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