_EXPORT void
extract_address(BString &address)
{
const char *string = address.String();
int32 first;
// first, remove all quoted text
if ((first = address.FindFirst('"')) >= 0) {
int32 last = first + 1;
while (string[last] && string[last] != '"')
last++;
if (string[last] == '"')
address.Remove(first, last + 1 - first);
}
// try to extract the address now
if ((first = address.FindFirst('<')) >= 0) {
// the world likes us and we can just get the address the easy way...
int32 last = address.FindFirst('>');
if (last >= 0) {
address.Truncate(last);
address.Remove(0, first + 1);
return;
}
}
// then, see if there is anything in parenthesis to throw away
if ((first = address.FindFirst('(')) >= 0) {
int32 last = first + 1;
while (string[last] && string[last] != ')')
last++;
if (string[last] == ')')
address.Remove(first, last + 1 - first);
}
// now, there shouldn't be much else left
trim_white_space(address);
}
_EXPORT void
get_address_list(BList &list, const char *string, void (*cleanupFunc)(BString &))
{
if (string == NULL || !string[0])
return;
const char *start = string;
while (true) {
if (string[0] == '"') {
const char *quoteEnd = ++string;
while (quoteEnd[0] && quoteEnd[0] != '"')
quoteEnd++;
if (!quoteEnd[0]) // string exceeds line!
quoteEnd = string;
string = quoteEnd + 1;
}
if (string[0] == ',' || string[0] == '\0') {
BString address(start, string - start);
trim_white_space(address);
if (cleanupFunc)
cleanupFunc(address);
list.AddItem(strdup(address.String()));
start = string + 1;
}
if (!string[0])
break;
string++;
}
}
_EXPORT void SubjectToThread (BString &string)
{
// a regex that matches a non-ASCII UTF8 character:
#define U8C \
"[\302-\337][\200-\277]" \
"|\340[\302-\337][\200-\277]" \
"|[\341-\357][\200-\277][\200-\277]" \
"|\360[\220-\277][\200-\277][\200-\277]" \
"|[\361-\367][\200-\277][\200-\277][\200-\277]" \
"|\370[\210-\277][\200-\277][\200-\277][\200-\277]" \
"|[\371-\373][\200-\277][\200-\277][\200-\277][\200-\277]" \
"|\374[\204-\277][\200-\277][\200-\277][\200-\277][\200-\277]" \
"|\375[\200-\277][\200-\277][\200-\277][\200-\277][\200-\277]"
#define PATTERN \
"^ +" \
"|^(\\[[^]]*\\])(\\<| +| *(\\<(\\w|" U8C "){2,3} *(\\[[^\\]]*\\])? *:)+ *)" \
"|^( +| *(\\<(\\w|" U8C "){2,3} *(\\[[^\\]]*\\])? *:)+ *)" \
"| *\\(fwd\\) *$"
if (gRebuf == NULL && atomic_add(&gLocker,1) == 0)
{
// the idea is to compile the regexp once to speed up testing
for (int i=0; i<256; ++i) gTranslation[i]=i;
for (int i='a'; i<='z'; ++i) gTranslation[i]=toupper(i);
gRe.translate = gTranslation;
gRe.regs_allocated = REGS_FIXED;
re_syntax_options = RE_SYNTAX_POSIX_EXTENDED;
const char *pattern = PATTERN;
// count subexpressions in PATTERN
for (unsigned int i=0; pattern[i] != 0; ++i)
{
if (pattern[i] == '\\')
++i;
else if (pattern[i] == '(')
++gNsub;
}
const char *err = re_compile_pattern(pattern,strlen(pattern),&gRe);
if (err == NULL)
gRebuf = &gRe;
else
fprintf(stderr, "Failed to compile the regex: %s\n", err);
}
else
{
int32 tries = 200;
while (gRebuf == NULL && tries-- > 0)
snooze(10000);
}
if (gRebuf)
{
struct re_registers regs;
// can't be static if this function is to be thread-safe
regs.num_regs = gNsub;
regs.start = (regoff_t*)malloc(gNsub*sizeof(regoff_t));
regs.end = (regoff_t*)malloc(gNsub*sizeof(regoff_t));
for (int start=0;
(start=re_search(gRebuf, string.String(), string.Length(),
0, string.Length(), ®s)) >= 0;
)
{
//
// we found something
//
// don't delete [bemaildaemon]...
