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/lib/asmEquivalent.c src/hg/lib/asmEquivalent.c index 917694c..64896b4 100644 --- src/hg/lib/asmEquivalent.c +++ src/hg/lib/asmEquivalent.c @@ -1,255 +1,255 @@ /* asmEquivalent.c was originally generated by the autoSql program, which also * generated asmEquivalent.h and asmEquivalent.sql. This module links the database and * the RAM representation of objects. */ #include "common.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "asmEquivalent.h" char *asmEquivalentCommaSepFieldNames = "source,destination,sourceAuthority,destinationAuthority,matchCount,sourceCount,destinationCount"; /* definitions for sourceAuthority column */ static char *values_sourceAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL}; static struct hash *valhash_sourceAuthority = NULL; /* definitions for destinationAuthority column */ static char *values_destinationAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL}; static struct hash *valhash_destinationAuthority = NULL; void asmEquivalentStaticLoad(char **row, struct asmEquivalent *ret) /* Load a row from asmEquivalent table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->source = row[0]; ret->destination = row[1]; ret->sourceAuthority = sqlEnumParse(row[2], values_sourceAuthority, &valhash_sourceAuthority); ret->destinationAuthority = sqlEnumParse(row[3], values_destinationAuthority, &valhash_destinationAuthority); ret->matchCount = sqlLongLong(row[4]); ret->sourceCount = sqlLongLong(row[5]); ret->destinationCount = sqlLongLong(row[6]); } struct asmEquivalent *asmEquivalentLoadByQuery(struct sqlConnection *conn, char *query) /* Load all asmEquivalent from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with asmEquivalentFreeList(). */ { struct asmEquivalent *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = asmEquivalentLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void asmEquivalentSaveToDb(struct sqlConnection *conn, struct asmEquivalent *el, char *tableName, int updateSize) /* Save asmEquivalent as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ { -struct dyString *update = newDyString(updateSize); +struct dyString *update = dyStringNew(updateSize); sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',(null),(null),%lld,%lld,%lld)", tableName, el->source, el->destination, el->sourceAuthority, el->destinationAuthority, el->matchCount, el->sourceCount, el->destinationCount); sqlUpdate(conn, update->string); -freeDyString(&update); +dyStringFree(&update); } struct asmEquivalent *asmEquivalentLoad(char **row) /* Load a asmEquivalent from row fetched with select * from asmEquivalent * from database. Dispose of this with asmEquivalentFree(). */ { struct asmEquivalent *ret; AllocVar(ret); ret->source = cloneString(row[0]); ret->destination = cloneString(row[1]); ret->sourceAuthority = sqlEnumParse(row[2], values_sourceAuthority, &valhash_sourceAuthority); ret->destinationAuthority = sqlEnumParse(row[3], values_destinationAuthority, &valhash_destinationAuthority); ret->matchCount = sqlLongLong(row[4]); ret->sourceCount = sqlLongLong(row[5]); ret->destinationCount = sqlLongLong(row[6]); return ret; } struct asmEquivalent *asmEquivalentLoadAll(char *fileName) /* Load all asmEquivalent from a whitespace-separated file. * Dispose of this with asmEquivalentFreeList(). */ { struct asmEquivalent *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileRow(lf, row)) { el = asmEquivalentLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct asmEquivalent *asmEquivalentLoadAllByChar(char *fileName, char chopper) /* Load all asmEquivalent from a chopper separated file. * Dispose of this with asmEquivalentFreeList(). */ { struct asmEquivalent *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[7]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = asmEquivalentLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct asmEquivalent *asmEquivalentCommaIn(char **pS, struct asmEquivalent *ret) /* Create a asmEquivalent out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new asmEquivalent */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->source = sqlStringComma(&s); ret->destination = sqlStringComma(&s); ret->sourceAuthority = sqlEnumComma(&s, values_sourceAuthority, &valhash_sourceAuthority); ret->destinationAuthority = sqlEnumComma(&s, values_destinationAuthority, &valhash_destinationAuthority); ret->matchCount = sqlLongLongComma(&s); ret->sourceCount = sqlLongLongComma(&s); ret->destinationCount = sqlLongLongComma(&s); *pS = s; return ret; } void asmEquivalentFree(struct asmEquivalent **pEl) /* Free a single dynamically allocated asmEquivalent such as created * with asmEquivalentLoad(). */ { struct asmEquivalent *el; if ((el = *pEl) == NULL) return; freeMem(el->source); freeMem(el->destination); freez(pEl); } void asmEquivalentFreeList(struct asmEquivalent **pList) /* Free a list of dynamically allocated asmEquivalent's */ { struct asmEquivalent *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; asmEquivalentFree(&el); } *pList = NULL; } void asmEquivalentOutput(struct asmEquivalent *el, FILE *f, char sep, char lastSep) /* Print out asmEquivalent. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->source); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->destination); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); sqlEnumPrint(f, el->sourceAuthority, values_sourceAuthority); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); sqlEnumPrint(f, el->destinationAuthority, values_destinationAuthority); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%lld", el->matchCount); fputc(sep,f); fprintf(f, "%lld", el->sourceCount); fputc(sep,f); fprintf(f, "%lld", el->destinationCount); fputc(lastSep,f); } void asmEquivalentJsonOutput(struct asmEquivalent *el, FILE *f) /* Print out asmEquivalent in JSON format. */ { fputc('{',f); fputc('"',f); fprintf(f,"source"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->source); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"destination"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->destination); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"sourceAuthority"); fputc('"',f); fputc(':',f); fputc('"',f); sqlEnumPrint(f, el->sourceAuthority, values_sourceAuthority); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"destinationAuthority"); fputc('"',f); fputc(':',f); fputc('"',f); sqlEnumPrint(f, el->destinationAuthority, values_destinationAuthority); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"matchCount"); fputc('"',f); fputc(':',f); fprintf(f, "%lld", el->matchCount); fputc(',',f); fputc('"',f); fprintf(f,"sourceCount"); fputc('"',f); fputc(':',f); fprintf(f, "%lld", el->sourceCount); fputc(',',f); fputc('"',f); fprintf(f,"destinationCount"); fputc('"',f); fputc(':',f); fprintf(f, "%lld", el->destinationCount); fputc('}',f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */