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/makeDb/hgPepPred/hgPepPred.c src/hg/makeDb/hgPepPred/hgPepPred.c
index 0017eda..eb47747 100644
--- src/hg/makeDb/hgPepPred/hgPepPred.c
+++ src/hg/makeDb/hgPepPred/hgPepPred.c
@@ -1,411 +1,411 @@
 /* hgPepPred - Load peptide predictions from Ensembl or Genie. */
 
 /* 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 "options.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "hash.h"
 #include "jksql.h"
 #include "pepPred.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "hgPepPred - Load peptide predictions from Ensembl or Genie\n"
   "usage:\n"
   "   hgPepPred database type file(s)\n"
   "where type is either 'ensembl' or 'genie' or 'softberry'\n"
   "or\n"
   "   hgPepPred database generic table files(s)\n"
   "which will load the given table assuming the peptide name is\n"
   "in the fasta record\n"
   "or\n"
   "   hgPepPred database tab table file\n"
   "which will load the given table from a single tab separated file\n"
   "options:\n"
   "   -abbr=prefix  Abbreviate by removing prefix from names\n"
   "   -suffix=suffix - add suffix to each protein id\n"
   );
 }
 
 /* command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"abbr", OPTION_STRING},
     {"suffix", OPTION_STRING},
     {NULL, 0}
 };
 
 char *abbr = NULL;
 char *suffix = NULL;
 
 void makeCustomTable(char *database, char *table, char *defString)
 /* create/recreate table. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *ds = newDyString(2048);
+struct dyString *ds = dyStringNew(2048);
 
 sqlDyStringPrintf(ds, defString, table);
 sqlRemakeTable(conn, table, ds->string);
 sqlDisconnect(&conn);
-freeDyString(&ds);
+dyStringFree(&ds);
 }
 
 void loadTableFromTabFile(char *database, char *table, char *tabFile)
 /* Load up table from tab file. */
 {
 struct sqlConnection *conn = sqlConnect(database);
-struct dyString *ds = newDyString(2048);
+struct dyString *ds = dyStringNew(2048);
 sqlDyStringPrintf(ds, 
    "load data local infile '%s' into table %s", tabFile, table);
 sqlUpdate(conn, ds->string);
 sqlDisconnect(&conn);
-freeDyString(&ds);
+dyStringFree(&ds);
 }
 
 char *createString = 
 "CREATE TABLE %s (\n"
 "    name varchar(255) not null,	# Name of gene - same as in genePred\n"
 "    seq longblob not null,	# Peptide sequence\n"
 "              #Indices\n"
 "    PRIMARY KEY(name(64))\n"
 ")\n";
 
 char *findEnsTrans(struct lineFile *lf, char *line)
 /* Find transcript name out of ensemble line.  Squawk and die
  * if a problem. */
 {
 char *words[32];
 int wordCount, i;
 char *pat = "Translation:";
 int patSize = strlen(pat);
 
 wordCount = chopLine(line+1, words);
 for (i=0; i<wordCount; ++i)
     {
     if (startsWith(pat, words[i]))
         return words[i] + patSize;
     }
 // Ensembl appears to have changed their format recently; handle both formats.
 wordCount = chopString(line+1, "|", words, ArraySize(words));
 if (wordCount >= 3)
     {
     char *ptr = strchr(words[2], '.');
     if (ptr != NULL) *ptr = 0;
     return(words[2]);
     }
 errAbort("Couldn't find '%s' key for transcript name line %d of %s",
     pat, lf->lineIx, lf->fileName);
 return NULL;
 }
 
 void oneEnsFile(char *ensFile, struct hash *uniq, struct hash *pToT, FILE *f)
 /* Process one ensemble peptide prediction file into tab delimited
  * output f, using uniq hash to make sure no dupes. */
 {
 struct lineFile *lf = lineFileOpen(ensFile, TRUE);
 char *line;
 int lineSize;
 boolean firstTime = TRUE;
 char *translation;
 
