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/facetField.c src/hg/lib/facetField.c
index 8e44dc3..b80d7f8 100644
--- src/hg/lib/facetField.c
+++ src/hg/lib/facetField.c
@@ -1,484 +1,484 @@
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "fieldedTable.h"
 #include "facetField.h"
 #include "csv.h"
 
 int facetValCmpSelectCountDesc(const void *va, const void *vb)
 /* Compare two facetVal so as to sort them based on selectCount with most used first.
  * If two have same count, sort alphabetically on facet val.  */
 {
 struct facetVal *a = *((struct facetVal **)va);
 struct facetVal *b = *((struct facetVal **)vb);
 int result = b->selectCount - a->selectCount;
 if (result == 0)
     {
     result = strcmp(a->val, b->val);
     }
 return result;
 }
 
 static int facetValCmpUseCountDesc(const void *va, const void *vb)
 /* Compare two facetVal so as to sort them based on useCount with most used first */
 {
 struct facetVal *a = *((struct facetVal **)va);
 struct facetVal *b = *((struct facetVal **)vb);
 return b->useCount - a->useCount;
 }
 
 int facetValCmp(const void *va, const void *vb)
 /* Compare two facetVal alphabetically by val */
 {
 struct facetVal *a = *((struct facetVal **)va);
 struct facetVal *b = *((struct facetVal **)vb);
 return cmpWordsWithEmbeddedNumbers(a->val, b->val);
 }
 
 struct facetVal *facetsClone(struct facetVal *origList)
 /* Copy the facet vals list */
 {
 
 struct facetVal *newList = NULL;
 struct facetVal *o;  // original element
 for (o = origList; o != NULL; o = o->next)
     {
 
     struct facetVal *n;   // new element
     AllocVar(n);
     n->val = o->val;
     n->useCount = o->useCount;
     n->selected = o->selected;
     n->selectCount = o->selectCount;
 
     slAddHead(&newList, n);
     }
 
 /* Restore reversed order and return result */
 slReverse(&newList);
 
 return newList;
 }
 
 
 static struct facetVal *facetValNew(char *val, int useCount)
 /* Create new facetVal structure */
 {
 struct facetVal *facetVal;
 AllocVar(facetVal);
 facetVal->val = val;
 facetVal->useCount = useCount;
 return facetVal;
 }
 
 int facetFieldCountSelected(struct facetField *facetField)
 /* Return number of facets in list that are selected */
 {
 if (facetField->allSelected)
     return slCount(facetField->valList);
 else
     {
     int count = 0;
     struct facetVal *facetVal;
     for (facetVal = facetField->valList; facetVal != NULL; facetVal = facetVal->next)
 	if (facetVal->selected)
 	    ++count;
     return count;
     }
 }
 
 static void facetFieldAdd(struct facetField *facetField, char *tagVal, boolean selecting)
 /* Add information about tag to facetField */
 {
 if (!selecting)
     facetField->useCount += 1;
 struct facetVal *facetVal = hashFindVal(facetField->valHash, tagVal);
 if (facetVal == NULL)
     {
     AllocVar(facetVal);
     hashAddSaveName(facetField->valHash, tagVal, facetVal, &facetVal->val);
     slAddHead(&facetField->valList, facetVal);
     if (selecting)
 	{
 	facetVal->selected = TRUE;
 	facetField->allSelected = FALSE;
 	}
     if (facetField->allSelected)
 	facetVal->selected = TRUE;
     }
 if (!selecting)
     facetVal->useCount += 1;
 facetField->currentVal = facetVal;
 }
 
 static struct facetField *facetFieldNew(char *fieldName)
 /* Create a new facetField structure */
 {
 struct facetField *facetField;
 AllocVar(facetField);
 facetField->fieldName = cloneString(fieldName);
 facetField->valHash = hashNew(0);
 facetField->allSelected = TRUE;  // default to all values selected
 return facetField;
 }
 
