int parseMultiPart(char *boundary)
{
int bound_len=strlen(boundary), type, startat, finish=false;
char *name=NULL, *ctyp=NULL, *fname=NULL;
MFILE *mf=mfopen();
while((startat=miscFReadLn(stdin, mf))!=-1) {
if(strncmp(boundary, mfGetDataAt(mf, startat), bound_len))
continue;
/* new part found - insert old part and init new one...
* no insert at FIRST header ...
* at end of multipart ??? "--boundary--" line ? */
if(!strncmp("--", mfGetDataAt(mf, mfGetLength(mf)-4), 2))
finish=true;
mfSetLength(mf, startat);
if(name!=NULL) {
/* strip memfile, since one more <cr><lf> or only <lf> at end */
mf->used--;
if(*(char*)((int)mf->data+mf->used-1) == '\r') mf->used--;
if(type==CgiKindFile) {
listAddData(type, name, fname, ctyp, mf);
mf=mfopen();
} else
listAddData(type, name, mfGetData(mf), ctyp, NULL);
}
if(finish==true) return(true);
type=parseMultiHead(&name, &fname, &ctyp);
mfSetLength(mf, 0);
}
mfclose(mf);
free(name);
free(fname);
free(ctyp);
return true;
}
/*
* Read a sequence from a file "fnin" of format "format". If "format" is 0
* (ANY_FORMAT), we automatically determine the correct format.
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *read_reading(char *fn, int format) {
Read *read;
mFILE *fp;
#ifdef USE_BIOLIMS
if( !strncmp(fn,BIOLIMS_TAG,strlen(BIOLIMS_TAG))){
return spReadBiolimsReading(fn);
}
#endif
if (NULL == (fp = open_trace_mfile(fn, NULL))) {
errout("'%s': couldn't open\n", fn);
return NULL;
}
read = mfread_reading(fp, fn, format);
mfclose(fp);
return read;
}
/*!
* Read a sequence from a file "fnin" of format "format". If "format" is 0
* (ANY_FORMAT), we automatically determine the correct format.
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *read_reading(char *fn, int format) {
Read *read;
mFILE *fp;
#ifdef USE_BIOLIMS
if( !strncmp(fn,BIOLIMS_TAG,strlen(BIOLIMS_TAG))){
return spReadBiolimsReading(fn);
}
#endif
/*
* If we're asking for an Experiment file, read it.
* If the format is ANY then attempt EXP first following by trace.
* Otherwise use the trace search mechanism.
*
* Note this is purely for locating files and not for forcing the file
* format. It's here so that experiment files and trace files may be
* given identical names but accessed through different search paths
* (as is the case with the trace server).
*/
if (format == TT_EXP) {
if (NULL == (fp = open_exp_mfile(fn, NULL))) {
errout("'%s': couldn't open\n", fn);
return NULL;
}
} else {
fp = NULL;
if (format == TT_ANY)
fp = open_exp_mfile(fn, NULL);
if (!fp && NULL == (fp = open_trace_mfile(fn, NULL))) {
errout("'%s': couldn't open\n", fn);
return NULL;
}
}
read = mfread_reading(fp, fn, format);
mfclose(fp);
return read;
}
void LoadScriptFile(pzllst *lst,FManNode *filename, bool control, MList *controlst)
{
#ifdef TRACE
printf("Loading script file %s\n",filename->File);
#endif
if (control)
{
Rend_SetRenderer(RENDER_FLAT);
}
mfile *fl=mfopen(filename);
if (fl == NULL)
{
printf("Error opening file %s\n",filename->File);
exit(1);
return;
}
char buf[FILE_LN_BUF];
while(!mfeof(fl))
{
mfgets(buf,FILE_LN_BUF,fl);
char *str=PrepareString(buf);
if (strCMP(str,"puzzle")==0)
{
Parse_Puzzle(lst,fl,str);
}
else if (strCMP(str,"control")==0 && control )
{
Parse_Control(controlst,fl,str);
}
}
mfclose(fl);
}
/*
* Read a sequence from a FILE *fp of format "format". If "format" is 0
* (ANY_FORMAT), we automatically determine the correct format.
* We still pass a filename 'fn' although this isn't used other than for
* filling in the read->trace_name field.
