1 /*
2 * Copyright (c) 2005, 2007, 2010 Genome Research Ltd.
3 * Author(s): James Bonfield
4 *
5 * Redistribution and use in source and binary forms, with or without
6 * modification, are permitted provided that the following conditions are met:
7 *
8 * 1. Redistributions of source code must retain the above copyright notice,
9 * this list of conditions and the following disclaimer.
10 *
11 * 2. Redistributions in binary form must reproduce the above
12 * copyright notice, this list of conditions and the following
13 * disclaimer in the documentation and/or other materials provided
14 * with the distribution.
15 *
16 * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
17 * Institute nor the names of its contributors may be used to endorse
18 * or promote products derived from this software without specific
19 * prior written permission.
20 *
21 * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
22 * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
23 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
24 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
25 * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
26 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
27 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
28 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
29 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
30 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
31 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
32 */
33
34 /*
35 * Author(s): James Bonfield
36 *
37 * Copyright (c) 2001 MEDICAL RESEARCH COUNCIL
38 * All rights reserved
39 *
40 * Redistribution and use in source and binary forms, with or without
41 * modification, are permitted provided that the following conditions are met:
42 *
43 * 1 Redistributions of source code must retain the above copyright notice,
44 * this list of conditions and the following disclaimer.
45 *
46 * 2 Redistributions in binary form must reproduce the above copyright
47 * notice, this list of conditions and the following disclaimer in
48 * the documentation and/or other materials provided with the
49 * distribution.
50 *
51 * 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
52 * MOLECULAR BIOLOGY nor the names of its contributors may be used
53 * to endorse or promote products derived from this software without
54 * specific prior written permission.
55 *
56 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
57 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
58 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
59 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
60 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
61 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
62 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
63 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
64 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
65 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
66 * POSSIBILITY OF SUCH DAMAGE.
67 */
68
69 /*
70 * Fetches all or several specific comment(s) from a trace file TEXT section.
71 *
72 * Usage:
73 * get_comment [options] [field ...] < infile
74 *
75 * Options:
76 * -c Suppresses display of field-ID
77 * -h Help
78 *
79 * Return codes:
80 * 0 Success
81 * 1 At least one field was not found
82 * 2 Failed to read file, or usage message displayed
83 */
84
85 #ifdef HAVE_CONFIG_H
86 #include "io_lib_config.h"
87 #endif
88
89 #include <stdio.h>
90 #include <stdlib.h>
91 #include <string.h>
92 #include <unistd.h>
93
94 #include <io_lib/Read.h>
95
96 /* Nasty Microsoft bits */
97 #ifdef _MSC_VER
98 # define DLL_IMPORT __declspec(dllimport)
99 #else
100 # define DLL_IMPORT
101 #endif
102
103 /*
104 * From unistd.h
105 extern DLL_IMPORT char *optarg;
106 extern DLL_IMPORT int optind;
107 */
108
usage(void)109 void usage(void) {
110 puts("Usage:");
111 puts(" get_comment [options] [field ...] < infile");
112 puts("\nOptions:");
113 puts(" -c Suppresses display of field-ID");
114 puts(" -h Help");
115 puts("\nReturn codes:");
116 puts(" 0 Success");
117 puts(" 1 At least one field was not found");
118 puts(" 2 Failed to read file, or usage message displayed");
119 exit(2);
120 }
121
main(int argc,char ** argv)122 int main(int argc, char **argv) {
123 Read *r;
124 char *ident, *value;
125 int ident_len, value_len;
126 enum state_t {
127 NAME, EQUALS, VALUE, NL
128 } state;
129 size_t len;
130 int i, j, found;
131 int suppress = 0;
132 int *found_args = NULL;
133
134 /* Parse arguments */
135 for (argc--, argv++; argc > 0; argc--, argv++) {
136 if (**argv != '-')
137 break;
138
139 if (strcmp(*argv, "-c") == 0) {
140 suppress = 1;
141
142 } else {
143 usage();
144 }
145 }
146
147 /* Read the file */
148 read_sections(READ_COMMENTS);
149 if (NULL == (r = fread_reading(stdin, "(stdin)", TT_ANY))) {
150 fprintf(stderr, "failed to read trace from stdin\n");
151 return 2;
152 }
153
154 if (!r->info)
155 return 1;
156
157 if (argc == 0) {
158 /* Display all of them */
159 puts(r->info);
160
161 } else {
162 /* Display only the ones listed on the command line */
163
164 found_args = (int *)calloc(argc, sizeof(int));
165
166 len = strlen(r->info);
167 state = NAME;
168 ident = r->info;
169 found = 0;
170 /* Not needed, but avoids "might be used uninitialized" message */
171 value = NULL;
172 ident_len = value_len = 0;
173 for (i = 0; i <= len; i++) {
174 switch (state) {
175 case NAME:
176 if (r->info[i] == '=') {
177 state = EQUALS;
178 ident_len = &r->info[i] - ident;
179 value_len = 0;
180 }
181 break;
182
183 case EQUALS:
184 for (j = 0; j < argc; j++) {
185 if (strncmp(ident, argv[j], ident_len) == 0) {
186 found = 1;
187 found_args[j] = 1;
188 }
189 }
190 state = VALUE;
191 value = &r->info[i];
192
193 /* DELIBERATE FLOW THROUGH */
194
195 case VALUE:
196 if (r->info[i] == '\n' || r->info[i] == 0) {
197 value_len = &r->info[i] - value;
198 state = NL;
199 }
200 break;
201
202 case NL:
203 if (found) {
204 if (suppress) {
205 printf("%.*s\n",
206 value_len, value);
207 } else {
208 printf("%.*s=%.*s\n",
209 ident_len, ident, value_len, value);
210 }
211 }
212 state = NAME;
213 ident = &r->info[i];
214 found = 0;
215 break;
216 }
217 }
218 }
219
220 read_deallocate(r);
221
222 if (found_args) {
223 for (j = 0; j < argc; j++) {
224 if (found_args[j] == 0)
225 return 1;
226 }
227 }
228
229 return 0;
230 }
231