4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/visiGene/jackson/mysqlEscape/mysqlEscape.c src/hg/visiGene/jackson/mysqlEscape/mysqlEscape.c index 8f3c296..c611ac4 100644 --- src/hg/visiGene/jackson/mysqlEscape/mysqlEscape.c +++ src/hg/visiGene/jackson/mysqlEscape/mysqlEscape.c @@ -1,254 +1,254 @@ /* mysqlEscape - GALT BARBER 2006-03-31 * Reads data formatted with long string field and line terminators. * it can be used to just parse the data and count the fields and rows, * but it can also be used to do much more, i.e. convert to another set of terminators, * insert \N to mark NULL values for mysql, and escape the other fields generally. * It also serves as a model of how to parse for non-single-character punctuators * capable of operating quickly on large files while using a modest amount of memory * in a rolling overlapped buffer. */ /* Copyright (C) 2007 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "options.h" #include "dystring.h" #include <mysql.h> #define BUFSIZE 32768 boolean noOutput = FALSE; boolean noEscape = FALSE; boolean noNullFix = FALSE; boolean tabSep = FALSE; #define TTERM "<UCSCtabUCSC>" #define NTERM "<UCSCnewlineUCSC>" #define NULLMARK "\\N" /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"noNullFix" , OPTION_BOOLEAN}, {"noEscape" , OPTION_BOOLEAN}, {"noOutput" , OPTION_BOOLEAN}, {"tabSep" , OPTION_BOOLEAN}, {"-help" , OPTION_BOOLEAN}, {NULL, 0} }; static void usage(char *self) /* print usage message and exit */ { errAbort("Purpose:\n\tperform mysql escape on stdin, write to stdout.\n" "Usage:\n\t%s < input > output\n" "options:\n" " -noNullFix suppresses fixing NULLs for MySQL\n" " -noEscape suppresses escaping for MySQL\n" " -noOutput suppresses writing output\n" " -tabSep causes tab and newline to be used instead \n" ,self); } static void putOut(char *buf, int *pi, char *more, int len) /* buffer output to stdout to increase speed, use len==-1 to flush */ { int i = *pi; int bufSize = BUFSIZE*2 + 1; int leftover = len; while(leftover!=0) { len = leftover; if (len > bufSize) { len = bufSize; } if (((bufSize - i) < len) || (len < 0)) { mustWrite(stdout, buf, i); i = 0; } if (len>0) { memcpy(buf+i,more,len); i+=len; } leftover -= len; more += len; } *pi = i; } int main(int argc, char *argv[]) { char *buf=NULL; char *fix=NULL; char *out=NULL; int bi = 0; /* current index 0-based - where span starts */ int bii = 0; /* current index 0-based - where span ends */ int bn = -1; /* next newline token */ int bt = -1; /* next tab token */ int be = 0; /* end of data 0-based */ int nread = -1; int fieldCount = 0; int rowCount = 1; int lastFC = -1; char *match = NULL; int ns = strlen(NTERM); int ts = strlen(TTERM); int is = 0; int blimit = 0; int overlap = max(strlen(TTERM),strlen(NTERM)) - 1; int oi = 0; struct dyString *field = dyStringNew(0); char *tOut = TTERM; // this can be changed to desired character or string char *nOut = NTERM; char *iOut = NULL; optionInit(&argc, argv, optionSpecs); if (argc != 1 || optionExists("-help")) usage(argv[0]); noNullFix = optionExists("noNullFix"); noEscape = optionExists("noEscape"); noOutput = optionExists("noOutput"); tabSep = optionExists("tabSep"); if ((tabSep && noOutput) || (tabSep && noEscape)) errAbort("-tabSep should not be used with -noOutput or -noEscape"); if (tabSep) { tOut = "\t"; nOut = "\n"; } buf=needMem(BUFSIZE); out=needMem(BUFSIZE*2+1); dyStringClear(field); while (nread != 0) { //verbose(2,"reading more be=%d\n",be); while (be < BUFSIZE && (nread = fread(buf+be, 1, BUFSIZE-be, stdin))>0) { be += nread; //verbose(2,"read %d bytes, be=%d\n",nread,be); } if (nread < 0) errAbort("Error reading %lld bytes: %s", (long long)BUFSIZE, strerror(ferror(stdin))); blimit = be; if (be == BUFSIZE) blimit = BUFSIZE - overlap; bn = -1; bt = -1; while (bi < blimit) { if (bn < 0) { match = memMatch(NTERM, ns, buf+bi, be-bi); if (match) bn = match - buf; else bn = BUFSIZE; } if (bt < 0) { match = memMatch(TTERM, ts, buf+bi, be-bi); if (match) bt = match - buf; else bt = BUFSIZE; } if (bt < bn) /* tab field separator is next */ { bii = bt; bt = -1; is = ts; iOut = tOut; ++fieldCount; } else if (bn < bt) /* newline is next */ { bii = bn; bn = -1; is = ns; iOut = nOut; ++fieldCount; if (lastFC == -1) lastFC = fieldCount; if (lastFC != fieldCount) verbose(1,"expected %d fields, found %d in row %d\n", lastFC, fieldCount, rowCount); fieldCount = 0; ++rowCount; } else /* just a fragment continuing */ { bii = blimit; is = 0; } dyStringAppendN(field, buf+bi, bii - bi); if (is > 0) /* we have a complete tag and output desired */ { if (field->stringSize==0) { if (!noNullFix) dyStringAppend(field, NULLMARK); /* mark as NULL for mysql, when field is empty */ } else { if (!noEscape) { /* Don't call the function in jksql.c because it assumes it is a string * i.e. that has a terminating 0, * whereas in theory the input data itself could contain a nul. */ fix=needMem(field->stringSize*2+1); mysql_escape_string(fix, field->string, field->stringSize); dyStringClear(field); dyStringAppendN(field, fix, strlen(fix)); freez(&fix); if (strchr(field->string, '\t')) /* have to escape tabs separately */ { fix=replaceChars(field->string, "\t", "\\t"); dyStringClear(field); dyStringAppendN(field, fix, strlen(fix)); freez(&fix); } } } if (!noOutput) { putOut(out, &oi, field->string, field->stringSize); /* field value */ putOut(out, &oi, iOut, strlen(iOut)); /* field separator */ } dyStringClear(field); } bii += is; /* skip over input separator */ bi = bii; /* this becomes last */ } memcpy(buf,buf+bi,be-bi); /* scroll remainder overlap */ be -= bi; bi = 0; } /* any residual field value - actually it's probably some unescaped garbage, do not output. putOut(out, &oi, field->string, field->stringSize); */ /* flush to stdout */ putOut(out, &oi, NULL, -1); verbose(1,"#fields=%d (fieldCount var=%d), #rows=%d\n", lastFC, fieldCount, rowCount-1); return 0; }