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/snp/snpLoad/snpSplit.c src/hg/snp/snpLoad/snpSplit.c
index 9762fb4..fcca45c 100644
--- src/hg/snp/snpLoad/snpSplit.c
+++ src/hg/snp/snpLoad/snpSplit.c
@@ -1,437 +1,439 @@
 /* snpSplit - split the ContigLoc table by chrom. */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 
 #include "chromInfo.h"
 #include "dystring.h"
 #include "hash.h"
 #include "hdb.h"
 #include "snpTmp.h"
 
 
 /* these are described in b125_mapping.doc */
 /* Also snpFixed.LocTypeCode */
 char *locTypeStrings[] = {
     "range",
     "exact",
     "between",
     "rangeInsertion",
     "rangeSubstitution",
     "rangeDeletion",
 };
 
 char *functionStrings[] = {
 /* From snpFixed.SnpFunctionCode. */
     "unknown", 
     "locus", 
     "coding", 
     "coding-synon", 
     "coding-nonsynon", 
     "untranslated", 
     "intron", 
     "splice-site", 
     "cds-reference", 
 };
 
 char *snpDb = NULL;
 char *targetDb = NULL;
 char *contigGroup = NULL;
 static struct hash *chromHash = NULL;
 static struct slName *chromList = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
     "snpSplit - split the ContigLoc table by chrom\n"
     "usage:\n"
     "    snpSplit snpDb targetDb contigGroup\n");
 }
 
 /* Copied from hgLoadWiggle. */
 static struct hash *loadAllChromInfo()
 /* Load up all chromosome infos. */
 {
 struct chromInfo *el;
 struct sqlConnection *conn = sqlConnect(targetDb);
 struct sqlResult *sr = NULL;
 struct hash *ret;
 char **row;
 
 ret = newHash(0);
 
-sr = sqlGetResult(conn, NOSQLINJ "select * from chromInfo");
+char query[1024];
+sqlSafef(query, sizeof query, "select * from chromInfo");
+sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = chromInfoLoad(row);
     verbose(4, "Add hash %s value %u (%#lx)\n", el->chrom, el->size, (unsigned long)&el->size);
     hashAdd(ret, el->chrom, (void *)(& el->size));
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 return ret;
 }
 
 /* also copied from hgLoadWiggle. */
 static unsigned getChromSize(char *chrom)
 /* Return size of chrom.  */
 {
 struct hashEl *el = hashLookup(chromHash,chrom);
 
 if (el == NULL)
     errAbort("Couldn't find size of chrom %s", chrom);
     return *(unsigned *)el->val;
 }
 
 
 boolean setCoordsAndLocType(struct snpTmp *el, int locType, int lc_ngbr, int rc_ngbr,
                             char *startString, char *endString, int alleleSize)
 /* set coords and locType */
 {
 char *rangeString1, *rangeString2;
 int rangeInContig = 0;
 
 el->chromStart = atoi(startString);
 
 /* range */
 if (locType == 1) 
     {
     el->locType = locTypeStrings[0];
     rangeString1 = cloneString(endString);
     rangeString2 = strstr(rangeString1, "..");
     if (rangeString2 == NULL) 
         {
         verbose(1, "error processing range snp %s with phys_pos %s\n", rangeString1);
         return FALSE;
         }
     rangeString2 = rangeString2 + 2;
     el->chromEnd = atoi(rangeString2);
     if (el->chromEnd <= el->chromStart)
         {
         verbose(1, "unexpected range coords (end <= start) %s\n", el->name);
 	return FALSE;
 	}
     return TRUE;
     }
 
 /* exact */
 if (locType == 2)
     {
     el->locType = locTypeStrings[1];
     el->chromEnd = atoi(endString);
     if (el->chromEnd != el->chromStart + 1)
         {
 	verbose(1, "unexpected exact coords (end != start + 1) %s\n", el->name);
 	return FALSE;
 	}
     return TRUE;
     }
 
 /* between */
 if (locType == 3)
     {
     el->locType = locTypeStrings[2];
     // rangeString1 = cloneString(endString);
     // rangeString2 = strstr(rangeString1, "^");
     // if (rangeString2 == NULL) 
         // {
         // verbose(1, "error processing snp %s with phys_pos %s\n", rangeString1);
         // return FALSE;
 	// }
     el->chromEnd = el->chromStart;
     return TRUE;
     }
 
 /* rangeInsertion */
 if (locType == 4)
     {
     el->locType = locTypeStrings[3];
     rangeInContig = rc_ngbr - lc_ngbr - alleleSize;
     el->chromEnd = el->chromStart + rangeInContig;
     return TRUE;
     }
 