*
* NB this function should NOT be used when Biolims support is required
* (as biolims readings are not stored in a file)
*
* Returns:
* Read * for success
* NULLRead for failure
*/
Read *mfread_reading(mFILE *fp, char *fn, int format) {
Read *read;
mFILE *newfp;
if (!fn)
fn = "(unknown)";
newfp = freopen_compressed(fp, NULL);
if (newfp != fp) {
fp = newfp;
} else {
newfp = NULL;
}
#ifdef _WIN32
/*
* jkb 16/05/00 comment below
*
* On windows "prog < file.abi" will work wrongly (compared to
* "prog file.abi") because windows is rather stupid. It treats ascii
* and binary streams differently, it considers stdin to be ascii unless
* told otherwise, and it can only be told otherwise by using non-ansi
* windows-specific function calls.
*/
if (format != TT_EXP && format != TT_PLN && fp->fp)
_setmode(_fileno(fp->fp), _O_BINARY);
#endif
if (format == TT_ANY) {
format = fdetermine_trace_type(fp);
mrewind(fp);
}
switch (format) {
case TT_UNK:
case TT_ERR:
errout("File '%s' has unknown trace type\n", fn);
read = NULLRead;
break;
#ifdef IOLIB_SCF
case TT_SCF: {
Scf *scf;
scf = mfread_scf(fp);
if (scf) {
read = scf2read(scf);
scf_deallocate(scf);
} else
read = NULLRead;
break;
}
#endif
#ifdef IOLIB_CTF
case TT_CTF:
read = mfread_ctf(fp);
break;
#endif
#ifdef IOLIB_ZTR
case TT_ZTR:
case TT_ZTR1:
case TT_ZTR2:
case TT_ZTR3: {
ztr_t *ztr;
if ((ztr = mfread_ztr(fp))) {
uncompress_ztr(ztr);
read = ztr2read(ztr);
delete_ztr(ztr);
} else {
read = NULLRead;
}
break;
}
#endif
#ifdef IOLIB_ABI
case TT_ABI:
read = mfread_abi(fp);
break;
#endif
#ifdef IOLIB_ALF
case TT_ALF:
read = mfread_alf(fp);
break;
#endif
#ifdef IOLIB_EXP
case TT_EXP: {
/* FIXME: we shouldn't redirect like this */
Exp_info *e = exp_mfread_info(fp);
read = e ? exp2read(e,fn) : NULLRead;
break;
}
#endif
#ifdef IOLIB_PLN
case TT_PLN:
read = mfread_pln(fp);
break;
#endif
default:
errout("Unknown format %d specified to read_reading()\n", format);
read = NULLRead;
}
if (read != NULLRead && (read->trace_name = (char *)xmalloc(strlen(fn)+1)))
strcpy(read->trace_name, fn);
if (newfp) mfclose(newfp);
return read;
}
/* this is REALLY a f**k ... why didnt they put the fname in a own line :( */
int parseMultiHead(char **name, char **fname, char **ctyp)
{
char *endchars;
const char *contt="Content-Type: ", *line;
const char *contd="Content-Disposition: form-data; name=";
int i, ret=0;
MFILE *mf=mfopen(), *mfname=mfopen();
free(*ctyp);
(*ctyp)=strdup("");
/* read till empty line appears - end of header ... */
while((miscFReadLn(stdin, mf)>=0) && (line=mfGetData(mf)) &&
!(line[0]=='\n' || (line[0]!=0 && line[0]=='\r' && line[1]=='\n'))) {
/* make sure, next lines starts at beginn of file again... */
mfSetLength(mf, 0);
/* "Content-Type: what/ever" line */
if(!strncasecmp(line, contt, strlen(contt))) {
free(*ctyp);
(*ctyp)=miscStringDelCrLf((char*)strdup((char*)(line+strlen(contt))));
}
/* "Content-Disposition: form-data; name="whatever"; filename="C:\f**k.txt"" - line */
if(!strncasecmp(line, contd, strlen(contd))) {
i=strlen(contd);
if(line[i]=='"') {
endchars="\"\r\n\0";
i++;
}
else endchars=";\r\n\0";
/* parse name */
while(strchr(endchars, line[i])==NULL)
mfputc(line[i++], mfname);
*name=realloc(*name, mfGetLength(mfname)+1);
strcpy(*name, mfGetData(mfname));
mfSetLength(mfname, 0);
if(line[i]=='\"') i++;
if(line[i]!=';') {
ret=CgiKindValue;
continue;
}
else ret=CgiKindFile;
/* we have a filename= part here - parse filename */
while(line[i]!=0 && line[i]!='=') i++;
i++;
if(line[i]=='\"') {
endchars="\"\r\n\0";
i++;
}
else endchars=";\r\n\0";
while(strchr(endchars, line[i])==NULL)
mfputc(line[i++], mfname);
if(mfGetLength(mfname)>0) {
