44ccfacbe3a3d4b300f80d48651c77837a4b571e galt Tue Apr 26 11:12:02 2022 -0700 SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix. diff --git src/hg/protein/omimParseRec/omimParseRec.c src/hg/protein/omimParseRec/omimParseRec.c index 439abe3..03ff7b5 100644 --- src/hg/protein/omimParseRec/omimParseRec.c +++ src/hg/protein/omimParseRec/omimParseRec.c @@ -1,290 +1,290 @@ /* omimParseRec - parse text of OMIM records by different field types */ /* Copyright (C) 2011 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "localmem.h" #include "dystring.h" #include "portable.h" #include "obscure.h" FILE *fh2; /* 2nd file handle pointing to the OMIM text file */ FILE *recFh; FILE *fieldFh; void usage() /* Explain usage and exit. */ { errAbort( "omimParseRec - parse OMIM records by different field types\n" "usage:\n" " omimParseRec omimText outRecFile outFieldFile\n" ); } static struct optionSpec options[] = { {NULL, 0}, }; struct omimRecord /* An OMIM record. */ { char *id; /* OMIM ID */ char type; /* OMIM type */ char *title; /* OMIM title */ char *geneSymbol; /* gene symbol */ int startPos; int endPos; char *av; char *cd; char *cn; char *cs; char *ed; char *rf; char *sa; char *tx; }; struct omimField /* An OMIM field. */ { char *omimId; /* OMIM ID */ char *type; /* field type */ char *title; /* field title */ int startPos; int endPos; }; struct omimLitRef /* A OMIM literature reference. */ { struct omimLitRef *next; char *title; /* Title of article. */ char *cite; /* Journal/book/patent citation. */ struct slName *authorList; /* Author names in lastName, F.M. format. */ char *rp; /* Somewhat complex 'Reference Position' line. */ struct hashEl *rxList; /* Cross-references. */ struct hashEl *rcList; /* TISSUE=XXX X; STRAIN=YYY; parsed out. */ char *pubMedId; /* pubMed ID, may be NULL. */ char *medlineId; /* Medline ID, may be NULL. */ char *doiId; /* DOI ID, may be NULL. */ }; char buffer[80*10000]; void printField(struct omimField *omimFd, FILE *outf) /* print out field info */ { long bytesRead; fprintf(outf, "%s\t%s\t%d\t%d\n", omimFd->omimId, omimFd->type, omimFd->startPos, omimFd->endPos - omimFd->startPos + 1); fflush(stdout); if (((omimFd->endPos - omimFd->startPos + 1) + 1) >sizeof(buffer)) { fprintf(stderr, "field %s for OMIM record %s needs %d bytes, which exceeded buffer size of %d\n", omimFd->type, omimFd->omimId, (omimFd->endPos - omimFd->startPos + 1) + 1, (int)sizeof(buffer)); exit(1); } fseek(fh2, (long)(omimFd->startPos), SEEK_SET); bytesRead = (long)fread(buffer, (size_t)1, (size_t)(omimFd->endPos - omimFd->startPos + 1), fh2); *(buffer+bytesRead) = '\0'; } struct omimRecord *omimRecordNext(struct lineFile *lf, struct lm *lm, /* Local memory pool for this structure. */ struct dyString *dy, /* Scratch string to use. */ FILE *recFh, FILE *fieldFh) /* Read next record from file and parse it into omimRecord structure * that is allocated in memory. */ { char *line; struct omimRecord *omimr; char *chp; int lineSize; char *fieldType; boolean recDone, fieldDone; char *row[1]; boolean endOfFile = FALSE; boolean endOfRec = FALSE; boolean firstFieldDone = FALSE; struct omimField *omimFd = NULL; recDone = FALSE; /* Parse record number and title lines. */ if (!lineFileRow(lf, row)) return NULL; if (!sameString(row[0], "*RECORD*")) { errAbort("Expecting *RECORD* line %d of %s", lf->lineIx, lf->fileName); } lmAllocVar(lm, omimr); omimr->startPos = lf->lineStart + lf->bufOffsetInFile; if (!lineFileNext(lf, &line, &lineSize)) return