rc_t CC Usage (::Args const* args)
{
rc_t rc = 0;
const char* progname = UsageDefaultName;
const char* fullpath = UsageDefaultName;
if (args == NULL)
rc = RC(rcExe, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram(args, &fullpath, &progname);
UsageSummary (progname);
printf("Parameters:\n");
HelpParamLine ("src-db-path", param_usage_src);
HelpParamLine ("new-cache-db-path", param_usage_dst);
printf ("\nOptions:\n");
HelpOptionLine (AlignCache::ALIAS_ID_SPREAD_THRESHOLD, AlignCache::OPTION_ID_SPREAD_THRESHOLD, "value", AlignCache::USAGE_ID_SPREAD_THRESHOLD);
HelpOptionLine (NULL, AlignCache::OPTION_CURSOR_CACHE_SIZE, "value in MB", AlignCache::USAGE_CURSOR_CACHE_SIZE);
HelpOptionLine (NULL, AlignCache::OPTION_MIN_CACHE_COUNT, "count", AlignCache::USAGE_MIN_CACHE_COUNT);
XMLLogger_Usage();
printf ("\n");
HelpOptionsStandard ();
HelpVersion (fullpath, KAppVersion());
return rc;
}
rc_t CC Usage (const Args * args)
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
rc_t rc;
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
UsageSummary (progname);
KOutMsg ("Parameters:\n");
HelpParamLine ("source-file-path", first_usage);
HelpParamLine ("extract-path", second_usage);
KOutMsg ("Options:\n");
HelpOptionLine (ALIAS_XML, OPTION_XML, "XML-file", xml_usage);
HelpOptionLine (ALIAS_DIR, OPTION_DIR, "directoy-path", dir_usage);
HelpOptionLine (ALIAS_FORCE, OPTION_FORCE, NULL, force_usage);
HelpOptionsStandard ();
/* 1 2 3 4 5 6 7 8 */
/* 12345678901234567890123456789012345678901234567890123456789012345678901234567890 */
HelpVersion (fullpath, KAppVersion());
return rc;
}
rc_t CC Usage(const Args* args) {
rc_t rc = 0 ;
const char* progname = UsageDefaultName;
const char* fullpath = UsageDefaultName;
if (args == NULL)
{ rc = RC(rcExe, rcArgv, rcAccessing, rcSelf, rcNull); }
else
{ rc = ArgsProgram(args, &fullpath, &progname); }
UsageSummary(progname);
KOutMsg("Parameters:\n");
HelpParamLine ("db-path", param_usage);
KOutMsg ("\nOptions:\n");
HelpOptionLine (ALIAS_ALL, OPTION_ALL, NULL, USAGE_ALL);
HelpOptionLine (ALIAS_REF, OPTION_REF, NULL, USAGE_REF);
HelpOptionLine (ALIAS_BAM, OPTION_BAM, NULL, USAGE_BAM);
HelpOptionLine (ALIAS_QUA, OPTION_QUA, NULL, USAGE_QUA);
HelpOptionsStandard ();
HelpVersion (fullpath, KAppVersion());
return rc;
}
rc_t CC Usage (const Args * args)
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
char const *const file_crypt = de[0] == 'd'
? "file to decrypt"
: "file to encrypt";
char const *const dir_crypt = de[0] == 'd'
? "directory to decrypt"
: "directory to encrypt";
const char * const pline[] = {
file_crypt, NULL,
"name of resulting file", NULL,
"directory of resulting file", NULL,
dir_crypt, NULL
};
rc_t rc, orc;
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
orc = UsageSummary (progname);
if (rc == 0)
rc = orc;
KOutMsg ("Parameters:\n");
HelpParamLine ("source-file" , pline);
HelpParamLine ("destination-file" , pline + 2);
HelpParamLine ("destination-directory", pline + 4);
HelpParamLine ("directory" , pline + 6);
KOutMsg ("\nOptions:\n");
HelpOptionLine (ALIAS_FORCE, OPTION_FORCE, NULL, ForceUsage);
CryptOptionLines ();
HelpOptionsStandard ();
/* forcing editor alignment */
/* 12345678901234567890123456789012345678901234567890123456789012345678901234567890*/
KOutMsg (
"\n"
"Details:\n"
" All %scryptions are non-destructive until successful. No files are deleted or\n"
" replaced until the %scryptions are complete.\n"
"\n", de, de);
KOutMsg (
" The extension '.ncbi_enc' will be %s when a file is %scrypted.\n"
"\n", Decrypting ? "removed" : "added", de);
if (Decrypting) KOutMsg (
" NCBI Archive files that contain NCBI database objects will not be decrypted\n"
" unless the %s option is used. As these objects can be used without\n"
" decryption it is recommended they remain encrypted.\n"
"\n", OPTION_SRA);
else KOutMsg (
" NCBI Archive files that contain NCBI database objects will not have the\n"
" .ncbi_enc extension added.\n\n");
KOutMsg (
" If the only parameter is a file name then it will be replaced by a file that\n"
" is %scrypted with a possible changed extension.\n"
" \n", de);
KOutMsg (
" If the only parameter is a directory, all files in that directory including\n"
" all files in subdirectories will be replaced with a possible change\n"
" in the extension.\n"
"\n");
KOutMsg (
" If there are two parameters a copy is made but the copy will be %scrypted.\n"
" If the second parameter is a directory the new file might have a different\n"
" extension. If it is not a directory, the extension will be as given in the\n"
" the parameter.\n"
"\n", de);
KOutMsg (
" Missing directories in the destination path will be created.\n"
"\n");
KOutMsg (
" Already existing destination files will cause the program to end with\n"
" an error and will be left unchanged unless the --%s option is used to\n"
" force the files to be overwritten.\n"
"\n", OPTION_FORCE);
KOutMsg (
"Encryption key (file password):\n"
" The encryption key or file password is handled by configuration. If not yet\n"
" set, this program will fail.\n\n"
" You can set the encryption key by running:\n\n"
" perl configuration-assistant.perl\n"
"\n");
HelpVersion (fullpath, KAppVersion());
return rc;
}
rc_t CC Usage (const Args * args)
{
const char * progname = UsageDefaultName;
const char * fullpath = UsageDefaultName;
rc_t rc;
if (args == NULL)
rc = RC (rcApp, rcArgv, rcAccessing, rcSelf, rcNull);
else
rc = ArgsProgram (args, &fullpath, &progname);
UsageSummary (progname);
KOutMsg ("Parameters:\n");
HelpParamLine ("source-file-path", first_usage);
HelpParamLine ("destination-file-path", second_usage);
KOutMsg ("\nOptions:\n");
HelpOptionLine (ALIAS_FORCE, OPTION_FORCE, NULL, force_usage);
HelpOptionsStandard ();
OUTMSG (("\n"
"ncbi-file uri syntax:\n"
" 'ncbi-file' uris are based on a combination of the standard\n"
" 'file' and 'http' syntax familiar to browser users.\n"
" Enclosing questions marks are probably necessary.\n"
"\n"
" URI syntax is 'scheme:'hierarchical-part'?'query'#'fragment'\n"
" scheme:\n"
" ncbi-file\n"
" hierarchical-part:\n"
" this is the same as for scheme file and can be the native form or\n"));
OUTMSG ((" the ncbi 'posix' format that matches most flavors of Unix.\n"
" Environment variables and short hands such as '~' are not interpreted.\n"
" query:\n"
" Zero or two symbols separated by the '&'. The whole query can be omitted.\n"
" enc or encrypt\n"
" pwfile='path to a file containing a password'\n"
" pwfd='file descriptor where the password can be read'\n"
" If the encrypt is present exactly one of the other two must be present.\n"
" fragment:\n"
" No fragment is permitted.\n"));
OUTMSG (("\n"
"password contents:\n"
" The file or file descriptor containing the password is read enough to satisfy\n"
" the following restriction. The password is terminated by the end of file,\n"
" a carriage return or a line feed. The length must be no more than 4096 bytes.\n"
" The password file should have limited read access to protect it.\n"));
OUTMSG (("\n"
"Use examples:"
"\n"
" To encrypt a create a file named 'example' with a password from a file\n"
" named 'password-file' to a file named 'example.nenc' all in the current\n"
" directory:\n"
"\n"
" $ %s example \"ncbi-file:example.nenc?encrypt&pwfile=password-file\"\n",
progname));
OUTMSG (("\n"
" To decrypt a file named 'example.nenc' with a password from a file\n"
" named 'password-file' to a file named 'example' in directories implied\n"
" in the command:\n"
"\n"
" $ %s \"ncbi-file:/home/user/downloads/example.nenc?encrypt&pwfile=/home/user/password-file\" example\n",
progname));
OUTMSG (("\n"
" To change the encryption of a file from one password to another:\n"
"\n"
" $ %s \"ncbi-file:/home/user/downloads/example.nenc?encrypt&pwfile=old-password-file\" \\\n"
" \"ncbi-file:example.nenc?encrypt&pwfile=/home/user/new-password-file\"\n",
progname));
HelpVersion (fullpath, KAppVersion());
return rc;
}