Mercurial > repos > dawe > srf2fastq
annotate srf2fastq/io_lib-1.12.2/progs/hash_tar.c @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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rev | line source |
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0
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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
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1 #include <stdio.h> |
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2 #include <string.h> |
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3 #include <errno.h> |
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4 #include <stdlib.h> |
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5 #include <fcntl.h> |
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6 #include <io_lib/tar_format.h> |
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7 #include <io_lib/hash_table.h> |
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8 |
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9 typedef struct { |
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10 char member[256]; |
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11 uint64_t pos; |
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12 uint32_t size; |
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13 } tar_file; |
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14 |
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15 void seek_forward(FILE *fp, int size) { |
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16 if (fp != stdin) { |
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17 fseek(fp, size, SEEK_CUR); |
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18 } else { |
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19 /* Seeking on a pipe isn't supported, even for fwd seeks */ |
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20 char buf[8192]; |
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21 while (size) { |
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22 size -= fread(buf, 1, size > 8192 ? 8192 : size, fp); |
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23 } |
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24 } |
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25 } |
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26 |
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27 int main(int argc, char **argv) { |
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28 int directories = 0; |
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29 FILE *fp; |
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30 tar_block blk; |
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31 char member[256]; |
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32 size_t size, extra; |
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33 int LongLink = 0; |
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34 size_t offset = 0; |
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35 int verbose = 0; |
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36 HashFile *hf; |
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37 tar_file *files = NULL; |
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38 int nfiles = 1024; |
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39 int fileno = 0; |
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40 int i; |
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41 char *header = NULL, *footer = NULL; |
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42 int found_header, found_footer; |
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43 int basename = 0; |
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44 char *archive = NULL; |
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45 int append_mode = 0; |
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46 int prepend_mode = 0; |
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47 |
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48 files = (tar_file *)malloc(nfiles * sizeof(tar_file)); |
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49 |
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50 hf = HashFileCreate(0, HASH_DYNAMIC_SIZE); |
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51 |
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52 /* process command line arguments of the form -arg */ |
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53 for (argc--, argv++; argc > 0; argc--, argv++) { |
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54 if (**argv != '-' || strcmp(*argv, "--") == 0) |
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55 break; |
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56 |
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57 if (strcmp(*argv, "-a") == 0 && argc > 1) { |
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58 archive = argv[1]; |
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59 argv++; |
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60 argc--; |
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61 } |
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62 |
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63 if (strcmp(*argv, "-A") == 0) |
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64 append_mode = 1; |
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65 |
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66 if (strcmp(*argv, "-O") == 0) |
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67 prepend_mode = 1; |
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68 |
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69 if (strcmp(*argv, "-d") == 0) |
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70 directories = 1; |
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71 |
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72 if (strcmp(*argv, "-v") == 0) |
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73 verbose = 1; |
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74 |
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75 if (strcmp(*argv, "-b") == 0) |
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76 basename = 1; |
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77 |
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78 if (strcmp(*argv, "-h") == 0 && argc > 1) { |
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79 /* Common header */ |
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80 hf->headers = (HashFileSection *) |
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81 realloc(hf->headers, (hf->nheaders+1) * |
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82 sizeof(HashFileSection)); |
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83 header = argv[1]; |
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84 hf->nheaders++; |
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85 argv++; |
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86 argc--; |
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87 } |
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88 |
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89 if (strcmp(*argv, "-f") == 0 && argc > 1) { |
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90 /* Common footer */ |
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91 hf->footers = (HashFileSection *) |
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92 realloc(hf->footers, (hf->nfooters+1) * |
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93 sizeof(HashFileSection)); |
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94 footer = argv[1]; |
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95 hf->nfooters++; |
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96 argv++; |
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97 argc--; |
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98 } |
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99 } |
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100 |
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101 if (argc != 1 && !archive) { |
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102 fprintf(stderr, "Usage: hash_tar [options] [tarfile] > tarfile.hash\n"); |
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103 fprintf(stderr, " -a fname Tar archive filename: use if reading from stdin\n"); |
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104 fprintf(stderr, " -A Force no archive name (eg will concat to archive itself)\n"); |
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105 fprintf(stderr, " -O Set arc. offset to size of hash (use when prepending)\n"); |
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106 fprintf(stderr, " -v Verbose mode\n"); |
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107 fprintf(stderr, " -d Index directory names (useless?)\n"); |
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108 fprintf(stderr, " -h name Set tar entry 'name' to be a file header\n"); |
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109 fprintf(stderr, " -f name Set tar entry 'name' to be a file footer\n"); |
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110 fprintf(stderr, " -b Use only the filename portion of a pathname\n"); |
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111 return 1; |
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112 } |
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113 |
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114 /* open the tarfile */ |
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115 if (argc >= 1) { |
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116 archive = argv[0]; |
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117 if (NULL == (fp = fopen(archive, "rb"))) { |
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118 perror(archive); |
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119 return 1; |
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120 } |
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121 } else { |
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122 fp = stdin; |
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123 if (!archive) { |
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124 fprintf(stderr, "If reading from stdin you must use the " |
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125 "\"-a archivename\" option\n"); |
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126 return 1; |
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127 } |
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128 } |
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129 |
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130 /* Fill out the files[] array with the offsets, size and names */ |
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131 while(fread(&blk, sizeof(blk), 1, fp) == 1) { |
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132 /* |
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133 * If a directory is too large to fit in the name (>100) but short |
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134 * enough to fit in the prefix the name field will be empty, this is |
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135 * not the cas for ordinary files where the name field is always |
