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comparison GEMBASSY-1.0.3/include/gfile.c @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 /******************************************************************************
2 ** @source GEMBASSY file routines
3 **
4 ** @version 1.0
5 ** @modified December 27 2012 Hidetoshi Itaya Created this file
6 ** @@
7 **
8 ** This library is free software; you can redistribute it and/or
9 ** modify it under the terms of the GNU Library General Public
10 ** License as published by the Free Software Foundation; either
11 ** version 2 of the License, or (at your option) any later version.
12 **
13 ** This library is distributed in the hope that it will be useful,
14 ** but WITHOUT ANY WARRANTY; without even the implied warranty of
15 ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 ** Library General Public License for more details.
17 **
18 ** You should have received a copy of the GNU Library General Public
19 ** License along with this library; if not, write to the
20 ** Free Software Foundation, Inc., 59 Temple Place - Suite 330,
21 ** Boston, MA 02111-1307, USA.
22 ******************************************************************************/
23
24 #include "gfile.h"
25
26
27
28
29 /* @func gValID ***************************************************************
30 **
31 ** Checks if an input string is a valid ID
32 **
33 ** @param id [r] [AjPStr] ID to check
34 ** @return [AjBool]
35 ** @@
36 ******************************************************************************/
37
38 ajint gValID(AjPStr id){
39 AjPFilebuff buff = NULL;
40 AjPStr url = NULL;
41 AjPStr line = NULL;
42 AjPRegexp pval = NULL;
43
44 url = ajStrNewC("http://web.sfc.keio.ac.jp/~t11080hi/valID/valID.cgi?id=");
45 url = ajStrNew();
46 ajFmtPrintS(&url, "http://rest.g-language.org/%S", id);
47
48 //ajStrAppendS(&url, id);
49
50 if(!gFilebuffURLS(url, &buff)) {
51 return ajFalse;
52 }
53
54 return ajTrue;
55
56 ajBuffreadLine(buff, &line);
57
58 pval = ajRegCompC("^0");
59
60 if(ajRegExec(pval, line))
61 return ajFalse;
62
63 return ajTrue;
64 }
65
66
67
68
69 /* @func gStrAppendURLS *******************************************************
70 **
71 ** Downloads file from a specified URL and writes to given output file
72 **
73 ** @param [r] url [AjPStr] URL to download file from
74 ** @param [r] string [AjPStr] String to write into
75 ** @return [AjBool]
76 ** @@
77 ******************************************************************************/
78
79 AjBool gStrAppendURLS(AjPStr url, AjPStr* string){
80 AjPFilebuff buff = NULL;
81 AjPStr file = NULL;
82 AjPStr line = NULL;
83
84 if(!*string)
85 *string = ajStrNew();
86
87 if(!gFilebuffURLS(url, &buff))
88 return ajFalse;
89
90 while(ajBuffreadLine(buff, &line)){
91 ajStrAppendS(string, line);
92 }
93
94 ajFilebuffDel(&buff);
95
96 return ajTrue;
97 }
98
99
100
101
102 /* @func gStrAppendURLC *******************************************************
103 **
104 ** Downloads file from a specified URL and writes to given output file
105 **
106 ** @param [r] url [char*] URL to download file from
107 ** @param [r] string [AjPStr] String to write into
108 ** @return [AjBool]
109 ** @@
110 ******************************************************************************/
111
112 AjBool gStrAppendURLC(char* url, AjPStr* string){
113 if(!gStrAppendURLS(ajStrNewC(url), string))
114 {
115 return ajFalse;
116 }
117
118 return ajTrue;
119 }
120
121
122
123
124 /* @func gFileOutURLS *********************************************************
125 **
126 ** Downloads file from a specified URL and writes to given output file
127 **
128 ** @param [r] url [AjPStr] URL to download file from