 /* rangeSubstitution */
 if (locType == 5)
     {
     el->locType = locTypeStrings[4];
     el->chromEnd = el->chromStart + alleleSize;
     return TRUE;
     }
 
 /* rangeDeletion */
 if (locType == 6)
     {
     el->locType = locTypeStrings[5];
     rangeInContig = rc_ngbr - lc_ngbr - alleleSize;
     el->chromEnd = el->chromStart + rangeInContig;
     return TRUE;
     }
 
 verbose(1, "skipping snp %s with loc type %d\n", el->name, locType);
 return FALSE;
 }
 
 void lookupFunction(struct snpTmp *list)
 /* get function from ContigLocusId table */
 /* can be multiple matches */
 /* function values are defined in snpFixed.SnpFunctionCode */
 {
 struct snpTmp *el;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 int functionValue = 0;
 char snpName[32];
 struct dyString *dy = NULL;
 int funcCount = 0;
 int newSize = 0;
 
 for (el = list; el != NULL; el = el->next)
 {
-    dy = newDyString(256);
+    dy = dyStringNew(256);
     strcpy(snpName, el->name);
     stripString(snpName, "rs");
 
     sqlSafef(query, sizeof(query), "select count(*) from ContigLocusId where snp_id = %s and ctg_id = %s", snpName, el->contigName);
     funcCount = sqlQuickNum(conn, query);
     if (funcCount == 0)
         {
         el->func = cloneString("unknown");
         continue;
         }
 
     sqlSafef(query, sizeof(query), "select fxn_class from ContigLocusId where snp_id = %s and ctg_id = %s", snpName, el->contigName);
     sr = sqlGetResult(conn, query);
 
     while ((row = sqlNextRow(sr)) != NULL)
         {
         functionValue = atoi(row[0]);
         if (functionValue > 8)
             {
             verbose(1, "unexpected function value %d for %s; setting to 0 (zero)", functionValue, snpName);
             functionValue = 0;
             }
         dyStringPrintf(dy, "%s,", functionStrings[functionValue]);
         }
 
     // chop off the last character
     newSize = dy->stringSize - 1;
     dyStringResize(dy, newSize);
     el->func = cloneString(dy->string);
     sqlFreeResult(&sr);
-    freeDyString(&dy);
+    dyStringFree(&dy);
     }
 hFreeConn(&conn);
 }
 
 struct snpTmp *readSnps(char *chromName, struct slName *contigList)
 /* query ContigLoc for all snps in contig */
 {
 struct snpTmp *list=NULL, *el = NULL;
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 int locType;
 int pos;
 int snpCount = 0;
 int contigCount = 0;
 struct slName *contigPtr;
 
 verbose(1, "reading snps...\n");
 for (contigPtr = contigList; contigPtr != NULL; contigPtr = contigPtr->next)
     {
     contigCount++;
     verbose(1, "contig count = %d\n", contigCount);
     sqlSafef(query, sizeof(query), "select snp_id, ctg_id, loc_type, lc_ngbr, rc_ngbr, phys_pos_from, "
       "phys_pos, orientation, allele from ContigLoc where snp_type = 'rs' and ctg_id = '%s'", contigPtr->name);
     verbose(3, "ctg_id = %d\n", contigPtr->name);
 
     sr = sqlGetResult(conn, query);
     while ((row = sqlNextRow(sr)) != NULL)
         {
         pos = atoi(row[5]);
         if (pos == 0) 
             {
 	    verbose(5, "snp %s is unaligned\n", row[0]);
 	    continue;
 	    }
         locType = atoi(row[2]);
         if (locType < 1 || locType > 6) 
             {
 	    verbose(1, "skipping snp %s with loc_type %d\n", el->name, locType);
 	    continue;
 	    }
         AllocVar(el);
         el->name = cloneString(row[0]);
         el->chrom = chromName;
         if(!setCoordsAndLocType(el, locType, atoi(row[3]), atoi(row[4]), row[5], row[6], strlen(row[8])))
             {
             free(el);
 	    continue;
 	    }
         if (atoi(row[7]) == 0) 
             strcpy(el->strand, "+");
         else if (atoi(row[7]) == 1)
             strcpy(el->strand, "-");
         else
             strcpy(el->strand, "?");
         el->refNCBI = cloneString(row[8]);
 	// should this be reverseComplemented for negative strand??!!
 	if (sameString(el->locType, "between") && !sameString(el->refNCBI, "-"))
 	    verbose(1, "unexpected between allele %s for %s\n", el->refNCBI, el->name);
 	el->contigName = cloneString(contigPtr->name);
         slAddHead(&list,el);
 	snpCount++;
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 verbose(1, "%d snps found\n", snpCount);
 return list;
 }
 
