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/cgilib/ucscRetroInfo.c src/hg/cgilib/ucscRetroInfo.c
index 543d93b..ef90342 100644
--- src/hg/cgilib/ucscRetroInfo.c
+++ src/hg/cgilib/ucscRetroInfo.c
@@ -1,441 +1,441 @@
 /* ucscRetroInfo.c was originally generated by the autoSql program, which also 
  * generated ucscRetroInfo.h and ucscRetroInfo.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 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 "dystring.h"
 #include "jksql.h"
 #include "ucscRetroInfo.h"
 
 
 struct ucscRetroInfo *ucscRetroInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all ucscRetroInfo 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 ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void ucscRetroInfoSaveToDb(struct sqlConnection *conn, struct ucscRetroInfo *el, char *tableName, int updateSize)
 /* Save ucscRetroInfo 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. Strings are automatically escaped to allow insertion into the database. */
 {
-struct dyString *update = newDyString(updateSize);
+struct dyString *update = dyStringNew(updateSize);
 char  *blockSizesArray, *chromStartsArray;
 blockSizesArray = sqlSignedArrayToString(el->blockSizes, el->blockCount);
 chromStartsArray = sqlSignedArrayToString(el->chromStarts, el->blockCount);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,%d,'%s','%s',%d,%d,'%s','%s',%d,%d,'%s',%u,%u,%u,%d,%d,%u,%u,%u,%u,%u,%u,%u,%d,%u,%d,%d,%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%d,%d,'%s',%g,%u)", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->blockCount,  blockSizesArray ,  chromStartsArray ,  el->retroExonCount,  el->axtScore,  el->type,  el->gChrom,  el->gStart,  el->gEnd,  el->gStrand,  el->parentSpliceCount,  el->geneOverlap,  el->polyA,  el->polyAstart,  el->exonCover,  el->intronCount,  el->bestAliCount,  el->matches,  el->qSize,  el->qEnd,  el->tReps,  el->coverage,  el->label,  el->milliBad, el->alignGapCount,  el->processedIntrons,  el->conservedSpliceSites,  el->maxOverlap,  el->refSeq,  el->rStart,  el->rEnd,  el->mgc,  el->mStart,  el->mEnd,  el->kgName,  el->kStart,  el->kEnd,  el->overName,  el->overStart,  el->overExonCover,  el->overStrand,  el->posConf,  el->polyAlen);
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 freez(&blockSizesArray);
 freez(&chromStartsArray);
 }
 
 
 struct ucscRetroInfo *ucscRetroInfoLoad(char **row)
 /* Load a ucscRetroInfo from row fetched with select * from ucscRetroInfo
  * from database.  Dispose of this with ucscRetroInfoFree(). */
 {
 struct ucscRetroInfo *ret;
 