 /* Do cursory sanity check. */
 if (!lineFileNext(lf, &line, &lineSize))
     errAbort("%s is empty", ensFile);
 if (line[0] != '>')
     errAbort("%s is badly formatted, doesn't begin with '>'", ensFile);
 lineFileReuse(lf);
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '>')
         {
 	char *upperCase;
 	char *transcript;
 	/* End last line. */
 	if (firstTime)
 	    firstTime = FALSE;
 	else
 	    fputc('\n', f);
 	translation = findEnsTrans(lf, line);
 	if (hashLookupUpperCase(uniq, translation) != NULL)
 	    errAbort("Duplicate (case insensitive) '%s' line %d of %s", translation, lf->lineIx, lf->fileName);
 	upperCase = cloneString(translation);
 	touppers(upperCase);
 	hashAdd(uniq, upperCase, NULL);
 	freeMem(upperCase);
 	transcript = hashFindVal(pToT, translation);
 	if (transcript == NULL)
 	    errAbort("Can't find transcript for %s", translation);
 	fprintf(f, "%s\t", transcript);
 	}
     else
         {
 	mustWrite(f, line, lineSize-1);
 	}
     }
 fputc('\n', f);
 lineFileClose(&lf);
 }
 
 struct hash *ensProtToTrans(char *database)
 /* Use ensGtp table to create hash keyed by protein and
  * returning transcript values. */
 {
 char *table = "ensGtp";
 struct sqlConnection *conn = sqlConnect(database);
 char query[256], **row;
 struct sqlResult *sr;
 struct hash *hash = newHash(16);
 
 if (!sqlTableExists(conn, table))
      errAbort("No %s table, need to build that first", table);
 sqlSafef(query, sizeof(query), "select protein,transcript from %s", table);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     chopSuffix(row[0]);
     chopSuffix(row[1]);
     hashAdd(hash, row[0], cloneString(row[1]));
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 return hash;
 }
 
 void ensPepPred(char *database, int fileCount, char *fileNames[])
 /* Load Ensembl peptide predictions into database. */
 {
 int i;
 char *fileName;
 char *tempName = "ensPep.tab";
 FILE *f = mustOpen(tempName, "w");
 struct hash *uniq = newHash(16);
 struct hash *pToT = ensProtToTrans(database);
 
 makeCustomTable(database, "ensPep", createString);
 for (i=0; i<fileCount; ++i)
     {
     fileName = fileNames[i];
     printf("Processing %s\n", fileName);
     oneEnsFile(fileName, uniq, pToT, f);
     }
 carefulClose(&f);
 loadTableFromTabFile(database, "ensPep", tempName);
 freeHash(&uniq);
 }
 
 
 void oneGenieFile(char *fileName, struct hash *uniq, FILE *f)
 /* Process one genie peptide prediction file into known and alt tab files. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line;
 int lineSize;
 boolean firstTime = TRUE;
 char *trans;
 boolean skip = FALSE;
 
 /* Do cursory sanity check. */
 if (!lineFileNext(lf, &line, &lineSize))
     errAbort("%s is empty", fileName);
 if (line[0] != '>')
     errAbort("%s is badly formatted, doesn't begin with '>'", fileName);
 lineFileReuse(lf);
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '>')
         {
 	/* End last line. */
 	if (firstTime)
 	    firstTime = FALSE;
 	else
 	    fputc('\n', f);
 	trans = firstWordInLine(line+1);
 	if (abbr != NULL && startsWith(abbr, trans))
 	    trans += strlen(abbr);
 	if (hashLookupUpperCase(uniq, trans) != NULL)
 	    {
 	    warn("Duplicate (case insensitive) '%s' line %d of %s. Ignoring all but first.", trans, lf->lineIx, lf->fileName);
 	    skip = TRUE;
 	    }
 	else
 	    {
 	    char *upperCase;
 	    upperCase = cloneString(trans);
 	    touppers(upperCase);
 	    hashAdd(uniq, upperCase, NULL);
 	    freeMem(upperCase);
 	    fprintf(f, "%s\t", trans);
 	    skip = FALSE;
 	    }
 	}
     else if (!skip)
         {
 	mustWrite(f, line, lineSize-1);
 	}
     }
 fputc('\n', f);
 lineFileClose(&lf);
 }
 
 void geniePepPred(char *database, int fileCount, char *fileNames[])
 /* Load Genie peptide predictions into database. */
 {
 char *altTab = "alt.tab";
 FILE *alt =  mustOpen(altTab, "w");
 struct hash *uniq = newHash(16);
 int i;
 char *fileName;
 
 makeCustomTable(database, "genieAltPep", createString);
 for (i=0; i<fileCount; ++i)
     {
     fileName = fileNames[i];
     printf("Processing %s\n", fileName);
     oneGenieFile(fileName, uniq, alt);
     }
 carefulClose(&alt);
 loadTableFromTabFile(database, "genieAltPep", altTab);
 freeHash(&uniq);
 }
 
 void genericOne(char *fileName, struct hash *uniq, FILE *f)
 /* Process one ensemble peptide prediction file into tab delimited
  * output f, using uniq hash to make sure no dupes. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *line;
 int lineSize;
 boolean firstTime = TRUE;
 char *trans, transBuf[128];
 