if (start == regs.start[1])
start = regs.start[2];
string.Remove(start,regs.end[0]-start);
if (start) string.Insert(' ',1,start);
}
free(regs.start);
free(regs.end);
}
// Finally remove leading and trailing space. Some software, like
// tm-edit 1.8, appends a space to the subject, which would break
// threading if we left it in.
trim_white_space(string);
}
_EXPORT void
extract_address_name(BString &header)
{
BString name;
const char *start = header.String();
const char *stop = start + strlen (start);
// Find a string S in the header (email foo) that matches:
// Old style name in brackets: [email protected] (S)
// New style quotes: "S" <*****@*****.**>
// New style no quotes if nothing else found: S <*****@*****.**>
// If nothing else found then use the whole thing: S
for (int i = 0; i <= 3; i++) {
// Set p1 to the first letter in the name and p2 to just past the last
// letter in the name. p2 stays NULL if a name wasn't found in this
// pass.
const char *p1 = NULL, *p2 = NULL;
switch (i) {
case 0: // [email protected] (S)
if ((p1 = strchr(start,'(')) != NULL) {
p1++; // Advance to first letter in the name.
size_t nest = 1; // Handle nested brackets.
for (p2 = p1; p2 < stop; ++p2)
{
if (*p2 == ')')
--nest;
else if (*p2 == '(')
++nest;
if (nest <= 0)
break;
}
if (nest != 0)
p2 = NULL; // False alarm, no terminating bracket.
}
break;
case 1: // "S" <*****@*****.**>
if ((p1 = strchr(start, '\"')) != NULL)
p2 = strchr(++p1, '\"');
break;
case 2: // S <*****@*****.**>
p1 = start;
if (name.Length() == 0)
p2 = strchr(start, '<');
break;
case 3: // S
p1 = start;
if (name.Length() == 0)
p2 = stop;
break;
}
// Remove leading and trailing space-like characters and save the
// result if it is longer than any other likely names found.
if (p2 != NULL) {
while (p1 < p2 && (isspace (*p1)))
++p1;
while (p1 < p2 && (isspace (p2[-1])))
--p2;
int newLength = p2 - p1;
if (name.Length() < newLength)
name.SetTo(p1, newLength);
}
}
int32 lessIndex = name.FindFirst('<');
int32 greaterIndex = name.FindLast('>');
if (lessIndex == 0) {
// Have an address of the form <address> and nothing else, so remove
// the greater and less than signs, if any.