 boolean perRowFacetFields(int fieldCount, char **row, char *nullVal, struct facetField *ffArray[])
 /* Process each row of a resultset updating use and select counts. 
  * Returns TRUE if row passes selected facet values filter and should be included in the final result set. */
 {
 boolean result = FALSE;
 int totalSelectedFacets = 0;
 int facetCount = 0;  // non-NULL facet count
 int i;
 for (i=0; i<fieldCount; ++i)
     {
     struct facetField *ff = ffArray[i];
     char *val = row[i];
     if (val == NULL)
 	val = nullVal;
     if (val != NULL)
 	{
 	facetFieldAdd(ff, val, FALSE);
 	if (ff->currentVal->selected)
 	    ++totalSelectedFacets;
 	++facetCount;
 	}
     else
 	{
 	ff->currentVal = NULL;
 	}
     }
 
 if ((totalSelectedFacets == facetCount) && (facetCount > 0))
     {
     // include this row in the final resultset
     result = TRUE;
     }
 for (i=0; i<fieldCount; ++i)
     {
     struct facetField *ff = ffArray[i];
     if (ff->currentVal) // disregard null values
 	{
 	// disregard one's self.
 	if ((totalSelectedFacets - (int)ff->currentVal->selected) == (facetCount - 1))
 	    ff->currentVal->selectCount++;
 	    // shown on GUI to guide choosing by user
 	}
     }
 return result;
 }
 
 #define facetValStringPunc '~'
 
 char *linearizeFacetVals(struct facetField *selectedList)
 /* Linearize selected fields vals into a string. fieldVal must be selected. */
 {
-struct dyString *dy = newDyString(1024);
+struct dyString *dy = dyStringNew(1024);
 struct facetField *sff = NULL;
 for (sff = selectedList; sff; sff=sff->next)
     {
     dyStringPrintf(dy, "%s %d%d ", sff->fieldName, sff->showAllValues, sff->isMerged);
     boolean first = TRUE;
     struct facetVal *el;
     for (el=sff->valList; el; el=el->next)
 	{
 	if (el->selected)
 	    {
 	    if (first)
 		{
 		first = FALSE;
 		}
 	    else
 		dyStringAppendC(dy, ',');
 	    // TODO encode as csv val to support doubled internal quote value?
 	    dyStringPrintf(dy, "\"%s\"", el->val);  
 	    }
 	}
     dyStringAppendC(dy, facetValStringPunc);
     }
 return dyStringCannibalize(&dy);
 }
 
 void selectedListFacetValUpdate(struct facetField **pSelectedList, char *facetName, char *facetValue, char *op)
 /* Add or remove by changing selected boolean
  * Reset entire facet by setting all vals to selected = false for the facet */
 {
 struct facetField *selectedList = *pSelectedList;
 struct facetField *sff = NULL;
 if (sameString(op, "resetAll"))  // remove all selections
     {
     *pSelectedList = NULL;
     return;
     }
 
 for (sff = selectedList; sff; sff=sff->next)
     {
     if (sameString(sff->fieldName, facetName))
 	{
 	break;
 	}
     }
 if (!sff)
     {
     sff = facetFieldNew(facetName);
     slAddHead(&selectedList, sff);
     }
 
 if (sameString(op, "add"))
     {
     facetFieldAdd(sff, facetValue, TRUE);
     sff->currentVal->selected = TRUE;
     }
 else if (sameString(op, "remove"))
     {
     facetFieldAdd(sff, facetValue, TRUE);
     sff->currentVal->selected = FALSE;
     }
 else if (sameString(op, "showAllValues"))  // show all facet values
     {
     sff->showAllValues = TRUE;
     }
 else if (sameString(op, "showSomeValues"))  // show all facet values
     {
     sff->showAllValues = FALSE;
     }
 else if (sameString(op, "reset"))
     {
     sff->showAllValues = FALSE;
     sff->isMerged = FALSE;
     struct facetVal *el;
     for (el=sff->valList; el; el=el->next)
 	{
 	el->selected = FALSE;
 	}
     }
 else if (sameString(op, "merge"))
     {
     sff->isMerged = TRUE;
     }
 else if (sameString(op, "unmerge"))
     {
     sff->isMerged = FALSE;
     }
 *pSelectedList = selectedList;
 }
 
