824cd5d39b0a42abe0394e0cee41b705259c63bd
braney
  Tue Aug 30 11:15:38 2011 -0700
use safef instead of strcpy.  What was I thinking?
diff --git src/hg/lib/hubConnect.c src/hg/lib/hubConnect.c
index 1673481..ce1798a 100644
--- src/hg/lib/hubConnect.c
+++ src/hg/lib/hubConnect.c
@@ -1,585 +1,585 @@
 /* hubConnect - stuff to manage connections to track hubs.  Most of this is mediated through
  * the hubConnect table in the hgCentral database.  Here there are routines to translate between
  * hub symbolic names and hub URLs,  to see if a hub is up or down or sideways (up but badly
  * formatted) etc.  Note that there is no C structure corresponding to a row in the hubConnect 
  * table by design.  We just want field-by-field access to this. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "dystring.h"
 #include "sqlNum.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "net.h"
 #include "trackHub.h"
 #include "hubConnect.h"
 #include "hui.h"
 #include "errCatch.h"
 #include "obscure.h"
 
 
 boolean isHubTrack(char *trackName)
 /* Return TRUE if it's a hub track. */
 {
 return startsWith(hubTrackPrefix, trackName);
 }
 
 boolean hubConnectTableExists()
 /* Return TRUE if the hubConnect table exists. */
 {
 struct sqlConnection *conn = hConnectCentral();
 boolean exists = sqlTableExists(conn, hubPublicTableName);
 hDisconnectCentral(&conn);
 return exists;
 }
 
 void hubConnectStatusFree(struct hubConnectStatus **pHub)
 /* Free hubConnectStatus */
 {
 struct hubConnectStatus *hub = *pHub;
 if (hub != NULL)
     {
     freeMem(hub->shortLabel);
     freeMem(hub->longLabel);
     freeMem(hub->hubUrl);
     freeMem(hub->errorMessage);
     if (hub->dbArray)
         {
 	freeMem(hub->dbArray[0]);
 	freeMem(hub->dbArray);
 	}
     freez(pHub);
     }
 }
 
 void hubConnectStatusFreeList(struct hubConnectStatus **pList)
 /* Free a list of dynamically allocated hubConnectStatus's */
 {
 struct hubConnectStatus *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     hubConnectStatusFree(&el);
     }
 *pList = NULL;
 }
 
 static void hubConnectRemakeTrackHubVar(struct cart *cart)
 /* Remake trackHub cart variable if need be from various check box vars. */
 {
 if (cartVarExists(cart, hgHubConnectRemakeTrackHub))
     {
     struct slPair *hubVarList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
     int prefixLength = strlen(hgHubConnectHubVarPrefix);
     struct dyString *trackHubs = dyStringNew(0);
     struct slPair *hubVar;
     boolean firstOne = TRUE;
     for (hubVar = hubVarList; hubVar != NULL; hubVar = hubVar->next)
         {
 	if (cartBoolean(cart, hubVar->name))
 	    {
 	    if (firstOne)
 		firstOne = FALSE;
 	    else
 		dyStringAppendC(trackHubs, ' ');
 	    dyStringAppend(trackHubs, hubVar->name + prefixLength);
 	    }
 	}
     slPairFreeList(&hubVarList);
     cartSetString(cart, hubConnectTrackHubsVarName, trackHubs->string);
     dyStringFree(&trackHubs);
     cartRemove(cart, hgHubConnectRemakeTrackHub);
     }
 }
 
 struct slName *hubConnectHubsInCart(struct cart *cart)
 /* Return list of track hub ids that are turned on. */
 {
 hubConnectRemakeTrackHubVar(cart);
 char *trackHubString = cartOptionalString(cart, hubConnectTrackHubsVarName);
 return slNameListFromString(trackHubString, ' ');
 }
 
 static struct hubConnectStatus *hubConnectStatusForIdDb(struct sqlConnection *conn, int id)
 /* Given a hub ID return associated status. Returns NULL if no such hub.  If hub
  * exists but has problems will return with errorMessage field filled in. */
 {
 struct hubConnectStatus *hub = NULL;
 char query[1024];
 safef(query, sizeof(query), 
     "select id,shortLabel,longLabel,hubUrl,errorMessage,dbCount,dbList,status from %s where id=%d",
     hubStatusTableName, id);
 struct sqlResult *sr = sqlGetResult(conn, query);
 char **row = sqlNextRow(sr);
 if (row != NULL)
     {
     AllocVar(hub);
     hub->id = sqlUnsigned(row[0]);
     hub->shortLabel = cloneString(row[1]);
     hub->longLabel = cloneString(row[2]);
     hub->hubUrl = cloneString(row[3]);
     hub->errorMessage = cloneString(row[4]);
     hub->dbCount = sqlUnsigned(row[5]);
     int sizeOne;
     sqlStringDynamicArray(row[6], &hub->dbArray, &sizeOne);
     assert(sizeOne == hub->dbCount);
     hub->status = sqlUnsigned(row[7]);
     }
 sqlFreeResult(&sr);
 return hub;
 }
 