if (greaterIndex > 0)
name.Remove(greaterIndex, 1);
name.Remove(lessIndex, 1);
} else if (lessIndex > 0 && lessIndex < greaterIndex) {
// Yahoo stupidly inserts the e-mail address into the name string, so
// this bit of code fixes: "Joe <*****@*****.**>" <*****@*****.**>
name.Remove(lessIndex, greaterIndex - lessIndex + 1);
}
trim_white_space(name);
header = name;
}
void shell()
{
current_database = -1;
char entrada[1000], nomeBD[TAM_NOME_BANCO];
int resultado = 0, codDB = -1;
nomeBD[0]='\0';
char *current_db_name = strdup(">");//inicializa com nenhum banco conectado
char *start;
start = strdup("dbms-start");//este comando posteriormente como start do banco, no momento ele é automatico
printf("\nWelcome to the DBMS Interface.\nType 'help' '\\h' for help.\n\n");
/**
* ****************************
*
* Comandos do shell
*
* ****************************
*/
using_history ();//função para usar o histórico
read_history (".history_file");
while(1)
{
int nTokens;
strcpy(entrada, readline(current_db_name));
/**
* Adiciona ao histórico
*/
if (entrada[0])
{
char *expansion;
int result;
result = history_expand (entrada, &expansion);
if (result)
fprintf (stderr, "%s", expansion);
if (result < 0 || result == 2)
{
free (expansion);
continue;
}
add_history (expansion);
strncpy (entrada, expansion, sizeof (entrada) - 1);
free (expansion);
write_history (".history_file");//adiciona no histórico
}
char **tokens = tokenize( trim_white_space(remove_newline(entrada)),' ',&nTokens);
/**
* Opção para criar tabela e banco de dados
*/
if (strcmp(strtolower(tokens[0]),"create")==0)
{
if(strcmp(strtolower(tokens[1]),"table")==0)
{
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
createTable(entrada,current_database);
}
else if(strcmp(strtolower(tokens[1]),"database")==0)
{
if (nTokens >= 5)
{
printf("Invalid command. Type help to show de interface usage.\n");
continue;
}
if (strlen(tokens[2]) > TAM_NOME_BANCO )
{
printf("Database name too big.\n");
continue;
}
resultado = checkCreateDB( remove_semicolon(tokens[2]) );//verifica a existência do nome e grava-o no arquivo
if(resultado==-1)
{
printf("Error creating database file.\n");
}
if(resultado==-3)
{
printf("Database exists.\n");
}
else
{
printf("Database created successfully.\n");
}
}
else
{
printf("Invalid command. Type help to show de interface usage.\n");
continue;
}
}
/**
* Conecta ao banco de dados passado como parâmetro
*/
else if(strcmp(strtolower(tokens[0]),"\\c") == 0){
if (nTokens != 2)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
continue;
}
char *name_db = remove_semicolon(tokens[1]);
codDB = busca(name_db,1); //função chamada para conecção no banco, retorna o codigo do banco ao conectar
if (codDB >= 0)
{
strcpy(nomeBD, name_db); //passa o nome do bd, para a variavel mostrar ao usuario qual o banco conectado
free(current_db_name);
current_db_name = (char*) malloc (sizeof(char)*(strlen(name_db)+3));
if (current_db_name == NULL)
{
printf("Out of memory.\nAborting...\n");
}
strcpy(current_db_name,name_db);
current_database = codDB;
strcat(current_db_name,"=#");
current_db_name[strlen(current_db_name)] = '\0';
}
else
{
printf("No such database '%s'.\n", name_db);
continue;
}
}
/**
* Insere tuplas em uma tabela
*/
else if(strcmp(strtolower(tokens[0]),"insert")==0)
{
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
insert(entrada,current_database);
}
/**
* Imprime as tabelas do banco de dados atual
* ou o esquema de uma tabela
*/
else if(strcmp(strtolower(tokens[0]),"\\d")==0)
{
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
if (nTokens >= 3)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
continue;
}
else if (nTokens == 1)
{
//imprime tabelas do banco de dados
listaTabelas(current_database);
}
else
{
//imprime o esquema de uma tabela