 /* Do cursory sanity check. */
 if (!lineFileNext(lf, &line, &lineSize))
     errAbort("%s is empty", fileName);
 if (line[0] != '>')
     errAbort("%s is badly formatted, doesn't begin with '>'", fileName);
 lineFileReuse(lf);
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '>')
         {
 	char *upperCase;
 	/* End last line. */
 	if (firstTime)
 	    firstTime = FALSE;
 	else
 	    fputc('\n', f);
 	trans = firstWordInLine(line+1);
 	if (abbr != NULL && startsWith(abbr, trans))
 	    trans += strlen(abbr);
         if (suffix != NULL)
             {
             safef(transBuf, sizeof(transBuf), "%s%s", trans, suffix);
             trans = transBuf;
             }
 	if (hashLookupUpperCase(uniq, trans) != NULL)
 	    errAbort("Duplicate (case insensitive) '%s' line %d of %s", trans, lf->lineIx, lf->fileName);
 	upperCase = cloneString(trans);
 	touppers(upperCase);
 	hashAdd(uniq, upperCase, NULL);
 	freeMem(upperCase);
 	fprintf(f, "%s\t", trans);
 	}
     else
         {
 	mustWrite(f, line, lineSize-1);
 	}
     }
 fputc('\n', f);
 lineFileClose(&lf);
 }
 
 
 void genericPepPred(char *database, int fileCount, char *fileNames[], char *table)
 /* Load a generic (simple) peptide file. */
 {
 int i;
 char *fileName;
 char tempName[256];
 FILE *f;
 struct hash *uniq = newHash(16);
 
 sprintf(tempName, "%s.tab", table);
 f = mustOpen(tempName, "w");
 makeCustomTable(database, table, createString);
 for (i=0; i<fileCount; ++i)
     {
     fileName = fileNames[i];
     printf("Processing %s\n", fileName);
     genericOne(fileName, uniq, f);
     }
 carefulClose(&f);
 loadTableFromTabFile(database, table, tempName);
 freeHash(&uniq);
 }
 
 void tabPepPred(char *database, int fileCount, char *fileNames[], char *table)
 /* Load a tab separated peptide file. */
 {
 struct hash *uniq = newHash(16);
 struct lineFile *lf = lineFileOpen(fileNames[0], TRUE);
 char *words[2];
 
 if (fileCount != 1)
     errAbort("Only one file allowed for tab separated peptides");
 
 makeCustomTable(database, table, createString);
 
 printf("Processing %s\n", fileNames[0]);
 while (lineFileRow(lf, words))
     {
     char *upperCase;
     if (hashLookupUpperCase(uniq, words[0]) != NULL)
 	errAbort("Duplicate (case insensitive) '%s' line %d of %s", words[0], lf->lineIx, lf->fileName);
     upperCase = cloneString(words[0]);
     touppers(upperCase);
     hashAdd(uniq, upperCase, NULL);
     freeMem(upperCase);
     }
 lineFileClose(&lf);
 printf("Loading %s\n", fileNames[0]);
 loadTableFromTabFile(database, table, fileNames[0]);
 freeHash(&uniq);
 }
 
 void softberryPepPred(char *database, int fileCount, char *fileNames[])
 /* Load Softberry peptide predictions into database. */
 {
 genericPepPred(database, fileCount, fileNames, "softberryPep");
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 char *type;
 optionInit(&argc, argv, optionSpecs);
 if (argc < 4)
     usage();
 abbr = optionVal("abbr", abbr);
 suffix = optionVal("suffix", abbr);
 type = argv[2];
 if (sameWord(type, "ensembl"))
     ensPepPred(argv[1], argc-3, argv+3);
 else if (sameWord(type, "genie"))
     geniePepPred(argv[1], argc-3, argv+3);
 else if (sameWord(type, "softberry"))
     softberryPepPred(argv[1], argc-3, argv+3);
 else if (sameWord(type, "generic"))
     genericPepPred(argv[1], argc-4, argv+4, argv[3]);
 else if (sameWord(type, "tab"))
     tabPepPred(argv[1], argc-4, argv+4, argv[3]);
 else
     usage();
 return 0;
 }