 boolean isHubUnlisted(struct hubConnectStatus *hub) 
 /* Return TRUE if it's an unlisted hub */
 {
     return (hub->status & HUB_UNLISTED);
 }
 
 struct hubConnectStatus *hubConnectStatusForId(struct sqlConnection *conn, int id)
 /* Given a hub ID return associated status. Returns NULL if no such hub.  If hub
  * exists but has problems will return with errorMessage field filled in. */
  /* If the id is negative, then the hub is private and the number is the
   * offset into the private hubfile in the trash */
 {
 struct hubConnectStatus *hub = NULL;
 
 hub = hubConnectStatusForIdDb(conn, id);
 
 return hub;
 }
 
 
 struct hubConnectStatus *hubConnectStatusListFromCartAll(struct cart *cart)
 /* Return list of all track hubs that are referenced by cart. */
 {
 struct hubConnectStatus *hubList = NULL, *hub;
 struct slPair *pair, *pairList = cartVarsWithPrefix(cart, hgHubConnectHubVarPrefix);
 struct sqlConnection *conn = hConnectCentral();
 for (pair = pairList; pair != NULL; pair = pair->next)
     {
     int id = hubIdFromCartName(pair->name);
     hub = hubConnectStatusForId(conn, id);
     if (hub != NULL)
 	{
         slAddHead(&hubList, hub);
 	}
     }
 slFreeList(&pairList);
 hDisconnectCentral(&conn);
 slReverse(&hubList);
 return hubList;
 }
 
 struct hubConnectStatus *hubConnectStatusListFromCart(struct cart *cart)
 /* Return list of track hubs that are turned on by user in cart. */
 {
 struct hubConnectStatus *hubList = NULL, *hub;
 struct slName *name, *nameList = hubConnectHubsInCart(cart);
 struct sqlConnection *conn = hConnectCentral();
 for (name = nameList; name != NULL; name = name->next)
     {
     int id = sqlSigned(name->name);
     hub = hubConnectStatusForId(conn, id);
     if (hub != NULL)
 	{
         slAddHead(&hubList, hub);
 	}
     }
 slFreeList(&nameList);
 hDisconnectCentral(&conn);
 slReverse(&hubList);
 return hubList;
 }
 
 int hubIdFromCartName(char *cartName)
 /* Given something like "hgHubConnect.hub.123" return 123 */
 {
 assert(startsWith("hgHubConnect.hub.", cartName));
 
 char *ptr1 = strchr(cartName, '.');
 char *ptr2 = strchr(ptr1 + 1, '.');
 
 return sqlUnsigned(ptr2+1);
 }
 
 unsigned hubIdFromTrackName(char *trackName)
 /* Given something like "hub_123_myWig" return 123 */
 {
 assert(startsWith("hub_", trackName));
 char *ptr1 = trackName;
 ptr1 += 4;
 char *ptr2 = strchr(ptr1, '_');
 
 if (ptr2 == NULL)
     errAbort("hub track %s not in correct format\n", trackName);
 char save = *ptr2;
 *ptr2 = 0;
 unsigned val = sqlUnsigned(ptr1);
 *ptr2 = save;
 return  val;
 }
 
 char *hubConnectSkipHubPrefix(char *trackName)
 /* Given something like "hub_123_myWig" return myWig.  Don't free this, it's not allocated */
 {
 assert(startsWith("hub_", trackName));
 trackName += 4;
 trackName = strchr(trackName, '_');
 assert(trackName != NULL);
 return trackName + 1;
 }
 
 struct trackHub *trackHubFromId(unsigned hubId)
 /* Given a hub ID number, return corresponding trackHub structure. 
  * ErrAbort if there's a problem. */
 {
 struct sqlConnection *conn = hConnectCentral();
 struct hubConnectStatus *status = hubConnectStatusForId(conn, hubId);
 hDisconnectCentral(&conn);
 if (status == NULL)
     errAbort("The hubId %d was not found", hubId);
 if (!isEmpty(status->errorMessage))
     errAbort("Hub %s at %s has the error: %s", status->shortLabel, 
 	    status->hubUrl, status->errorMessage);
 char hubName[16];
 safef(hubName, sizeof(hubName), "hub_%u", hubId);
 struct trackHub *hub = trackHubOpen(status->hubUrl, hubName);
 hubConnectStatusFree(&status);
 return hub;
 }
 
 static struct trackDb *findSuperTrack(struct trackDb *tdbList, char *trackName)
 /*  discover any supertracks, and if there are some add them 
  *  to the subtrack list of the supertrack */
 {
 struct trackDb *tdb;
 struct trackDb *p = NULL;
 struct trackDb *next;
 