char *t = table_name_real(remove_semicolon(tokens[1]),current_database);
if(!verificaNomeTabela(t)){
printf("Invalid table name.\n");
free(t);
continue;
}
struct fs_objects objeto = leObjeto(t);//para verificar se a tabela esta no banco
show_schema(objeto,tokens[1]);
free(t);
}
}
/**
* Comando temporário para imprimir tabela
*/
else if (strcmp(strtolower(tokens[0]),"select")==0)
{
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
selectTable(entrada,current_database);
}
/**
* Imprime os registros da tabela passada
*/
else if (strcmp(strtolower(tokens[0]),"show")==0)
{
if (nTokens != 2)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
continue;
}
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
if (verificaNomeTabela(table_name_real(remove_semicolon(tokens[1]),current_database) ) == 0 )
{
printf("Table %s doesn't exist.\n",remove_semicolon(tokens[1]));
continue;
}
char *t = table_name_real(remove_semicolon(tokens[1]),current_database);
char *file = table_name_real(remove_semicolon(tokens[1]),current_database);
strcat(file,".dat");
if (existeArquivo(file) == 0)
{
printf("Table is empty.\n" );
continue;
}
imprime(t);
free(file);
free(t);
}
/**
* Lista os bancos existentes
*/
else if(strcmp(strtolower(tokens[0]),"\\l")==0)
{
if (nTokens != 1)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
continue;
}
//LISTA os bancos existentes
listaBancos();
}
/**
* Opção para deletar o banco de dados e tabelas
*/
else if(strcmp(strtolower(tokens[0]),"drop")==0)
{
if (nTokens != 3)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
continue;
}
else if(strcmp(strtolower(tokens[1]),"table") == 0){
if (current_database == -1)
{
printf("Not connected to any database.\n");
continue;
}
if (verificaNomeTabela(table_name_real(remove_semicolon(tokens[2]),current_database) ) == 0 )
{
printf("Table %s doesn't exist.\n",remove_semicolon(tokens[2]));
continue;
}
char *t = table_name_real(remove_semicolon(tokens[2]),current_database);
char *exist = table_name_real(remove_semicolon(tokens[2]),current_database);
int ok = excluirTabela(t);
if (ok == SUCCESS)
{
printf("Table deleted successfully.\n");
}
free(exist);
free(t);
}
else if(strcmp(strtolower(tokens[1]),"database") == 0){
char *exist = table_name_real(remove_semicolon(tokens[2]),current_database);
strcat(exist,".dat");
if (existeArquivo(exist) != 0)
{
printf("The database is not empty for drop, there are existing tables.\n" );
continue;
}
exist = remove_semicolon(tokens[2]);
codDB = busca(exist,1);
if(codDB == current_database)
{
printf("Cannot drop the currently open database.\n");
continue;
}
int drop = dropDatabase(remove_semicolon(tokens[2]));
if(drop == 1)printf("Database deleted successfully.\n");
free(exist);
}
}
/**
* Ajuda ao usuário com exemplos da sintaxe dos comandos
*/
else if (strcmp(strtolower(tokens[0]),"help")==0 || strcmp(strtolower(tokens[0]),"\\h")==0)
{
if (nTokens != 1)
{
printf("Invalid number of arguments. Type help to show the interface usage.\n");
}
help();
}
/**
* Imprime mensagem de copyright
*/
else if(strcmp(strtolower(remove_semicolon(tokens[0])),"\\copyright")==0)
{
printf("\nDatabase Management System\n");
printf("\nPermission to use, copy, modify, and distribute this software and its\ndocumentation for any purpose, without fee, and without a written agreement\nis hereby granted, provided that the above copyright notice and this\nparagraph and the following two paragraphs appear in all copies.\n");
printf("\nTHIS SOFTWARE IS BEING DEVELOPED BY STUDENTS OF DATABASE II CLASS AT UNIVERSIDADE FEDERAL DA FRONTEIRA SUL.\n\n");
}
/**
* Comando de saída
*/
else if(strcmp(strtolower(remove_semicolon(tokens[0])),"exit")==0)
{
break;
}
else if(strcmp(strtolower(remove_semicolon(tokens[0])),"quit")==0)
{
break;
}