129 ** @param [r] outf [AjPFile] File object to write into
130 ** @return [AjBool]
131 ** @@
132 ******************************************************************************/
133
134 AjBool gFileOutURLS(AjPStr url, AjPFile* outf){
135 AjPFilebuff buff = NULL;
136 AjPStr file = NULL;
137 AjPStr line = NULL;
138
139 if(!gFilebuffURLS(url, &buff))
140 return ajFalse;
141
142 while(ajBuffreadLine(buff, &line)){
143 ajWriteline(*outf, line);
144 }
145
146 ajFilebuffDel(&buff);
147
148 return ajTrue;
149 }
150
151
152
153
154 /* @func gFileOutURLC *********************************************************
155 **
156 ** Downloads file from a specified URL and writes to given output file
157 **
158 ** @param [r] url [char*] URL to download file from
159 ** @param [r] outf [AjPFile] File object to write into
160 ** @return [AjBool]
161 ** @@
162 ******************************************************************************/
163
164 AjBool gFileOutURLC(char* url, AjPFile* outf){
165 if(!gFileOutURLS(ajStrNewC(url), outf))
166 {
167 return ajFalse;
168 }
169
170 return ajTrue;
171 }
172
173
174
175
176 /* @func gFilebuffURLS ********************************************************
177 **
178 ** Downloads file from a specified URL and inputs in file buffer
179 **
180 ** @param [r] url [AjPStr] URL to download file from
181 ** @param [r] buff [AjPFilebuff] File buffer to set
182 ** @return [AjBool]
183 ** @@
184 ******************************************************************************/
185
186 AjBool gFilebuffURLS(AjPStr url, AjPFilebuff* buff){
187 AjPStr line = NULL;
188 AjPStr host = NULL;
189 AjPStr path = NULL;
190 ajint port = 80;
191
192 ajHttpUrlDeconstruct(url, &port, &host, &path);
193
194 *buff = ajHttpRead(NULL, NULL, NULL, host, port, path);
195
196 if(!*buff)
197 return ajFalse;
198
199 ajFilebuffHtmlNoheader(*buff);
200
201 return ajTrue;
202 }
203
204
205
206
207 /* @func gFilebuffURLC ********************************************************
208 **
209 ** Downloads file from a specified URL and inputs in file buffer
210 **
211 ** @param [r] url [char*] URL to download file from
212 ** @param [r] buff [AjPFilebuff] File buffer to set
213 ** @return [AjBool]
214 ** @@
215 ******************************************************************************/
216
217 AjBool gFilebuffURLC(char* url, AjPFilebuff* buff){
218 gFilebuffURLS(ajStrNewC(url), buff);
219
220 if(!*buff)
221 return ajFalse;
222
223 return ajTrue;
224 }
225
226
227
228
229 /* @func gAssignUniqueName ****************************************************
230 **
231 ** Creates a unique filename
232 **
233 ** @return [AjPStr] the unique filename
234 ** @@
235 ******************************************************************************/
236
237 void gAssignUniqueName(AjPStr *string) {
238 static char ext[2] = "A";
239
240 ajFmtPrintS(string, "%08d%s", getpid(), ext);
241
242 if( ++ext[0] > 'Z' ) {
243 ext[0] = 'A';
244 }
245 }
246
247
248
249
250 /* @func gCreateUniqueName ****************************************************
251 **
252 ** Returns a unique filename
253 **
254 ** @return [AjPStr] the unique filename
255 ** @@
256 ******************************************************************************/
257
258 AjPStr gCreateUniqueName() {
259 AjPStr string;
260
261 gAssignUniqueName(&string);
262
263 return string;
264 }
265
266
267
268
269 /* @func gFormatGenbank *******************************************************
270 **
271 ** Creates a genbank format string with sequence and features
272 **
273 ** @param [r] seq [AjPSeq] Sequence object to write
274 ** @param [r] inseq [AjPStr] String to write to
275 ** @return [AjBool]
276 ** @@
277 ******************************************************************************/