 struct slName *getContigs(char *chromName)
 /* get list of contigs that are from chrom */
 {
 char query[512];
 struct sqlConnection *conn = hAllocConn();
 struct sqlResult *sr;
 char **row;
 struct slName *contigList = NULL;
 struct slName *el = NULL;
 int count = 0;
 
 verbose(1, "getting contigs...\n");
 sqlSafef(query, sizeof(query), "select ctg_id from ContigInfo where contig_chr = '%s' and group_term = '%s'", chromName, contigGroup);
 verbose(5, "query = %s\n", query);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     verbose(5, "contig = %s\n", row[0]);
     el = newSlName(row[0]);
     slAddHead(&contigList, el);
     count++;
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 verbose(1, "contigs found = %d\n", count);
 return(contigList);
 }
 
 
 void writeToTabFile(FILE *f, struct snpTmp *list)
 /* write tab separated file */
 {
 struct snpTmp *el;
 int count = 0;
 
 verbose(1, "writing to tab file...\n");
 for (el = list; el != NULL; el = el->next)
     {
     if (sameString(el->chrom, "ERROR")) continue;
     fprintf(f, "chr%s\t", el->chrom);
     fprintf(f, "%d\t", el->chromStart);
     fprintf(f, "%d\t", el->chromEnd);
     fprintf(f, "rs%s\t", el->name);
     fprintf(f, "%s\t", el->strand);
     fprintf(f, "%s\t", el->refNCBI);
     fprintf(f, "%s\t", el->locType);
     fprintf(f, "%s\t", el->func);
     /* don't need this going forward, but easier to write it */
     /* since using snpTmp.h */
     fprintf(f, "%s\t", el->contigName);
     fprintf(f, "\n");
     count++;
     }
 verbose(1, "%d lines written\n", count);
 }
 
 
 
 
 void loadDatabase(char *chromName, struct snpTmp *list)
 {
 FILE *f;
 struct sqlConnection *conn2 = hAllocConn2();
 char fileName[64];
 
 strcpy(fileName, "chr");
 strcat(fileName, chromName);
 strcat(fileName, "_snpTmp");
 f = hgCreateTabFile(".", fileName);
 writeToTabFile(f, list);
 snpTmpTableCreate(conn2, fileName);
 verbose(1, "loading...\n");
 hgLoadTabFile(conn2, ".", fileName, &f);
 hFreeConn2(&conn2);
 }
 
 int main(int argc, char *argv[])
 /* Check args; read and load . */
 {
 struct snpTmp *list=NULL, *el;
 struct slName *chromPtr, *contigList;
 char tableName[64];
 struct sqlConnection *conn;
 
 if (argc != 4)
     usage();
 
 /* TODO: look in jksql for existence check for non-hgcentral database */
 snpDb = argv[1];
 targetDb = argv[2];
 contigGroup = argv[3];
 // if(!hDbExists(targetDb))
     // errAbort("%s does not exist\n", targetDb);
 
 hSetDb(snpDb);
 hSetDb2(targetDb);
 chromHash = loadAllChromInfo();
 chromList = hAllChromNamesDb(targetDb);
 
 /* check for needed tables */
 if(!hTableExistsDb(snpDb, "ContigLoc"))
     errAbort("no ContigLoc table in %s\n", snpDb);
 if(!hTableExistsDb(snpDb, "ContigInfo"))
     errAbort("no ContigInfo table in %s\n", snpDb);
 if(!hTableExistsDb(snpDb, "ContigLocusId"))
     errAbort("no ContigLocusId table in %s\n", snpDb);
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     {
     stripString(chromPtr->name, "chr");
     }
 
 for (chromPtr = chromList; chromPtr != NULL; chromPtr = chromPtr->next)
     {
 
     conn = sqlConnect(targetDb);
     strcpy(tableName, "chr");
     strcat(tableName, cloneString(chromPtr->name));
     strcat(tableName, "_snpTmp");
     if (sqlTableExists(conn, tableName)) continue;
     sqlDisconnect(&conn);
 
     verbose(1, "chrom = %s\n", chromPtr->name);
     contigList = getContigs(chromPtr->name);
     if (contigList == NULL) continue;
     list = readSnps(chromPtr->name, contigList);
     slFreeList(&contigList);
     if (list == NULL)
         {
 	verbose(1, "no SNPs found\n");
 	continue;
 	}
     lookupFunction(list);
     slSort(&list, snpTmpCmp);
     loadDatabase(chromPtr->name, list);
     slFreeList(&list);
     }
 
 return 0;
 }