else if(strcmp(strtolower(remove_semicolon(tokens[0])),"bye")==0)
{
break;
}
else if(strcmp(strtolower(remove_semicolon(tokens[0])),"\\q")==0)
{
break;
}
else
{
printf("Invalid command. Type help to show the interface usage.\n");
continue;
}
}
free(start);
free(current_db_name);
}
Exp_info *exp_read_staden_info(mFILE *fp, char *filename)
/*
* Read a staden file into an Exp_info data structure
*/
{
Exp_info *e;
char *seq;
char *fn;
/* find last / in filename */
for(fn=filename+strlen(filename)-1;fn>filename && *fn!='/';fn--);
if (*fn=='/') fn++;
if ( (e = exp_create_info()) != NULL ) {
char line[128];
/* an upper limit for the file size */
int max_seq_size = file_size(filename);
int left, right, len, i;
int lineno;
int formatIsBap;
int CS_from, CS_to;
int SR;
CS_from = CS_to = SR = 0;
/*ID*/
(void)ArrayRef(e->entries[EFLT_ID],e->Nentries[EFLT_ID]++);
exp_get_entry(e,EFLT_ID) = (char *)strdup(fn);
/*EN*/
(void)ArrayRef(e->entries[EFLT_EN],e->Nentries[EFLT_EN]++);
exp_get_entry(e,EFLT_EN) = (char *)strdup(fn);
/*CC*/
(void)ArrayRef(e->entries[EFLT_CC],e->Nentries[EFLT_CC]++);
exp_get_entry(e,EFLT_CC) = (char *)strdup("Created from a staden format sequence assembly file");
seq = (char *) xmalloc(max_seq_size+1);
if (!seq)
return NULL;
left = 0;
right = 0;
len = 0;
lineno = 0;
formatIsBap = 1;
while (mfgets(line,sizeof(line),fp)!=NULL) {
char *s;
lineno++;
if (lineno == 1) {
int pos, ret;
char *cp;
/*
* This maybe a fasta format file.
*/
if (line[0] == '>') {
if (cp = strchr(line, ' '))
*cp = 0;
if (cp = strchr(line, '\t'))
*cp = 0;
if (cp = strchr(line, '\n'))
*cp = 0;
exp_set_entry(e, EFLT_ID, strdup(line+1));
exp_set_entry(e, EFLT_EN, strdup(line+1));
continue;
}
/*
* This maybe a file created from 'output consensus',
* in which case it'll have the Staden format style of:
* " <-----T2.00047----->" header on the first line.
*
* We strip this off. Argh - why don't Suns have the
* ANSI function memmove() ?
*/
ret = sscanf(line, " <%*18s>%n", &pos);
if (ret && pos == 21) {
int i, e = sizeof(line)-21;
for (i=0; i < e; i++)
line[i] = line[i+21];
/* memmove((void *)line,
* (void *)(line + 21),
* sizeof(line)-21);
*/
}
}
if (line[0] == ';') {
/********************************************
* Title line parsing
*******************************************/
if (lineno==1 &&
!(line[1] == ';' || line[1] == '<' || line[1] == '>')
) {
/* format of line is:
* <ln> ::= ;<i6><i6><i6><c4><c+>
* <i6> ::= <s><s><s><s><s><d> | ... <d><d><d><d><d><d>
* <c4> ::= <C><C><C><s>
* <c+> ::= <a><c+> | <a>
* <a> is [a-zA-Z0-9.]
* <s> is ' '
* <d> is [0-9]
* <C> is [A-Z]
*/
int d;
if (sscanf(line,";%6d%6d%6d",&d,&d,&d)==3 &&
strlen(line)>23) {
/* trim off trailing white space */
trim_white_space(line+23);
/*LN*/
(void)ArrayRef(e->entries[EFLT_LN],e->Nentries[EFLT_LN]++);
exp_get_entry(e,EFLT_LN) = (char *)strdup(line+23); line[23]='\0';
/*LT*/
(void)ArrayRef(e->entries[EFLT_LT],e->Nentries[EFLT_LT]++);
/* trim off trace type white space */
trim_white_space(line+19);
exp_get_entry(e,EFLT_LT) = (char *)strdup(line+19);
}
} else if (formatIsBap) {
switch (line[1]) {
case '<':
for(s=&line[2];*s;s++) {
if(!isspace(*s) && isprint(*s))
seq[left++] = *s;
}
break;
case '>':
for(s=&line[2];*s;s++) {
if(!isspace(*s) && isprint(*s))
seq[max_seq_size-right++] = *s;
}
break;
case ';':
/*TG*/
#if 0
trim_white_space(line);
(void)ArrayRef(e->entries[EFLT_TG],e->Nentries[EFLT_TG]++);
/* convert format from Staden format to
* Experiment file format
*/
{
char *cp;
int pos, len;
char type[5];
cp = (char *)xmalloc(strlen(line)+20);
if (cp == NULL)
break;
sscanf(line, ";;%4s %6d %6d",
type, &pos, &len);
/*
* Need to add 'left' to each start position
* in tag. ASSUMPTION: 'left' has already been
* defined. Ie that the ;< lines are before
* any ;; lines.
