last index of interest
231  size_t end =
232  min(start + kMaxIdsInQueryString, query_uids.size());
233  for (size_t i = start; i < end; ++i) {
234  subset_query_uids.push_back(query_uids[i]);
235  }
236  // This relies on the fact that FilterIds appends to result
237  FilterIds(subset_query_uids, db, query_string, result_uids);
238  }
239  }
240 }
241 
242 
244 CEntrez2Client::GetDocsums(const vector<TUid>& uids,
245  const string& db)
246 {
247  CEntrez2_id_list ids;
248  ids.AssignUids(uids);
249  ids.SetDb().Set(db);
250  return AskGet_docsum(ids);
251 }
252 
253 
254 /// Retrieve the docsums for a single UID
256 CEntrez2Client::GetDocsums(TUid uid, const string& db)
257 {
258  vector<TUid> uids;
259  uids.push_back(uid);
260  return GetDocsums(uids, db);
261 }
262 
263 
264 string
266 {
267  const CE2Request& e2req = request.GetRequest();
268  const CEntrez2_db_id* db = 0;
269 
270  switch (e2req.Which()) {
272  db = &e2req.GetEval_boolean().GetQuery().GetDb();
273  break;
275  db = &e2req.GetGet_docsum().GetDb();
276  break;
278  db = &e2req.GetGet_term_pos().GetDb();
279  break;
281  db = &e2req.GetGet_term_list().GetDb();
282  break;
284  db = &e2req.GetGet_term_hierarchy().GetDb();
285  break;
287  db = &e2req.GetGet_links().GetUids().GetDb();
288  break;
290  db = &e2req.GetGet_linked().GetUids().GetDb();
291  break;
293  db = &e2req.GetGet_link_counts().GetDb();
294  break;
295  default:
296  break;
297  }
298 
299  if (db && !db->Get().empty()) {
300  return "DB=" + db->Get();
301  } else {
302  return kEmptyStr;
303  }
304 }
305 
306 
307 #ifdef NCBI_STRICT_GI
308 
310  const string& db_from,
311  const string& db_to,
312  vector<TGi>& neighbor_uids)
313 {
314  vector<TUid> vi_neighbor_uids;
315  GetNeighbors(GI_TO(TUid, query_uid), db_from, db_to, vi_neighbor_uids);
316  ITERATE(vector<TUid>, it, vi_neighbor_uids) {
317  neighbor_uids.push_back(GI_FROM(TUid, *it));
318  }
319 }
320 
321 void CEntrez2Client::GetNeighbors(const vector<TGi>& query_uids,
322  const string& db,
323  const string& link_type,
324  vector<TGi>& neighbor_uids)
325 {
326  vector<TUid> vi_query_uids;
327  ITERATE(vector<TGi>, it, query_uids) {
328  vi_query_uids.push_back(GI_TO(TUid, *it));
329  }
330  vector<TUid> vi_neighbor_uids;
331  GetNeighbors(vi_query_uids, db, link_type, vi_neighbor_uids);
332  ITERATE(vector<TUid>, it, vi_neighbor_uids) {
333  neighbor_uids.push_back(GI_FROM(TUid, *it));
334  }
335 }
336 
338  const string& db_from,
339  const string& db_to)
340 {
341  return GetNeighbors(GI_TO(TUid, query_uid), db_from, db_to);
342 }
343 
345  const string& db_from,
346  const string& db_to)
347 {
348  vector<TUid> vi_query_uids;
349  ITERATE(vector<TGi>, it, query_uids) {
350  vi_query_uids.push_back(GI_TO(TUid, *it));
351  }
352  return GetNeighbors(vi_query_uids, db_from, db_to);
353 }
354 
356  const string& db)
357 {
358  return GetNeighborCounts(GI_TO(TUid, query_uid), db);
359 }
360 
361 void CEntrez2Client::Query(const string& query,
362  const string& db,
363  vector<TGi>& result_uids,
364  size_t start_offs,
365  size_t count,
366  TReply* reply)
367 {
368  vector<TUid> vi_result_uids;
369  Query(query, db, vi_result_uids, start_offs, count, reply);
370  ITERATE(vector<TUid>, it, vi_result_uids) {
371  result_uids.push_back(GI_FROM(TUid, *it));
372  }
373 }
374 
375 void CEntrez2Client::FilterIds(const vector<TGi>& query_uids,
376  const string& db,
377  const string& query_string,
378  vector<TGi>& result_uids)
379 {
380  vector<TUid> vi_query_uids;
381  ITERATE(vector<TGi>, it, query_uids) {
382  vi_query_uids.push_back(GI_TO(TUid, *it));
383  }
384  vector<TUid> vi_result_uids;
385  FilterIds(vi_query_uids, db, query_string, vi_result_uids);
386  ITERATE(vector<TUid>, it, vi_result_uids) {
387  result_uids.push_back(GI_FROM(TUid, *it));
388  }
389 }
390 
392  const string& db)
393 {
394  vector<TUid> vi_uids;
395  ITERATE(vector<TGi>, it, uids) {
396  vi_uids.push_back(GI_TO(TUid, *it));
397  }
398  return GetDocsums(vi_uids, db);
399 }
400 
402  const string& db)
403 {
404  return GetDocsums(GI_TO(TUid, uid), db);
405 }
406 
407 #endif
408 
409 END_objects_SCOPE // namespace ncbi::objects::
410 
412 
413 /* Original file checksum: lines: 64, chars: 1896, CRC32: cd6a8df4 */
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
CE2Request –.