 AllocVar(ret);
 ret->blockCount = sqlSigned(row[9]);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 ret->reserved = sqlUnsigned(row[8]);
 {
 int sizeOne;
 sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 {
 int sizeOne;
 sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
 assert(sizeOne == ret->blockCount);
 }
 ret->retroExonCount = sqlSigned(row[12]);
 ret->axtScore = sqlSigned(row[13]);
 ret->type = cloneString(row[14]);
 ret->gChrom = cloneString(row[15]);
 ret->gStart = sqlSigned(row[16]);
 ret->gEnd = sqlSigned(row[17]);
 safecpy(ret->gStrand, sizeof(ret->gStrand), row[18]);
 ret->parentSpliceCount = sqlUnsigned(row[19]);
 ret->geneOverlap = sqlUnsigned(row[20]);
 ret->polyA = sqlUnsigned(row[21]);
 ret->polyAstart = sqlSigned(row[22]);
 ret->exonCover = sqlSigned(row[23]);
 ret->intronCount = sqlUnsigned(row[24]);
 ret->bestAliCount = sqlUnsigned(row[25]);
 ret->matches = sqlUnsigned(row[26]);
 ret->qSize = sqlUnsigned(row[27]);
 ret->qEnd = sqlUnsigned(row[28]);
 ret->tReps = sqlUnsigned(row[29]);
 ret->coverage = sqlUnsigned(row[30]);
 ret->label = sqlSigned(row[31]);
 ret->milliBad = sqlUnsigned(row[32]);
 ret->alignGapCount = sqlSigned(row[33]);
 ret->processedIntrons = sqlSigned(row[34]);
 ret->conservedSpliceSites = sqlSigned(row[35]);
 ret->maxOverlap = sqlSigned(row[36]);
 ret->refSeq = cloneString(row[37]);
 ret->rStart = sqlSigned(row[38]);
 ret->rEnd = sqlSigned(row[39]);
 ret->mgc = cloneString(row[40]);
 ret->mStart = sqlSigned(row[41]);
 ret->mEnd = sqlSigned(row[42]);
 ret->kgName = cloneString(row[43]);
 ret->kStart = sqlSigned(row[44]);
 ret->kEnd = sqlSigned(row[45]);
 ret->overName = cloneString(row[46]);
 ret->overStart = sqlSigned(row[47]);
 ret->overExonCover = sqlSigned(row[48]);
 safecpy(ret->overStrand, sizeof(ret->overStrand), row[49]);
 ret->posConf = sqlFloat(row[50]);
 ret->polyAlen = sqlUnsigned(row[51]);
 return ret;
 }
 
 struct ucscRetroInfo *ucscRetroInfoLoadAll(char *fileName) 
 /* Load all ucscRetroInfo from a whitespace-separated file.
  * Dispose of this with ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[52];
 
 while (lineFileRow(lf, row))
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ucscRetroInfo *ucscRetroInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all ucscRetroInfo from a chopper separated file.
  * Dispose of this with ucscRetroInfoFreeList(). */
 {
 struct ucscRetroInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[52];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = ucscRetroInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct ucscRetroInfo *ucscRetroInfoCommaIn(char **pS, struct ucscRetroInfo *ret)
 /* Create a ucscRetroInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new ucscRetroInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->blockCount = sqlSignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->blockSizes, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->blockSizes[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->chromStarts, ret->blockCount);
 for (i=0; i<ret->blockCount; ++i)
     {
     ret->chromStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 ret->retroExonCount = sqlSignedComma(&s);
 ret->axtScore = sqlSignedComma(&s);
 ret->type = sqlStringComma(&s);
 ret->gChrom = sqlStringComma(&s);
 ret->gStart = sqlSignedComma(&s);
 ret->gEnd = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->gStrand, sizeof(ret->gStrand));
 ret->parentSpliceCount = sqlUnsignedComma(&s);
 ret->geneOverlap = sqlUnsignedComma(&s);
 ret->polyA = sqlUnsignedComma(&s);
 ret->polyAstart = sqlSignedComma(&s);
 ret->exonCover = sqlSignedComma(&s);
 ret->intronCount = sqlUnsignedComma(&s);
 ret->bestAliCount = sqlUnsignedComma(&s);
 ret->matches = sqlUnsignedComma(&s);
 ret->qSize = sqlUnsignedComma(&s);
 ret->qEnd = sqlUnsignedComma(&s);
 ret->tReps = sqlUnsignedComma(&s);
 ret->coverage = sqlUnsignedComma(&s);
 ret->label = sqlSignedComma(&s);
 ret->milliBad = sqlUnsignedComma(&s);
 ret->alignGapCount = sqlSignedComma(&s);
 ret->processedIntrons = sqlSignedComma(&s);
 ret->conservedSpliceSites = sqlSignedComma(&s);
 ret->maxOverlap = sqlSignedComma(&s);
 ret->refSeq = sqlStringComma(&s);
 ret->rStart = sqlSignedComma(&s);
 ret->rEnd = sqlSignedComma(&s);
 ret->mgc = sqlStringComma(&s);
 ret->mStart = sqlSignedComma(&s);
 ret->mEnd = sqlSignedComma(&s);
 ret->kgName = sqlStringComma(&s);
 ret->kStart = sqlSignedComma(&s);
 ret->kEnd = sqlSignedComma(&s);
 ret->overName = sqlStringComma(&s);
 ret->overStart = sqlSignedComma(&s);
 ret->overExonCover = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->overStrand, sizeof(ret->overStrand));
 ret->posConf = sqlFloatComma(&s);
 ret->polyAlen = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void ucscRetroInfoFree(struct ucscRetroInfo **pEl)
 /* Free a single dynamically allocated ucscRetroInfo such as created
  * with ucscRetroInfoLoad(). */
 {
 struct ucscRetroInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->blockSizes);
 freeMem(el->chromStarts);
 freeMem(el->type);
 freeMem(el->gChrom);
 freeMem(el->refSeq);
 freeMem(el->mgc);
 freeMem(el->kgName);
 freeMem(el->overName);
 freez(pEl);
 }
 