NULL; if (!sameString(line, "*FIELD* NO")) errAbort("Expecting *FIELD* NO line %d of %s", lf->lineIx, lf->fileName); if (!lineFileNextReal(lf, &line)) errAbort("%s ends in middle of a record", lf->fileName); omimr->id = lmCloneString(lm, line); if (!lineFileNextReal(lf, &line)) errAbort("%s ends in middle of a record", lf->fileName); if (!sameString(line, "*FIELD* TI")) errAbort("Expecting *FIELD* TI line %d of %s ---%s---", lf->lineIx, lf->fileName, line); if (!lineFileNext(lf, &line, &lineSize)) errAbort("%s ends in middle of a record", lf->fileName); if (!isdigit(*line)) { omimr->type = *line; } else { omimr->type = '\0'; } /* some records may not have gene symbol */ omimr->geneSymbol = ""; chp = strstr(line, ";"); if (chp != NULL) { *chp = '\0'; chp++; if (*chp == ' ') chp++; if (*chp != '\0') omimr->geneSymbol = cloneString(chp); } chp = strstr(line, omimr->id); if (chp == NULL) { errAbort("Expecting TI line for record %s, %d of %s ---%s===", omimr->id, lf->lineIx, lf->fileName, line); } chp = chp + strlen(omimr->id); chp++; omimr->title = lmCloneString(lm, chp); // !!! need to enhance it later to include startPos and length info. fprintf(recFh, "%s\t%c\t%s\t%s\n", omimr->id, omimr->type, omimr->geneSymbol, omimr->title); /* !!! temporarily skip lines before first FIELD after title */ /* further processing TBD */ while (strstr(line, "*FIELD*") == NULL) { lineFileNext(lf, &line, &lineSize); } lineFileReuse(lf); /* process a field */ firstFieldDone = FALSE; fieldDone = FALSE; while (!recDone) { if (!lineFileNext(lf, &line, &lineSize)) { endOfFile = TRUE; } /* "*THEEND*" signals the end of the OMIM text file */ if (sameWord(line, "*THEEND*")) endOfFile = TRUE; if (!endOfFile && (strstr(line, "*RECORD*") != NULL)) { endOfRec = TRUE; } /* handle termination of record here */ if (endOfFile || endOfRec) { lineFileReuse(lf); recDone = TRUE; if (firstFieldDone) { /* extra minus 1 to get rid of empty line at the end */ omimr ->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; omimFd->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; /* End of record or end of line also means end of a field. Print the field info */ printField(omimFd, fieldFh); } break; } chp = strstr(line, "*FIELD*"); if (chp != NULL) { fieldType = chp + strlen("*FIELD* "); if (!firstFieldDone) { lmAllocVar(lm, omimFd); firstFieldDone = TRUE; /* do not print anything at the first "*FIELD*" line */ } else { /* extra minus 1 to get rid of empty line at the end */ omimFd->endPos = lf->lineStart + lf->bufOffsetInFile - 1 - 1; /* print previous field info */ printField(omimFd, fieldFh); } /* fill in current field info */ omimFd->omimId = cloneString(omimr->id); omimFd->type = cloneString(fieldType); omimFd->startPos = lf->lineEnd + lf->bufOffsetInFile; } } if (endOfFile) return NULL; return omimr; } void omimParseRec(char *omimTextFile, FILE *recFh, FILE *fieldFh) /* omimParseRec - parse OMIM flat text file. */ { struct lineFile *lf = lineFileOpen(omimTextFile, TRUE); struct omimRecord *omimr; -struct dyString *dy = newDyString(4096); +struct dyString *dy = dyStringNew(4096); for (;;) { struct lm *lm = lmInit(8*1024); omimr = omimRecordNext(lf, lm, dy, recFh, fieldFh); if (omimr == NULL) break; lmCleanup(&lm); } dyStringFree(&dy); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); fh2 = mustOpen(argv[1], "r"); recFh = mustOpen(argv[2], "w"); fieldFh = mustOpen(argv[3], "w"); omimParseRec(argv[1], recFh, fieldFh); return 0; }