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/utils/ccCp/ccCp.c src/utils/ccCp/ccCp.c
index 2feb882..9bb3195 100644
--- src/utils/ccCp/ccCp.c
+++ src/utils/ccCp/ccCp.c
@@ -1,440 +1,440 @@
 /* ccCp - copy file to the cluster efficiently.  Uses child process
  * tracking mechanism. */
 
 /* Copyright (C) 2011 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 "dlist.h"
 #include "portable.h"
 #include "dystring.h"
 #include "options.h"
 #include <sys/wait.h>
 
 
 int crossSwitchMax = 40;		/* Max copies between switches at once. */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
 "ccCp - copy a file to cluster."
 "usage:\n"
 "   ccCp sourceFile destFile [hostList]\n"
 "This will copy sourceFile to destFile for all machines in\n"
 "hostList\n"
 "options\n"
 "    -crossMax=N (default %d) - maximum copies across switches\n"
 "example:\n"
 "   ccCp h.zip /var/tmp/h.zip newHosts"
 	, crossSwitchMax);
 }
 
 enum 	/* Constants. */
     {
     maxErrCount = 3,	/* Max number of errors before giving up. */
     };
 
 struct netSwitch
 /* Keep track of a network switch. */
     {
     struct netSwitch *next;	/* Next switch. */
     char *name;			/* Switch name. */
     int machCount;              /* Number of machines on this switch. */
     struct machine *machList;	/* The machines this is hooked to. */
     };
 
 struct machine
 /* Keep track of one machine in cluster. */
     {
     struct machine *next;
     char *name;		/* Name (like cc08) */
     struct netSwitch *netSwitch;  /* Which switch this is on. */
     int errCount;       /* Number of times have gotten error. */
     int pid;            /* Process ID if copying. */
     int status;         /* Status. */
     struct dlNode *sourceNode; /* Source node in copy. */
     };
 
 int crossSwitchCount = 0;	/* Current copies between switches. */
 
 boolean matchMaker(struct dlList *finList, struct dlList *toDoList, 
 	struct dlNode **retSourceNode, struct dlNode **retDestNode)
 /* Find a copy to make from the finished list to the toDo list. */
 {
 struct dlNode *sourceNode, *destNode = NULL;
 struct machine *source, *dest;
 bool gotIt = FALSE;
 
 for (sourceNode = finList->head; sourceNode->next != NULL; sourceNode = sourceNode->next)
     {
     source = sourceNode->val;
     for (destNode = toDoList->head; destNode->next != NULL; destNode = destNode->next)
 	{
 	dest = destNode->val;
 	if (dest->netSwitch == source->netSwitch)
 	    {
 	    gotIt = TRUE;
 	    break;
 	    }
 	if (crossSwitchCount < crossSwitchMax)
 	    {
 	    ++crossSwitchCount;
 	    gotIt = TRUE;
 	    break;
 	    }
 	}
     if (gotIt)
 	break;
     }
 if (!gotIt)
     return FALSE;
 dlRemove(sourceNode);
 dlRemove(destNode);
 *retSourceNode = sourceNode;
 *retDestNode = destNode;
 //uglyf("Matched (%s %s) and (%s %s) cross %d\n",
 //	source->name, source->netSwitch->name,
 //	dest->name, dest->netSwitch->name, crossSwitchCount);
 return TRUE;
 }
 
 struct netSwitch *findSwitch(struct netSwitch *nsList, char *name)
 /* Return matching switch or NULL if none. */
 {
 struct netSwitch *ns;
 for (ns = nsList; ns != NULL; ns = ns->next)
     if (sameString(ns->name, name))
 	return ns;
 return NULL;
 }
 
 int netSwitchCmp(const void *va, const void *vb)
 /* Compare two netSwitchs to sort with most nodes first. */
 {
 const struct netSwitch *a = *((struct netSwitch **)va);
 const struct netSwitch *b = *((struct netSwitch **)vb);
 return b->machCount - a->machCount;
 }
 
 char *fullPathName(char *relName)
 /* Return full version of path name. */
 {
 char firstChar = relName[0];
 char fullPath[512];
 char dir[512];
 
 if (firstChar == '/' || firstChar == '~')
     return cloneString(relName);
 if (getcwd(dir, sizeof(dir)) == NULL)
     errAbort("fullPathName: getcwd failed!");
 sprintf(fullPath, "%s/%s", dir, relName);
 return cloneString(fullPath);
 }
 
 struct machine *shuffleSwitches(struct netSwitch *nsList)
 /* Return machine list that is shuffled from switch to switch. */
 {
 struct netSwitch *ns;
 struct machine *machList = NULL, *mach;
 bool gotAny = TRUE;
 int iteration = 0;
 int machineIx;
 