278
279 AjBool gFormatGenbank(AjPSeq seq, AjPStr *inseq){
280 AjPSeqout seqout = NULL;
281 AjPFeattabOut featout = NULL;
282 AjPFeattable feat = NULL;
283 AjPStr seqline = NULL;
284 AjPStr featline = NULL;
285 AjPFile seqfile = NULL;
286 AjPFile featfile = NULL;
287 AjPStr filename = NULL;
288 AjBool hasfeats = ajTrue;
289
290 gAssignUniqueName(&filename);
291 feat = ajSeqGetFeatCopy(seq);
292
293 if(!feat) {
294 hasfeats = ajFalse;
295 }
296
297 seqout = ajSeqoutNew();
298
299 if(!ajSeqoutOpenFilename(seqout,filename))
300 embExitBad();
301
302 ajSeqoutSetFormatS(seqout,ajStrNewC("genbank"));
303 ajSeqoutWriteSeq(seqout,seq);
304 ajSeqoutClose(seqout);
305 ajSeqoutDel(&seqout);
306
307 seqfile = ajFileNewInNameS(filename);
308 ajSysFileUnlinkS(filename);
309
310 if(hasfeats) {
311 featout = ajFeattabOutNew();
312
313 if(!ajFeattabOutOpen(featout,filename))
314 return ajFalse;
315
316 ajFeattableWriteGenbank(featout,feat);
317
318 ajFeattableDel(&feat);
319 //ajFeattabOutDel(&featout);
320 ajFileClose(&(featout->Handle));
321
322 featfile = ajFileNewInNameS(filename);
323 ajSysFileUnlinkS(filename);
324 }
325
326 while(ajReadline(seqfile,&seqline)){
327 if(hasfeats && ajStrMatchC(seqline,"ORIGIN\n")){
328 while(ajReadline(featfile,&featline)){
329 ajStrAppendS(inseq, featline);
330 }
331 }
332 ajStrAppendS(inseq, seqline);
333 }
334
335 ajStrDel(&seqline);
336 ajStrDel(&featline);
337 ajStrDel(&filename);
338 ajFileClose(&seqfile);
339 ajFileClose(&featfile);
340
341 return hasfeats;
342 }
343
344
345
346
347 /* @func gGetFileContent ******************************************************
348 **
349 ** Reads file content and sets it to string pointer
350 **
351 ** @param [r] content [AjPSeq] String to write to
352 ** @param [r] filename [AjPSeq] Filename to open
353 ** @return [AjBool]
354 ** @@
355 ******************************************************************************/
356
357 AjBool gGetFileContent(AjPStr* content, AjPStr filename){
358 AjPFile file = NULL;
359 AjPStr line = NULL;
360
361 if((file = ajFileNewInNameS(filename)) == NULL)
362 return ajFalse;
363
364 while(ajReadline(file, &line))
365 ajStrAppendS(content, line);
366
367 if(file)
368 ajFileClose(&file);
369
370 ajSysFileUnlinkS(filename);
371
372 return ajTrue;
373 }
374
375
376
377
378 /* @func gtaiFileOutURLS ******************************************************
379 **
380 ** Downloads file from a specified URL and inputs in file buffer
381 **
382 ** @param [r] url [AjPStr] URL to download file from
383 ** @param [r] buff [AjPFilebuff] File buffer to set
384 ** @return [AjBool]
385 ** @@
386 ******************************************************************************/
387
388 AjBool gtaiFileOutURLS(AjPStr url, AjPFile* outf, AjBool tai){
389 if(tai)
390 {
391 CURL *curl;
392 CURLcode curl_res;
393
394 Memory *mem = malloc(sizeof(Memory*));
395
396 mem->size = 0;
397 mem->memory = NULL;
398
399 curl_global_init(CURL_GLOBAL_ALL);
400
401 curl = curl_easy_init();
402
403 if(curl)
404 {
405 curl_easy_setopt(curl, CURLOPT_URL, ajCharNewS(url));
406 curl_easy_setopt(curl, CURLOPT_FOLLOWLOCATION, 1);
407 curl_easy_setopt(curl, CURLOPT_WRITEFUNCTION, curl_write);
408 curl_easy_setopt(curl, CURLOPT_WRITEDATA, mem);
409 }
410
411 curl_res = curl_easy_perform(curl);
412
413 if(CURLE_OK == curl_res)
414 {
415 char* redir;
416 curl_res = curl_easy_getinfo(curl, CURLINFO_EFFECTIVE_URL, &redir);
417
418 if((CURLE_OK == curl_res) && redir) {
419 ajStrAssignC(&url, redir);
420 ajStrExchangeCC(&url, "cai.csv", "tai.csv");
421 }
422 }
423
424 free(mem);
425 curl_easy_cleanup(curl);
426 curl_global_cleanup();
427 }
428
429 return gFileOutURLS(url, outf);
430 }