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136 * non-empty |
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137 */ |
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138 if (!blk.header.name[0] && !blk.header.prefix[0]) |
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139 break; |
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140 |
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141 /* get size of member, rounded to a multiple of TBLOCK */ |
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142 size = strtoul(blk.header.size, NULL, 8); |
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143 extra = TBLOCK*((size+TBLOCK-1)/TBLOCK) - size; |
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144 |
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145 /* skip directories unless requested */ |
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146 if (directories || blk.header.typeflag != DIRTYPE) { |
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147 |
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148 /* |
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149 * extract member name (prefix + name), unless last member |
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150 * was ././@LongLink |
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151 */ |
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152 if (LongLink == 0) { |
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153 (void) strncpy(member, blk.header.prefix, 155); |
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154 if (strlen(blk.header.prefix) > 0 && blk.header.name[0]) |
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155 (void) strcat(member, "/"); |
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156 (void) strncat(member, blk.header.name, 100); |
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157 } |
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158 |
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159 /* account for gtar ././@LongLink */ |
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160 if (strcmp(member, "././@LongLink") == 0) { |
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161 /* still expect filenames to fit into 256 bytes */ |
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162 if (size > 256) { |
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163 fread(member, 1, size > 256 ? 256 : size, fp); |
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164 fprintf(stderr,"././@LongLink too long size=%ld\n", |
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165 (long)size); |
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166 fprintf(stderr,"%s...\n", member); |
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167 exit(1); |
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168 } |
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169 /* |
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170 * extract full name of next member then rewind to start |
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171 * of header |
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172 */ |
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173 fread(member, 1, size > 256 ? 256 : size, fp); |
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174 fseek(fp, -size, SEEK_CUR); |
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175 LongLink = 1; |
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176 } else { |
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177 /* output offset, member name */ |
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178 /* printf("%lu %.256s\n", (long)offset, member); */ |
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179 LongLink = 0; |
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180 |
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181 if (fileno >= nfiles) { |
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182 nfiles *= 2; |
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183 files = (tar_file *)realloc(files,nfiles*sizeof(tar_file)); |
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184 } |
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185 if (basename) { |
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186 char *cp = strrchr(member, '/'); |
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187 strcpy(files[fileno].member, cp ? cp+1 : member); |
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188 } else { |
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189 strcpy(files[fileno].member, member); |
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190 } |
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191 files[fileno].pos = offset+sizeof(blk); |
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192 files[fileno].size = size; |
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193 if (verbose) |
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194 fprintf(stderr, "File %d: pos %010ld+%06d: %s\n", |
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195 fileno, |
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196 (long)files[fileno].pos, |
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197 files[fileno].size, |
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198 files[fileno].member); |
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199 |
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200 fileno++; |
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201 } |
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202 } |
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203 |
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204 /* increment offset */ |
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205 size += extra; |
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206 seek_forward(fp, size); |
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207 offset += sizeof(blk) + size; |
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208 } |
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209 |
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210 /* |
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211 * Find the header/footer if specified. For now we only support one of |
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212 * each. |
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213 */ |
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214 found_header = found_footer = 0; |
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215 for (i = 0; i < fileno; i++) { |
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216 if (header && strncmp(header, files[i].member, 256) == 0) { |
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217 hf->headers[0].pos = files[i].pos; |
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218 hf->headers[0].size = files[i].size; |
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219 hf->headers[0].cached_data = NULL; |
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220 found_header++; |
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221 } |
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222 if (footer && strncmp(footer, files[i].member, 256) == 0) { |
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223 hf->footers[0].pos = files[i].pos; |
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224 hf->footers[0].size = files[i].size; |
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225 hf->footers[0].cached_data = NULL; |
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226 found_footer++; |
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227 } |
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228 } |
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229 if (header && !found_header) { |
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230 fprintf(stderr, "Warning: could not find header '%s' in file\n", |
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231 header); |
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232 hf->nheaders = 0; |
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233 } |
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234 if (footer && !found_footer) { |
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235 fprintf(stderr, "Warning: could not find footer '%s' in file\n", |
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236 footer); |
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237 hf->nfooters = 0; |
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238 } |
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239 |
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240 /* |
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241 * Construct the hash |
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242 */ |
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243 for (i = 0; i < fileno; i++) { |
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244 HashData hd; |
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245 HashFileItem *hfi = (HashFileItem *)calloc(1, sizeof(*hfi)); |
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246 |
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247 /* Just use the last head/foot defined as we only allow 1 at the mo. */ |
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248 hfi->header = hf->nheaders; |
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249 hfi->footer = hf->nfooters; |
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250 hfi->pos = files[i].pos; |
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251 hfi->size = files[i].size; |
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252 hd.p = hfi; |
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253 HashTableAdd(hf->h, files[i].member, strlen(files[i].member), |
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254 hd, NULL); |
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255 } |
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256 |
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257 fclose(fp); |
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258 |
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259 HashTableStats(hf->h, stderr); |
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260 if (!append_mode) |
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261 hf->archive = strdup(archive); |
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262 |
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263 #ifdef _WIN32 |
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264 _setmode(_fileno(stdout), _O_BINARY); |
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265 #endif |
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266 HashFileSave(hf, stdout, prepend_mode ? HASHFILE_PREPEND : 0); |
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267 HashFileDestroy(hf); |
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268 |
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269 free(files); |
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270 |
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271 return 0; |
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272 } |