 while (gotAny)
     {
     ++iteration;
     machineIx = 0;
     gotAny = FALSE;
     for (ns = nsList; ns != NULL; ns = ns->next)
 	{
 	++machineIx;
 	if (ns->machList != NULL)
 	    {
 	    mach = ns->machList;
 	    ns->machList = mach->next;
 	    slAddHead(&machList, mach);
 	    gotAny = TRUE;
 	    if (machineIx >= iteration)	  /* Seed biggest switches first. */
 		break;
 	    }
 	}
     }
 slReverse(&machList);
 return machList;
 }
 
 void readHosts(char *hostList, struct machine **retMachineList, struct netSwitch **retNsList)
 /* Create list of all machines from hostList. */
 {
 struct lineFile *lf = lineFileOpen(hostList, TRUE);
 struct machine *machList = NULL, *mach;
 struct netSwitch *nsList = NULL, *ns;
 char *line, *words[4];
 int lineSize, wordCount;
 char *switchName;
 
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '#')
 	continue;
     wordCount = chopLine(line, words);
     if (wordCount < 1 || wordCount > 2)
 	errAbort("Expecting one or two words line %d of %s", lf->lineIx, lf->fileName);
     AllocVar(mach);
     mach->name = cloneString(words[0]);
     if (wordCount > 1)
 	switchName = words[1];
     else
     	switchName = "1";
     if ((ns = findSwitch(nsList, switchName)) == NULL)
 	{
 	AllocVar(ns);
 	ns->name = cloneString(switchName);
 	slAddHead(&nsList, ns);
 	}
     mach->netSwitch = ns;
     ns->machCount += 1;
     slAddHead(&ns->machList, mach);
     }
 for (ns = nsList; ns != NULL; ns = ns->next)
     slReverse(&ns->machList);
 slSort(&nsList, netSwitchCmp);
 machList = shuffleSwitches(nsList);
 *retMachineList = machList;
 *retNsList = nsList;
 }
 
 void dlAddMiddle(struct dlList *list, struct dlNode *node)
 /* Add node to approximate middle of list. */
 {
 int listSize = dlCount(list);
 int midPos = listSize/2;
 if (midPos <= 0)
     dlAddTail(list, node);
 else
     {
     struct dlNode *ln = list->head;
     int i;
     for (i=0; i<midPos; ++i)
 	ln = ln->next;
     dlAddAfter(ln, node);
     }
 }
 
 void startCopy(struct machine *source, struct machine *dest, char *file, 
 	char *thisHost, struct dyString *cmd)
 /* Copy file from source to dest machine by executing rcp on dest, using cmd as
  * place to put the system call command. */
 {
 int childPid;
 
 dyStringClear(cmd);
 if (!sameString(thisHost, dest->name))
     dyStringPrintf(cmd, "rsh %s ", dest->name);
 dyStringPrintf(cmd, "rcp %s:%s %s", source->name, file, file);
 childPid = fork();
 if (childPid)
     {
     dest->pid = childPid;
     }
 else
     {
     int err;
     err = system(cmd->string);
     if (err != 0)
 	err = -1;
     exit(err);
     }
 }
 
 void ccCp(char *source, char *dest, char *hostList)
 /* Copy source to dest on all files in hostList. */
 {
 time_t startTime = time(NULL);
 time_t curTime, lastTime = 0;
 struct machine *machineList = NULL;
 struct netSwitch *nsList;
 struct machine *m, *m2;
 struct dlList *toDoList = newDlList();          /* We haven't done these. */
 struct dlList *finishedList = newDlList();	/* All done here. */
 struct dlList *sourceList = newDlList();        /* These are sources for copies. */
 struct dlList *workingList = newDlList();       /* These are copying data to themselves. */
 struct dlList *errList = newDlList();           /* These are messed up 3x or more. */
 struct dlNode *finNode, *node, *sourceNode, *destNode;
-struct dyString *cmd = newDyString(256);
+struct dyString *cmd = dyStringNew(256);
 int machineCount;
 int machinesFinished = 0;
 char *thisHost = getenv("HOST");
 off_t size;
 int goodMachines;
 double grandTotal;
 
 /* Get host and switch info. */
 readHosts(hostList, &machineList, &nsList);
 machineCount = slCount(machineList);
 
 /* Make sure file exists.... */
 if (!fileExists(source))
     errAbort("%s doesn't exist\n", source);
 size = fileSize(source);
 printf("Copying %s (%lld bytes) to %d machines\n", source, (unsigned long long)size, machineCount);
 
