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/encode/docId/lib/docIdSub.c src/hg/encode/docId/lib/docIdSub.c
index 2ae1bde..e22f941 100644
--- src/hg/encode/docId/lib/docIdSub.c
+++ src/hg/encode/docId/lib/docIdSub.c
@@ -1,311 +1,311 @@
 /* docIdSub.c was originally generated by the autoSql program, which also 
  * generated docIdSub.h and docIdSub.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* 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 "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "docId.h"
 #include "portable.h"
 
 //char *docIdTable = "docIdSub";
 
 void docIdSubStaticLoad(char **row, struct docIdSub *ret)
 /* Load a row from docIdSub table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->ix = sqlSigned(row[0]);
 ret->status = sqlSigned(row[1]);
 ret->assembly = row[2];
 ret->submitDate = row[3];
 ret->md5sum = row[4];
 ret->valReport = row[5];
 ret->valVersion = row[6];
 ret->metaData = row[7];
 ret->submitPath = row[8];
 ret->submitter = row[9];
 }
 
 struct docIdSub *docIdSubLoad(char **row)
 /* Load a docIdSub from row fetched with select * from docIdSub
  * from database.  Dispose of this with docIdSubFree(). */
 {
 struct docIdSub *ret;
 
 AllocVar(ret);
 ret->ix = sqlSigned(row[0]);
 ret->status = sqlSigned(row[1]);
 ret->assembly = cloneString(row[2]);
 ret->submitDate = cloneString(row[3]);
 ret->md5sum = cloneString(row[4]);
 ret->valReport = cloneString(row[5]);
 ret->valVersion = cloneString(row[6]);
 ret->metaData = cloneString(row[7]);
 ret->submitPath = cloneString(row[8]);
 ret->submitter = cloneString(row[9]);
 return ret;
 }
 
 struct docIdSub *docIdSubLoadAll(char *fileName) 
 /* Load all docIdSub from a whitespace-separated file.
  * Dispose of this with docIdSubFreeList(). */
 {
 struct docIdSub *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileRow(lf, row))
     {
     el = docIdSubLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct docIdSub *docIdSubLoadAllByChar(char *fileName, char chopper) 
 /* Load all docIdSub from a chopper separated file.
  * Dispose of this with docIdSubFreeList(). */
 {
 struct docIdSub *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[10];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = docIdSubLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct docIdSub *docIdSubCommaIn(char **pS, struct docIdSub *ret)
 /* Create a docIdSub out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new docIdSub */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->ix = sqlSignedComma(&s);
 ret->status = sqlSignedComma(&s);
 ret->assembly = sqlStringComma(&s);
 ret->submitDate = sqlStringComma(&s);
 ret->md5sum = sqlStringComma(&s);
 ret->valReport = sqlStringComma(&s);
 ret->valVersion = sqlStringComma(&s);
 ret->metaData = sqlStringComma(&s);
 ret->submitPath = sqlStringComma(&s);
 ret->submitter = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void docIdSubFree(struct docIdSub **pEl)
 /* Free a single dynamically allocated docIdSub such as created
  * with docIdSubLoad(). */
 {
 struct docIdSub *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->assembly);
 freeMem(el->submitDate);
 freeMem(el->md5sum);
 freeMem(el->valReport);
 freeMem(el->valVersion);
 freeMem(el->metaData);
 freeMem(el->submitPath);
 freeMem(el->submitter);
 freez(pEl);
 }
 
 void docIdSubFreeList(struct docIdSub **pList)
 /* Free a list of dynamically allocated docIdSub's */
 {
 struct docIdSub *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     docIdSubFree(&el);
     }
 *pList = NULL;
 }
 
 void docIdSubOutput(struct docIdSub *el, FILE *f, char sep, char lastSep) 
 /* Print out docIdSub.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%d", el->ix);
 fputc(sep,f);
 fprintf(f, "%d", el->status);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->assembly);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->submitDate);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->md5sum);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->valReport);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->valVersion);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->metaData);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->submitPath);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->submitter);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 char *docIdDecorate(char *composite, char *cellType, int num)
 {
 char buffer[10 * 1024];
 
 safef(buffer, sizeof buffer, "%s%sD%09d",composite, cellType, num);
 return cloneString(buffer);
 }
 
 
 boolean fileIsCompressed(char *fileName)
 {
 char *dot = strrchr(fileName, '.');
 
