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/gtexInfo.c src/hg/lib/gtexInfo.c index 3067250..e7f7d84 100644 --- src/hg/lib/gtexInfo.c +++ src/hg/lib/gtexInfo.c @@ -1,247 +1,247 @@ /* gtexInfo.c was originally generated by the autoSql program, which also * generated gtexInfo.h and gtexInfo.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 "gtexInfo.h" #include "gtexGeneBed.h" char *gtexInfoCommaSepFieldNames = "version,releaseDate,maxScore,maxMedianScore"; void gtexInfoStaticLoad(char **row, struct gtexInfo *ret) /* Load a row from gtexInfo table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->version = row[0]; ret->releaseDate = row[1]; ret->maxScore = sqlDouble(row[2]); ret->maxMedianScore = sqlDouble(row[3]); } struct gtexInfo *gtexInfoLoadByQuery(struct sqlConnection *conn, char *query) /* Load all gtexInfo 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 gtexInfoFreeList(). */ { struct gtexInfo *list = NULL, *el; struct sqlResult *sr; char **row; sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { el = gtexInfoLoad(row); slAddHead(&list, el); } slReverse(&list); sqlFreeResult(&sr); return list; } void gtexInfoSaveToDb(struct sqlConnection *conn, struct gtexInfo *el, char *tableName, int updateSize) /* Save gtexInfo 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',%g,%g)", tableName, el->version, el->releaseDate, el->maxScore, el->maxMedianScore); sqlUpdate(conn, update->string); -freeDyString(&update); +dyStringFree(&update); } struct gtexInfo *gtexInfoLoad(char **row) /* Load a gtexInfo from row fetched with select * from gtexInfo * from database. Dispose of this with gtexInfoFree(). */ { struct gtexInfo *ret; AllocVar(ret); ret->version = cloneString(row[0]); ret->releaseDate = cloneString(row[1]); ret->maxScore = sqlDouble(row[2]); ret->maxMedianScore = sqlDouble(row[3]); return ret; } struct gtexInfo *gtexInfoLoadAll(char *fileName) /* Load all gtexInfo from a whitespace-separated file. * Dispose of this with gtexInfoFreeList(). */ { struct gtexInfo *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[4]; while (lineFileRow(lf, row)) { el = gtexInfoLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct gtexInfo *gtexInfoLoadAllByChar(char *fileName, char chopper) /* Load all gtexInfo from a chopper separated file. * Dispose of this with gtexInfoFreeList(). */ { struct gtexInfo *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[4]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = gtexInfoLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct gtexInfo *gtexInfoCommaIn(char **pS, struct gtexInfo *ret) /* Create a gtexInfo out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new gtexInfo */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->version = sqlStringComma(&s); ret->releaseDate = sqlStringComma(&s); ret->maxScore = sqlDoubleComma(&s); ret->maxMedianScore = sqlDoubleComma(&s); *pS = s; return ret; } void gtexInfoFree(struct gtexInfo **pEl) /* Free a single dynamically allocated gtexInfo such as created * with gtexInfoLoad(). */ { struct gtexInfo *el; if ((el = *pEl) == NULL) return; freeMem(el->version); freeMem(el->releaseDate); freez(pEl); } void gtexInfoFreeList(struct gtexInfo **pList) /* Free a list of dynamically allocated gtexInfo's */ { struct gtexInfo *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; gtexInfoFree(&el); } *pList = NULL; } void gtexInfoOutput(struct gtexInfo *el, FILE *f, char sep, char lastSep) /* Print out gtexInfo. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->version); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->releaseDate); if (sep == ',') fputc('"',f); fputc(sep,f); fprintf(f, "%g", el->maxScore); fputc(sep,f); fprintf(f, "%g", el->maxMedianScore); fputc(lastSep,f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ void gtexInfoCreateTable(struct sqlConnection *conn, char *table) /* Create GTEx info table */ { char query[1024]; sqlSafef(query, sizeof(query), "CREATE TABLE %s (\n" " version varchar(255) not null, # GTEX data release (e.g. V4, V6)\n" " releaseDate varchar(255) not null, # Release date\n" " maxScore double not null, # Maximum score observed (use to scale display)\n" " maxMedianScore double not null, # Maximum score observed for a tissue median (use to scale display)\n" " #Indices\n" " PRIMARY KEY(version)\n" ")\n", table); sqlRemakeTable(conn, table, query); } char *gtexVersionSuffix(char *table) /* Return version string for a GTEx track table. Supporting V4, V6, V8 (default, no suffix )*/ { if (table) { if (endsWith(table, "V4")) return("V4"); /* TODO: Handle default case more generically if (endsWith(table, "V6")) return("V6"); */ if (endsWith(table, "V8")) return("V8"); } return(""); } char *gtexVersion(char *table) /* Return version string based on table suffix. Default version tables have no suffix */ { char *suffix = gtexVersionSuffix(table); return (sameString(suffix, "")) ? GTEX_DEFAULT_VERSION : suffix; } char *gtexVersionSuffixFromVersion(char *version) /* Return version table suffix for a version */ { if (!version) version = GTEX_DEFAULT_VERSION; return (sameString(version, GTEX_DEFAULT_VERSION)) ? "" : version; } double gtexMaxMedianScore(char *version) /* Retrieve max median score for latest (or named) version */ { char query[1024]; struct sqlConnection *conn = hAllocConn("hgFixed"); if (!conn) return 0; if (!version || sameString(version, "")) version = GTEX_DEFAULT_VERSION; sqlSafef(query, sizeof query, "select maxMedianScore from gtexInfo where version='%s'", version); double score = sqlQuickDouble(conn, query); if (score == 0.0) errAbort("Internal error: GTEx version \"%s\" not found in gtexInfo table", version); hFreeConn(&conn); return score; } char *gtexExprUnit(char *version) /* Units of gene expression */ { return (sameString(version, "V8") ? "TPM" : "RPKM"); }