 /* Add everything to the to-do list. */
 for (m = machineList; m != NULL; m = m->next)
     {
     dlAddValTail(toDoList, m);
     }
 
 
 /* Loop through to-do list trying to do first copy. */
 for (node = toDoList->head; node->next != NULL; node = node->next)
     {
     m = node->val;
     dyStringClear(cmd);
     m = node->val;
     if (sameString(thisHost, m->name))
 	{
 	if (sameString(source, dest))
 	    {
 	    /* Hey, this is too easy. */
 	    ++machinesFinished;
 	    break;
 	    }
 	else
 	    {
 	    dyStringPrintf(cmd, "cp %s %s", source, dest);
 	    }
 	}
     else
 	{
 	dyStringPrintf(cmd, "rcp %s %s:%s", source, m->name, dest);
 	}
     if (system(cmd->string) == 0)
 	{
 	dlRemove(node);
 	dlAddTail(finishedList, node);
 	++machinesFinished;
 	break;
 	}
     else  /* some error in rcp */
 	{
 	warn("Problem with %s\n", cmd->string);
 	m->errCount += 1;
 	}
     }
 
 /* Loop around launching child processes to copy and
  * wait for them to finish. */
 while (machinesFinished < machineCount)
     {
     int pid;
     int status;
 
     /* Start all possible copies. */
     while (matchMaker(finishedList, toDoList, &sourceNode, &destNode))
 	{
 	dlAddTail(sourceList, sourceNode);
 	dlAddTail(workingList, destNode);
 	m = destNode->val;
 	m->sourceNode = sourceNode;
 	startCopy(sourceNode->val, destNode->val, dest, thisHost, cmd);
 	}
 
     curTime = time(NULL);
     if (curTime - lastTime >= 3)
 	{
 	printf("%d finished in %d seconds, %d in progress, %d to start, %d errors, %d total\n",
 	    dlCount(finishedList) + dlCount(sourceList), (int)(curTime - startTime),
 	    dlCount(workingList), dlCount(toDoList), dlCount(errList), machineCount);
 	lastTime = curTime;
 	}
 
     /* Wait for a child to finish.  Figure out which machine it is. */
     pid = wait(&status);
     finNode = NULL;
     for (node = workingList->head; node->next != NULL; node = node->next)
 	{
 	m = node->val;
 	if (m->pid == pid)
 	    {
 	    finNode = node;
 	    break;
 	    }
 	}
     if (finNode == NULL)
 	{
 	errAbort("Returned from wait on unknown child %d\n", pid);
 	continue;
 	}
 
     m = finNode->val;
     m->pid = 0;
     dlRemove(finNode);
     dlRemove(m->sourceNode);
     m2 = m->sourceNode->val;
     if (m->netSwitch != m2->netSwitch)
 	--crossSwitchCount;
     dlAddTail(finishedList, m->sourceNode);
 
     if (WIFEXITED(status) && WEXITSTATUS(status) == 0)
 	{
 	/* Good return - move self and source node to finished list. */
 	++machinesFinished;
 	dlAddTail(finishedList, finNode);
 	}
     else
 	{
 	/* Bad return.  Increment error count, and maybe move it to
 	 * error list. */
 	if (++m->errCount >= maxErrCount)
 	    {
 	    ++machinesFinished;
 	    dlAddTail(errList, finNode);
 	    fprintf(stderr, "Gave up on %s\n", m->name);
 	    }
 	else
 	    {
 	    dlAddMiddle(toDoList, finNode);
 	    fprintf(stderr, "Retry %d on %s\n", m->errCount, m->name);
 	    }
 	}
     }
 if (!dlEmpty(errList))
     {
     fprintf(stderr, "errors in:");
     for (node = errList->head; node->next != NULL; node = node->next)
 	{
 	m = node->val;
 	fprintf(stderr, " %s", m->name);
 	}
     fprintf(stderr, "\n");
     }
 goodMachines = dlCount(finishedList);
 grandTotal = (double)goodMachines * (double)size;
 printf("Copied to %d of %d machines (grand total %e bytes) in %d seconds\n", 
 	goodMachines, machineCount, grandTotal, (int)(time(NULL) - startTime));
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 char *source, *dest, *hostList;
 
 optionHash(&argc, argv);
 crossSwitchMax = optionInt("crossMax", crossSwitchMax);
 if (argc != 3 && argc != 4)
     usage();
 source = argv[1];
 dest = argv[2];
 if (argc == 4)
     {
     hostList = argv[3];
     hostList = fullPathName(hostList);
     }
 else
     hostList = "/projects/compbio/experiments/hg/switchList";
 ccCp(source, dest, hostList);
 return 0;
 }