*/
pos += left;
values2tag(cp, type, pos, pos + len - 1,
2, &line[20]);
exp_get_entry(e,EFLT_TG) = cp;
}
if (strncmp(line+2,"IGNC",4)==0 ||
strncmp(line+2,"CVEC",4)==0) {
CS_from = atoi(&line[2+4+1]);
} else if (strncmp(line+2,"IGNS",4)== 0 ||
strncmp(line+2,"SVEC",4)== 0) {
SR = 1;
}
#endif
break;
default:
break;
}
}
} else {
/********************************************
* The actual sequence bit
*******************************************/
formatIsBap = 0; /* turn off title line parsing stuff */
for (s=line;*s;s++) {
if(!isspace(*s) && isprint(*s))
seq[left+len++] = *s;
}
}
}
/*
* The right cutoff has been stashed into the end of the array
* Move to correct place
*/
for(i=(max_seq_size-(left+len))/2;i>=0;i--) {
char temp;
/* swap */
temp = seq[left+len+i];
seq[left+len+i] = seq[max_seq_size-i];
seq[max_seq_size-i] = temp;
}
/* null terminate */
seq[left+len+right] = '\0';
/*SQ*/
(void)ArrayRef(e->entries[EFLT_SQ],e->Nentries[EFLT_SQ]++);
exp_get_entry(e,EFLT_SQ) = seq;
/*SL*/
sprintf(line,"%d",left);
(void)ArrayRef(e->entries[EFLT_SL],e->Nentries[EFLT_SL]++);
exp_get_entry(e,EFLT_SL) = (char *)strdup(line);
/*SR*/
if (SR) {
sprintf(line,"%d",left+len+1);
(void)ArrayRef(e->entries[EFLT_SR],e->Nentries[EFLT_SR]++);
exp_get_entry(e,EFLT_SR) = (char *)strdup(line);
}
/*CS*/
if (CS_from) {
if (CS_from == 1) {
CS_to = left;
} else {
CS_from = left + len + 1;
CS_to = left + len + right;
}
sprintf(line,"%d..%d",CS_from,CS_to);
(void)ArrayRef(e->entries[EFLT_CS],e->Nentries[EFLT_CS]++);
exp_get_entry(e,EFLT_CS) = (char *)strdup(line);
}
/*QR*/
if (!SR && !CS_from) {
sprintf(line,"%d",left+len+1);
(void)ArrayRef(e->entries[EFLT_QR],e->Nentries[EFLT_QR]++);
exp_get_entry(e,EFLT_QR) = (char *)strdup(line);
}
#if 0
/*TG*/
{
int i;
/* need to add LEFT to each start position in tag */
for(i=0;i<e->Nentries[EFLT_TG];i++) {
sprintf(line,"%4.4s %6d%s",
arr(char *,e->entries[EFLT_TG],i),
atoi(arr(char *,e->entries[EFLT_TG],i)+5)+left,
arr(char *,e->entries[EFLT_TG],i)+11);
xfree(arr(char *,e->entries[EFLT_TG],i));
arr(char *,e->entries[EFLT_TG],i) = (char *)strdup(line);
}
}
#endif
}