 struct facetField *deLinearizeFacetValString(char *selectedFields)
 /* Turn linearized selected fields string back into facet structures */
 {
 if (selectedFields == NULL) return NULL;  // Empty input means empty output
 struct facetField *ffList = NULL, *ff;
 boolean done = FALSE;
 while (!done)
     {
     if (sameString(selectedFields, ""))
 	break;
     char *end = strchr(selectedFields, facetValStringPunc);
     if (!end)
 	{
 	end = selectedFields + strlen(selectedFields);
 	done = TRUE;
 	}
     char saveEnd = *end;
     *end = 0;
     char *spc = strchr(selectedFields, ' ');
     if (!spc)
 	errAbort("expected space separating fieldname from showAllValues boolean");
     *spc = 0;
 
     char *flagsBoolean = spc+1;
     char *spc2 = strchr(flagsBoolean, ' ');
     if (!spc2)
 	errAbort("expected space separating showAllValues boolean from facet values list");
     *spc2 = 0;
 
     char *vals = spc2+1;
     struct slName *valList = NULL;
     if (*vals != 0)  // we have something
 	valList = csvParse(vals);
 
     ff = facetFieldNew(selectedFields);
     ff->showAllValues = (flagsBoolean[0] == '1');
     ff->isMerged = (flagsBoolean[1] == '1');
 
     slAddHead(&ffList, ff);
     struct slName *el;
     for (el=valList; el; el=el->next)
 	{
 	facetFieldAdd(ff, el->name, TRUE);
 	}
     
     *spc  = ' ';  // restore
     *spc2 = ' ';  // restore
     *end = saveEnd;
     selectedFields = end+1;
     }
 slReverse(&ffList);
 return ffList;
 }
 
 
 struct facetField *facetFieldsFromSqlTableInit(char *fields[], int fieldCount, char *selectedFields, struct facetField *ffArray[])
 /* Initialize ffList and ffArray and selected facet values */
 {
 /* Create facetField list and table. */
 struct facetField *ffList = NULL, *ff;
 int i;
 for (i=0; i<fieldCount; ++i)
     {
     ff = ffArray[i] = facetFieldNew(fields[i]);
     slAddHead(&ffList, ff);
     }
 slReverse(&ffList);
 
 /* Initialize selected facet values */
 if (selectedFields)
     {
     struct facetField *selectedList = deLinearizeFacetValString(selectedFields);
     struct facetField *sff = NULL;
     for (sff = selectedList; sff; sff=sff->next)
 	{
 	for (i=0; i<fieldCount; ++i)
 	    {
 	    if (sameString(ffArray[i]->fieldName, sff->fieldName))
 		{
 		ffArray[i]->showAllValues = sff->showAllValues;
 		ffArray[i]->isMerged = sff->isMerged;
 		struct facetVal *el;
 		for (el=sff->valList; el; el=el->next)
 		    {
 		    facetFieldAdd(ffArray[i], el->val, TRUE);
 		    }
 		}
 	    }
         
 	}
     }
 return ffList;
 }
 
 void facetFieldsFromSqlTableFinish(struct facetField *ffList, int (*compare )(const void *elem1,  const void *elem2))
 /* Do final cleanup after passing over rows */
 {
 /* Sort lists */
 struct facetField *ff;
 for (ff = ffList; ff != NULL; ff = ff->next)
     slSort(&ff->valList, compare);
 }
 
 
 struct facetField *facetFieldsFromSqlTable(struct sqlConnection *conn, char *table, char *fields[], int fieldCount, 
     char *nullVal, char *where, char *selectedFields, int *pSelectedRowCount)
 /* Return a list of facetField, one for each field of given table */
 {
 