 if (dot == NULL)
     return FALSE;
 
 dot++;
 
 if (sameString(dot, "bam") ||
     sameString(dot, "bigWig") ||
     sameString(dot, "gz"))
     return TRUE;
 
 return FALSE;
 }
 
 char *docDecorateType(char *type)
 // add .gz for types that should be compressed
 {
 if (sameString(type, "bam") ||
     sameString(type, "bigWig"))
         return type;
 
 char *ptr;
 
 if ((ptr = strchr(type, ' ')) != NULL)
     *ptr = 0;
 
 char buffer[10 * 1024];
 
 safef(buffer, sizeof buffer, "%s.gz", type);
 
 if (ptr)
     *ptr = ' ';
 
 return cloneString(buffer);
 }
 
 char *docIdGetPath(char *docId, char *docIdDir, char *type, char *submitPath)
 {
 char *ptr = docId + strlen(docId) - 1;
-struct dyString *dy = newDyString(20);
+struct dyString *dy = dyStringNew(20);
 char *suffix = docDecorateType(type);
 
 dyStringPrintf(dy, "%s/", docIdDir);
 for (; ptr != docId; ptr--)
     {
     dyStringPrintf(dy, "%c/", *ptr);   
     }
 
 dyStringPrintf(dy, "%s.%s", docId, suffix);
 
 return dyStringCannibalize(&dy);
 }
 
 char *nullString = "";
 
 void fillNull(char **val)
 {
 if (*val == NULL)
     *val = nullString;
 }
 
 char *docIdSubmit(struct sqlConnection *conn, char *docIdTable, struct docIdSub *docIdSub, 
     char *docIdDir, char *type)
 {
 
 verbose(2, "Submitting------\n");
 verbose(2, "status %d\n", docIdSub->status);
 verbose(2, "assembly %s\n", docIdSub->assembly);
 verbose(2, "submitDate %s\n", docIdSub->submitDate);
 verbose(2, "md5sum %s\n", docIdSub->md5sum);
 verbose(2, "valReport %s\n", docIdSub->valReport);
 verbose(2, "valVersion %s\n", docIdSub->valVersion);
 verbose(2, "metaData %s\n", docIdSub->metaData);
 verbose(2, "submitPath %s\n", docIdSub->submitPath);
 verbose(2, "submitter %s\n", docIdSub->submitter);
 verbose(2, "type %s\n", type);
 
 char query[1024 * 1024];
 
 fillNull(&docIdSub->valReport);
 fillNull(&docIdSub->md5sum);
 
 sqlSafef(query, sizeof query, "insert into %s (status, assembly, submitDate, md5sum, valReport, valVersion, metaData, submitPath, submitter) values (\"%d\",\"%s\",\"%s\",\"%s\", \"%s\", \"%s\", \"%s\",\"%s\",\"%s\")\n", docIdTable,
     docIdSub->status, docIdSub->assembly, docIdSub->submitDate, docIdSub->md5sum, docIdSub->valReport, docIdSub->valVersion, docIdSub->metaData, docIdSub->submitPath, docIdSub->submitter);
     //docIdSub->submitDate, docIdSub->md5sum, docIdSub->valReport, "null", docIdSub->submitPath, docIdSub->submitter);
 //printf("query is %s\n", query);
 char *response = sqlQuickString(conn, query);
 
 printf("submitted got response %s\n", response);
 
 sqlSafef(query, sizeof query, "select last_insert_id()");
 char *docId = cloneString(sqlQuickString(conn, query));
 
 printf("submitted got docId %s\n", docId);
 
 
 if (!fileExists(docIdSub->submitPath))
     errAbort("cannot open %s\n", docIdSub->submitPath);
 char *linkToFile = docIdGetPath(docId, docIdDir, type, docIdSub->submitPath);
 
 printf("linking %s to file %s\n", docIdSub->submitPath, linkToFile);
 char *slash = strrchr(linkToFile, '/');
 if (slash == NULL)
     errAbort("can't find slash in path %s\n", linkToFile);
 
 *slash = 0;
 makeDirsOnPath(linkToFile);
 *slash = '/';
 if (link(docIdSub->submitPath, linkToFile) < 0)
     errnoAbort("can't link %s to file %s\n", docIdSub->submitPath, linkToFile);
 
 return docId;
 }