Definition: E2Request.hpp:66
CRef< CEntrez2_docsum_list > GetDocsums(const vector< TUid > &uids, const string &db)
Retrieve the docsums for a set of UIDs.
virtual string GetAffinity(const CEntrez2_request &request) const
Get DB affinity of the request.
CRef< CEntrez2_link_count_list > GetNeighborCounts(TUid query_uid, const string &db)
Retrieve counts of the various types of neighbors available.
void FilterIds(const vector< TUid > &query_uids, const string &db, const string &query_string, vector< TUid > &result_uids)
Given some uids, a database, and an entrez query string, determine which of these uids match the quer...
void Query(const string &query, const string &db, vector< TUid > &result_uids, size_t start_offs=0, size_t count=0, TReply *reply=0)
Some other simplified interfaces.
void GetNeighbors(TUid query_uid, const string &db_from, const string &db_to, vector< TUid > &neighbor_uids)
A simplified interface for getting neighbors (links)
CEntrez2_boolean_element –.
CEntrez2_boolean_exp –.
CEntrez2_db_id –.
CEntrez2_eval_boolean –.
void AssignUids(const vector< TUid > &uids)
CEntrez2_id –.
Definition: Entrez2_id.hpp:66
CEntrez2_reply –.
CEntrez2_request –.
CRef –.
Definition: ncbiobj.hpp:618
#define GI_FROM(T, value)
Definition: ncbimisc.hpp:1086
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
Int8 TIntId
Definition: ncbimisc.hpp:999
#define ENTREZ_ID_FROM(T, value)
Definition: ncbimisc.hpp:1098
#define GI_TO(T, gi)
Definition: ncbimisc.hpp:1085
const TPrim & Get(void) const
Definition: serialbase.hpp:347
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define kEmptyStr
Definition: ncbistr.hpp:123
static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)
Convert numeric value to string.
Definition: ncbistr.hpp:673
virtual CRef< CEntrez2_link_set > AskGet_links(const CEntrez2_get_links &req, TReply *reply=0)
void SetDb(const TDb &value)
Assign a value to Db data member.
const TGet_docsum & GetGet_docsum(void) const
Get the variant data.
Definition: E2Request_.cpp:160
const TDb & GetDb(void) const
Get the Db member data.
const TEval_boolean & GetEval_boolean(void) const
Get the variant data.
Definition: E2Request_.cpp:138
const TGet_term_list & GetGet_term_list(void) const
Get the variant data.
Definition: E2Request_.cpp:204
virtual CRef< CEntrez2_link_count_list > AskGet_link_counts(const CEntrez2_id &req, TReply *reply=0)
const TUids & GetUids(void) const
Get the Uids member data.
const TGet_term_pos & GetGet_term_pos(void) const
Get the variant data.
Definition: E2Request_.cpp:182
const TGet_linked & GetGet_linked(void) const
Get the variant data.
Definition: E2Request_.cpp:270
void SetUids(TUids &value)
Assign a value to Uids data member.
void SetLimits(TLimits &value)
Assign a value to Limits data member.
void SetUid(TUid value)
Assign a value to Uid data member.
const TGet_links & GetGet_links(void) const
Get the variant data.
Definition: E2Request_.cpp:248
const TDb & GetDb(void) const
Get the Db member data.
void SetReturn_UIDs(TReturn_UIDs value)
Assign a value to Return_UIDs data member.
const TGet_link_counts & GetGet_link_counts(void) const
Get the variant data.
Definition: E2Request_.cpp:292
TExp & SetExp(void)
Assign a value to Exp data member.
const TDb & GetDb(void) const
Get the Db member data.
const TRequest & GetRequest(void) const
Get the Request member data.
const TDb & GetDb(void) const
Get the Db member data.
virtual CRef< CEntrez2_boolean_reply > AskEval_boolean(const CEntrez2_eval_boolean &req, TReply *reply=0)
void SetLinktype(const TLinktype &value)
Assign a value to Linktype data member.
void SetDb(const TDb &value)
Assign a value to Db data member.
const TQuery & GetQuery(void) const
Get the Query member data.
E_Choice Which(void) const
Which variant is currently selected.
Definition: E2Request_.hpp:416
void SetQuery(TQuery &value)
Assign a value to Query data member.
const TDb & GetDb(void) const
Get the Db member data.
virtual CRef< CEntrez2_docsum_list > AskGet_docsum(const CEntrez2_id_list &req, TReply *reply=0)
const TGet_term_hierarchy & GetGet_term_hierarchy(void) const
Get the variant data.
Definition: E2Request_.cpp:226
void SetDb(const TDb &value)
Assign a value to Db data member.
const TDb & GetDb(void) const
Get the Db member data.
@ e_Get_term_pos
get position in term list
Definition: E2Request_.hpp:98
@ e_Get_link_counts
get all links from one UID
Definition: E2Request_.hpp:103
@ e_Get_docsum
get the DocSums
Definition: E2Request_.hpp:97
@ e_Get_linked
get subset of UID list which has links
Definition: E2Request_.hpp:102
@ e_Get_links
get specific links from a UID list
Definition: E2Request_.hpp:101
@ e_Get_term_list
get Term list by position
Definition: E2Request_.hpp:99
@ e_Get_term_hierarchy
get a hierarchy from a term
Definition: E2Request_.hpp:100
@ e_Eval_boolean
Boolean lookup.
Definition: E2Request_.hpp:96
int i
T min(T x_, T y_)
static string query
Modified on Sun Apr 14 05:26:49 2024 by modify_doxy.py rev. 669887