 void ucscRetroInfoFreeList(struct ucscRetroInfo **pList)
 /* Free a list of dynamically allocated ucscRetroInfo's */
 {
 struct ucscRetroInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     ucscRetroInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void ucscRetroInfoOutput(struct ucscRetroInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out ucscRetroInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 fprintf(f, "%d", el->blockCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->blockSizes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->blockCount; ++i)
     {
     fprintf(f, "%d", el->chromStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(sep,f);
 fprintf(f, "%d", el->retroExonCount);
 fputc(sep,f);
 fprintf(f, "%d", el->axtScore);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->type);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gChrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->gStart);
 fputc(sep,f);
 fprintf(f, "%d", el->gEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->parentSpliceCount);
 fputc(sep,f);
 fprintf(f, "%u", el->geneOverlap);
 fputc(sep,f);
 fprintf(f, "%u", el->polyA);
 fputc(sep,f);
 fprintf(f, "%d", el->polyAstart);
 fputc(sep,f);
 fprintf(f, "%d", el->exonCover);
 fputc(sep,f);
 fprintf(f, "%u", el->intronCount);
 fputc(sep,f);
 fprintf(f, "%u", el->bestAliCount);
 fputc(sep,f);
 fprintf(f, "%u", el->matches);
 fputc(sep,f);
 fprintf(f, "%u", el->qSize);
 fputc(sep,f);
 fprintf(f, "%u", el->qEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->tReps);
 fputc(sep,f);
 fprintf(f, "%u", el->coverage);
 fputc(sep,f);
 fprintf(f, "%d", el->label);
 fputc(sep,f);
 fprintf(f, "%u", el->milliBad);
 fputc(sep,f);
 fprintf(f, "%d", el->alignGapCount);
 fputc(sep,f);
 fprintf(f, "%d", el->processedIntrons);
 fputc(sep,f);
 fprintf(f, "%d", el->conservedSpliceSites);
 fputc(sep,f);
 fprintf(f, "%d", el->maxOverlap);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->refSeq);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->rStart);
 fputc(sep,f);
 fprintf(f, "%d", el->rEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->mgc);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mStart);
 fputc(sep,f);
 fprintf(f, "%d", el->mEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->kgName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->kStart);
 fputc(sep,f);
 fprintf(f, "%d", el->kEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->overName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->overStart);
 fputc(sep,f);
 fprintf(f, "%d", el->overExonCover);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->overStrand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->posConf);
 fputc(sep,f);
 fprintf(f, "%u", el->polyAlen);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 struct ucscRetroInfo *ucscRetroInfoQuery(struct sqlConnection *conn,
                                        char *table, char *mappedId)
 /* load a single retro object for an mapped id from a table,
  * or error if not found */
 {
 return sqlQueryObjs(conn, (sqlLoadFunc)ucscRetroInfoLoad,
                     sqlQuerySingle,
                     "SELECT * FROM %s WHERE name = \"%s\"",
                     table, mappedId);
 }