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/gtexGeneBed.c src/hg/lib/gtexGeneBed.c
index 00946fb..869a213 100644
--- src/hg/lib/gtexGeneBed.c
+++ src/hg/lib/gtexGeneBed.c
@@ -1,309 +1,309 @@
 /* gtexGeneBed.c was originally generated by the autoSql program, which also 
  * generated gtexGeneBed.h and gtexGeneBed.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 "gtexGeneBed.h"
 
 
 
 char *gtexGeneBedCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,geneId,geneType,expCount,expScores";
 
 struct gtexGeneBed *gtexGeneBedLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all gtexGeneBed 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 gtexGeneBedFreeList(). */
 {
 struct gtexGeneBed *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gtexGeneBedLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gtexGeneBedSaveToDb(struct sqlConnection *conn, struct gtexGeneBed *el, char *tableName, int updateSize)
 /* Save gtexGeneBed 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);
 char  *expScoresArray;
 expScoresArray = sqlFloatArrayToString(el->expScores, el->expCount);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s','%s','%s',%u,'%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->geneId,  el->geneType,  el->expCount,  expScoresArray );
 sqlUpdate(conn, update->string);
-freeDyString(&update);
+dyStringFree(&update);
 freez(&expScoresArray);
 }
 
 struct gtexGeneBed *gtexGeneBedLoad(char **row)
 /* Load a gtexGeneBed from row fetched with select * from gtexGeneBed
  * from database.  Dispose of this with gtexGeneBedFree(). */
 {
 struct gtexGeneBed *ret;
 
 AllocVar(ret);
 ret->expCount = sqlUnsigned(row[8]);
 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->geneId = cloneString(row[6]);
 ret->geneType = cloneString(row[7]);
 {
 int sizeOne;
 sqlFloatDynamicArray(row[9], &ret->expScores, &sizeOne);
 assert(sizeOne == ret->expCount);
 }
 return ret;
 }
 
 struct gtexGeneBed *gtexGeneBedLoadAll(char *fileName) 
 /* Load all gtexGeneBed from a whitespace-separated file.
  * Dispose of this with gtexGeneBedFreeList(). */
 {
 struct gtexGeneBed *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileRow(lf, row))
     {
     el = gtexGeneBedLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexGeneBed *gtexGeneBedLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexGeneBed from a chopper separated file.
  * Dispose of this with gtexGeneBedFreeList(). */
 {
 struct gtexGeneBed *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexGeneBedLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexGeneBed *gtexGeneBedCommaIn(char **pS, struct gtexGeneBed *ret)
 /* Create a gtexGeneBed out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexGeneBed */
 {
 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->geneId = sqlStringComma(&s);
 ret->geneType = sqlStringComma(&s);
 ret->expCount = sqlUnsignedComma(&s);
 {
 int i;
 s = sqlEatChar(s, '{');
 AllocArray(ret->expScores, ret->expCount);
 for (i=0; i<ret->expCount; ++i)
     {
     ret->expScores[i] = sqlFloatComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 }
 *pS = s;
 return ret;
 }
 
 void gtexGeneBedFree(struct gtexGeneBed **pEl)
 /* Free a single dynamically allocated gtexGeneBed such as created
  * with gtexGeneBedLoad(). */
 {
 struct gtexGeneBed *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->geneId);
 freeMem(el->geneType);
 freeMem(el->expScores);
 freez(pEl);
 }
 
 void gtexGeneBedFreeList(struct gtexGeneBed **pList)
 /* Free a list of dynamically allocated gtexGeneBed's */
 {
 struct gtexGeneBed *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexGeneBedFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexGeneBedOutput(struct gtexGeneBed *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexGeneBed.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneType);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->expCount);
 fputc(sep,f);
 {
 int i;
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->expCount; ++i)
     {
     fprintf(f, "%g", el->expScores[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 }
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void gtexGeneBedCreateTable(struct sqlConnection *conn, char *table)
 /* Create expression record format table of given name. */
 {
 char query[1024];
 
 sqlSafef(query, sizeof(query),
 "CREATE TABLE %s (\n"
 "   chrom varchar(255) not null,	# Reference sequence chromosome or scaffold\n"
 "   chromStart int unsigned not null,	# Start position in chromosome\n"
 "   chromEnd int unsigned not null,	# End position in chromosome\n"
 "   name varchar(255) not null,	# Gene symbol\n"
 "   score int unsigned not null,	# Score from 0-1000\n"
 "   strand char(1) not null,	# + or - for strand\n"
 "   geneId varchar(255) not null,	# Ensembl gene ID, referenced in GTEx data tables\n"
 "   geneType varchar(255) not null,	# GENCODE gene biotype\n"
 "   expCount int unsigned not null,	# Number of experiment values\n"
 "   expScores longblob not null,	# Comma separated list of experiment scores\n"
           "#Indices\n"
 "   PRIMARY KEY(chrom,geneId)\n"
 "   INDEX(geneId)\n"
 "   INDEX(chrom,chromStart)\n"
 ")\n",
     table);
 sqlRemakeTable(conn, table, query);
 }
 
 char *gtexGeneClass(struct gtexGeneBed *geneBed)
 /* Return gene "class" (analogous to GENCODE transcriptClass) for a GENCODE gene biotype 
  * Mapped as follows:
 
  * coding: IG_C_gene, IG_D_gene, IG_J_gene, IG_V_gene, 
                TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene 
                polymorphic_pseudogene, protein_coding
 
  * pseudo: IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene,
                pseudogene 
 
  * nonCoding: 3prime_overlapping_ncrna, Mt_rRNA, Mt_tRNA, antisense, lincRNA, miRNA, 
                 misc_RNA, processed_transcript, rRNA, sense_intronic, sense_overlapping, 
                 snRNA, snoRNA
  * (MarkD request out for approval).
 */
 {
 char *geneType = geneBed->geneType;
 if (geneType == NULL)
     return "unknown";
 if (sameString(geneType, "coding") || sameString(geneType, "protein_coding") ||
         sameString(geneType, "polymorphic_pseudogene") || endsWith(geneType, "_gene"))
     return "coding";
 if (sameString(geneType, "pseudo") || sameString(geneType, "pseudogene") ||
         endsWith(geneType, "_pseudogene"))
     return "pseudo";
 // A bit of a cheat here -- better a mapping table
 return "nonCoding";
 }
 
 boolean gtexGeneIsCoding(struct gtexGeneBed *geneBed)
 /* Return TRUE if biotype indicates this is a protein coding gene */
 {
 return sameString("coding", gtexGeneClass(geneBed));
 }
 
 float gtexGeneTotalMedianExpression(struct gtexGeneBed *geneBed)
 /* Return total of all tissue medians */
 {
 int i;
 float sum = 0.0;
 for (i=0; i<geneBed->expCount; i++)
     sum += geneBed->expScores[i];
 return sum;
 }
 
 float gtexGeneHighestMedianExpression(struct gtexGeneBed *geneBed, int *tissueIdRet)
 /* Return tissue median and id of tissue with highest expression of this gene */
 {
 int i;
 float maxScore = 0.0;
 assert(tissueIdRet);
 for (i=0; i<geneBed->expCount; i++)
     {
     float score = geneBed->expScores[i];
     if (score > maxScore)
         {
         maxScore = score;
         *tissueIdRet = i;
         }
     }
 return maxScore;
 }