*fname=realloc(*fname, mfGetLength(mfname)+1);
strcpy(*fname, mfGetData(mfname));
mfSetLength(mfname, 0);
} else {
*fname=realloc(*fname, 16);
(*fname)[0]=0;
}
}
}
mfclose(mf);
mfclose(mfname);
return(ret);
}
int main(int argc, char **argv) {
int format = TT_ANY, r, prec = 0, version = 3, silent = 0;
int compress_mode = -1;
char *inf = NULL;
char *outf = NULL;
mFILE *ofp = mstdout();
int normalise = 0;
for (argc--, argv++; argc > 0; argc--, argv++) {
if (strcmp(*argv, "-8") == 0) {
prec = 1;
} else if (strcmp(*argv, "-2") == 0) {
version = 2;
} else if (strcmp(*argv, "-3") == 0) {
version = 3;
} else if (strcmp(*argv, "-normalise") == 0) {
normalise = 1;
} else if (strcmp(*argv, "-s") == 0) {
silent = 1;
} else if (strcasecmp(*argv, "-abi") == 0) {
format = TT_ABI;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-alf") == 0) {
format = TT_ALF;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-scf") == 0) {
format = TT_SCF;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-ztr") == 0) {
format = TT_ZTR;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-any") == 0) {
format = TT_ANY;
inf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-output") == 0) {
outf = *++argv;
argc--;
} else if (strcasecmp(*argv, "-compress") == 0) {
compress_mode = compress_str2int(*++argv);
argc--;
} else {
break;
}
}
/* if no args left than input file must have been specified */
if (!argc && !inf)
usage();
/* if outfile set, then using original syntax, so don't expect
any extra args */
if (argc && outf)
usage();
if (!silent) {
printf("makeSCF v3.06\n");
printf("Copyright (c) MRC Laboratory of Molecular Biology, 2001. All rights reserved.\n");
}
set_scf_version(version);
if(!argc) {
/* original calling syntax */
if (outf) {
ofp = mfopen(outf, "wb+");
if (NULL == ofp) {
perror(outf);
return 1;
}
}
r = convert(inf, ofp, outf, format, prec, compress_mode, normalise);
mfclose(ofp);
return r;
}
/* else */ {
/* new calling syntax, handling multiple files */
int result=0;
for (; argc > 0; argc--, argv++) {
if (inf) {
/* got infile, so get outfile and process */
outf= *argv;
ofp = mfopen(outf, "wb+");
if (NULL == ofp) {
perror(outf);
if(!result) result=1;
continue;
}
r = convert(inf, ofp, outf, format, prec, compress_mode,
normalise);
mfclose(ofp);
if(!result) /* keep track of the first error */
result=r;
/* now need to get another infile */
inf=NULL;
} else {
/* need infile */
inf= *argv;
}
}
return result;
}
}
int main(void)
{
MEMFILE *file, *file2, *file3;
char test[] = "This is a very long string that just goes on and on, but it can surely tell us a few things about how this code is working.";
char test2[] = "This is the second string, and should get cat'd right up behind the first string.";
char buffer[512];
printf("\n--------- open should fail (file doesn't exist)\n");
file = mfopen( "dummy", "r+b" );
printf("fopen(\"dummy\",\"r+b\") -> 0x%x\n", file );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- open should succeed (truncated on open)\n");
file = mfopen( "dummy", "w+b" );
printf("fopen(\"dummy\",\"w+b\") -> 0x%x\n", file );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("growth increment was %d\n", _mfsetgrowincrement( file, 64 ) );
printf("growth increment is now %d\n", _mfsetgrowincrement( file, 0 ) );
printf("\n--------- should be zero offset, and eof == false\n");
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should write %d bytes\n", strlen(test));
printf( "fwrite( [], %d, %d, file ) -> %d\n", strlen(test), sizeof(char),
mfwrite( test, strlen(test), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should read the string back in\n");