 /* Make query string */
 struct dyString *query = dyStringNew(0);
 sqlDyStringPrintf(query, "select %s", fields[0]);
 int i;
 for (i=1; i<fieldCount; ++i)
     {
     sqlDyStringPrintf(query, ",");
     sqlDyStringPrintf(query, "%s", fields[i]);
     }
 sqlDyStringPrintf(query, " from %s", table);
 if (where != NULL)
     sqlDyStringPrintf(query, " where %-s", where); // trusting where-clause
 
 
 struct facetField *ffArray[fieldCount];
 struct facetField *ffList = facetFieldsFromSqlTableInit(fields, fieldCount, selectedFields, ffArray);
 
 int selectedRowCount = 0;
 
 /* Scan through result saving it in list. */
 struct sqlResult *sr = sqlGetResult(conn, query->string);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (perRowFacetFields(fieldCount, row, nullVal, ffArray))
 	++selectedRowCount;
     }
 
 facetFieldsFromSqlTableFinish(ffList, facetValCmpUseCountDesc);
 
 /* Clean up and go home */
 dyStringFree(&query);
 sqlFreeResult(&sr);
 
 if (pSelectedRowCount)
     *pSelectedRowCount = selectedRowCount;
 return ffList;
 }
 
 // struct fieldedTable *facetFieldsFromFieldedTable(struct fieldedTable *ft, char *selectionKey,
 struct fieldedTable *facetFieldSelectRows(struct fieldedTable *ft, char *selectionKey,
     struct facetField *ffArray[])
 /* Return a tables that is just rows of table ft that pass selection key.  ffArray should
  * have same number of elements as ft->fieldCount */
 {
 int fieldCount = ft->fieldCount;
 struct fieldedTable *subTable = fieldedTableNew(ft->name, ft->fields, fieldCount);
 struct facetField *ffList = facetFieldsFromSqlTableInit(ft->fields, fieldCount, 
     selectionKey, ffArray);
 struct fieldedRow *fr;
 for (fr = ft->rowList; fr != NULL; fr = fr->next)
     {
     if (perRowFacetFields(fieldCount, fr->row, "", ffArray))
 	{
 	fieldedTableAdd(subTable, fr->row, fieldCount, fr->id);
 	}
     }
 facetFieldsFromSqlTableFinish(ffList, facetValCmpUseCountDesc);
 return subTable;
 }
 
 struct facetVal *facetValMajorPlusOther(struct facetVal *list, double minRatio)
 /* Return a list of only the tags that are over minRatio of total tags.
  * If there are tags that have smaller amounts than this, lump them together
  * under "other".  Returns a new list. Use slFreeList() to free the result.  */
 {
 /* Figure out total and minimum count to not be lumped into other */
 long total = 0;
 struct facetVal *tc;
 for (tc = list; tc != NULL; tc = tc->next)
     total += tc->useCount;
 long minCount = round(minRatio * total);
 
 /* Loop through and copy ones over threshold to new list, and lump rest
  * into other */
 struct facetVal *newList = NULL, *newTc;
 struct facetVal *other = NULL;
 int otherCount = 0;
 for (tc = list; tc != NULL; tc = tc->next)
     {
     if (tc->useCount >= minCount)
         {
 	newTc = facetValNew(tc->val, tc->useCount);
 	slAddHead(&newList, newTc);
 	}
     else
         {
 	if (other == NULL)
 	    other = facetValNew("", 0);
 	other->useCount += tc->useCount;
 	++otherCount;
 	}
     }
 
 /* Put other onto new list if it exists */
 if (other != NULL)
     {
     char label[64];
     safef(label, sizeof(label), "%d other", otherCount);
     other->val = cloneString(label);
     slAddHead(&newList, other);
     }
 
 /* Restore reversed order and return result */
 slReverse(&newList);
 return newList;
 }