printf( "rewind(file) \n" ); mrewind(file);
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should cat the second string to the first\n");
printf( "fwrite( [], %d, %d, file ) -> %d\n", sizeof(char), strlen(test2),
mfwrite( test2, strlen(test2), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- should read zero (fp is at eof)\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- seek test\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "seek(file,64,0)-> %d\n", mfseek( file, 64, SEEK_SET ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- read after seek test, should read filelen-64 bytes\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "-> \"%s\"\n", buffer );
printf("\n--------- change size test\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf( "ftruncate(fileno(file),10) -> %d\n", mftruncate( mfileno( file ), 10 ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- negative seek test\n");
printf( "fseek(file,-5,2)->%d\n", mfseek( file, -5, SEEK_END ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("\n--------- read after seek test, should read 5 bytes\n");
memset( buffer, 0, sizeof( buffer ));
printf( "fread( [], %d, %d, file ) -> %d\n", sizeof(buffer), sizeof(char),
mfread( buffer, sizeof(buffer), sizeof(char), file ) );
printf( "-> \"%s\"\n", buffer );
printf("\n--------- open and write a second file\n");
file2 = mfopen( "dummy2", "w+b" );
printf("fopen(\"dummy2\",\"w+b\") -> 0x%x\n", file2 );
printf( "fwrite( [], %d, %d, file2 ) -> %d\n", strlen("TEST"), sizeof(char),
mfwrite( "TEST", strlen("TEST"), sizeof(char), file2 ) );
printf( "filelength( fileno( file2 ) )-> %ld\n", mfilelength( mfileno( file2 ) ) );
printf( "ftell(file2) -> %ld feof(file2)-> %d\n", mftell( file2 ), mfeof( file2 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- open and write a third file\n");
file3 = mfopen( "dummy3", "w+b" );
printf("fopen(\"dummy3\",\"w+b\") -> 0x%x\n", file3 );
printf( "fwrite( [], %d, %d, file3 ) -> %d\n", strlen("BLAHBLAH"), sizeof(char),
mfwrite( "BLAHBLAH", strlen("BLAHBLAH"), sizeof(char), file3 ) );
printf( "filelength( fileno( file3 ) )-> %ld\n", mfilelength( mfileno( file3 ) ) );
printf( "ftell(file3) -> %ld feof(file3)-> %d\n", mftell( file3 ), mfeof( file3 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close second\n");
printf( "fclose(file2) -> %d\n", mfclose( file2 ) );
printf( "filelength( fileno( file2 ) )-> %ld\n", mfilelength( mfileno( file2 ) ) );
printf( "ftell(file2) -> %ld feof(file2)-> %d\n", mftell( file2 ), mfeof( file2 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- check first\n");
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- truncate to zero test\n");
printf( "ftruncate(fileno(file),0) -> %d\n", mftruncate( mfileno( file ), 0 ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close first\n");
printf( "fclose(file) -> %d\n", mfclose( file ) );
printf( "filelength( fileno( file ) )-> %ld\n", mfilelength( mfileno( file ) ) );
printf( "ftell(file) -> %ld feof(file)-> %d\n", mftell( file ), mfeof( file ) );
printf("#of open memstreams: %d\n", count_open_streams() );
printf("\n--------- close third\n");
printf( "fclose(file3) -> %d\n", mfclose( file3 ) );
printf( "filelength( fileno( file3 ) )-> %ld\n", mfilelength( mfileno( file3 ) ) );
printf( "ftell(file3) -> %ld feof(file3)-> %d\n", mftell( file3 ), mfeof( file3 ) );
printf("#of open memstreams: %d\n", count_open_streams() );
return 0;
}
int mfcloseall(void)
{
while ( __memstreambase )
mfclose( __memstreambase );
return 0;
}
int main(int argc, char *argv[]){
MFILE* fp = mfopen(argv[1], "a");
mfputs(argv[2], fp);
mfclose(fp);
return 0;
}