 for(tdb = tdbList; tdb; tdb = next)
     {
     /* save away the next pointer becuase we may detach this node and
      * add it to its supertrack parent */
     next = tdb->next;
     if (tdb->parent != NULL && sameString(trackName, tdb->parent->track))
 	{
 	/* found a supertrack with the right name, add this child */
 	p = tdb->parent;
 	slAddHead(&p->subtracks, tdb);
 	}
     }
 
 return p;
 }
 
 struct trackDb *hubConnectAddHubForTrackAndFindTdb( char *database, 
     char *trackName, struct trackDb **pTdbList, struct hash *trackHash)
 /* Go find hub for trackName (which will begin with hub_), and load the tracks
  * for it, appending to end of list and adding to trackHash.  Return the
  * trackDb associated with trackName. This will also fill in the html fields,
  * but just for that track and it's parents. */ 
 {
 unsigned hubId = hubIdFromTrackName(trackName);
 struct trackHub *hub = trackHubFromId(hubId);
 struct trackHubGenome *hubGenome = trackHubFindGenome(hub, database);
 struct trackDb *tdbList = trackHubTracksForGenome(hub, hubGenome);
 tdbList = trackDbLinkUpGenerations(tdbList);
 tdbList = trackDbPolishAfterLinkup(tdbList, database);
 rAddTrackListToHash(trackHash, tdbList, NULL, FALSE);
 if (pTdbList != NULL)
     *pTdbList = slCat(*pTdbList, tdbList);
 struct trackDb *tdb = hashFindVal(trackHash, trackName);
 if (tdb == NULL) 
     // superTracks aren't in the hash... look in tdbList
     tdb = findSuperTrack(tdbList, trackName);
 
 if (tdb == NULL) 
     errAbort("Can't find track %s in %s", trackName, hub->url);
 
 /* Add html for track and parents. */
 /* Note: this does NOT add the HTML for supertrack kids */
 struct trackDb *parent;
 for (parent = tdb; parent != NULL; parent = parent->parent)
     {
     char *simpleName = hubConnectSkipHubPrefix(tdb->track);
     char *url = trackHubRelativeUrl(hubGenome->trackDbFile, simpleName);
     char buffer[10*1024];
     safef(buffer, sizeof buffer, "%s.html", url);
 
     parent->html = netReadTextFileIfExists(buffer);
     freez(&url);
     }
 trackHubClose(&hub);
 
 return tdb;
 }
 
 static void enterHubInStatus(struct trackHub *tHub, boolean unlisted)
 /* put the hub status in the hubStatus table */
 {
 struct sqlConnection *conn = hConnectCentral();
 
 /* calculate dbList */
 struct dyString *dy = newDyString(1024);
 struct hashEl *hel;
 struct hashCookie cookie = hashFirst(tHub->genomeHash);
 int dbCount = 0;
 
 while ((hel = hashNext(&cookie)) != NULL)
     {
     dbCount++;
     dyStringPrintf(dy,"%s,", hel->name);
     }
 
 
 char query[512];
 safef(query, sizeof(query), "insert into %s (hubUrl,status,shortLabel, longLabel, dbList, dbCount) values (\"%s\",%d,\"%s\",\"%s\", \"%s\", %d)",
     hubStatusTableName, tHub->url, unlisted ? 1 : 0,
     tHub->shortLabel, tHub->longLabel,
     dy->string, dbCount);
 sqlUpdate(conn, query);
 hDisconnectCentral(&conn);
 }
 
 static unsigned getHubId(char *url, char **errorMessage)
 /* find id for url in hubStatus table */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 char **row;
 boolean foundOne = FALSE;
 int id = 0;
 
 safef(query, sizeof(query), "select id,errorMessage from %s where hubUrl = \"%s\"", hubStatusTableName, url);
 
 struct sqlResult *sr = sqlGetResult(conn, query);
 
 while ((row = sqlNextRow(sr)) != NULL)
     {
     if (foundOne)
 	errAbort("more than one line in %s with hubUrl %s\n", 
 	    hubStatusTableName, url);
 
     foundOne = TRUE;
 
     char *thisId = row[0], *thisError = row[1];
 
     if (!isEmpty(thisError))
 	*errorMessage = cloneString(thisError);
 
     id = sqlUnsigned(thisId);
     }
 sqlFreeResult(&sr);
 
 hDisconnectCentral(&conn);
 
 return id;
 }
 
 static boolean hubHasDatabase(unsigned id, char *database)
 /* check to see if hub specified by id supports database */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 
 safef(query, sizeof(query), "select dbList from %s where id=%d", 
     hubStatusTableName, id); 
 char *dbList = sqlQuickString(conn, query);
 boolean gotIt = FALSE;
 
 if (nameInCommaList(database, dbList))
     gotIt = TRUE;
 
 hDisconnectCentral(&conn);
 
 freeMem(dbList);
 
 return gotIt;
 }
 
 static boolean fetchHub(char *database, char *url, boolean unlisted)
 {
 struct errCatch *errCatch = errCatchNew();
 struct trackHub *tHub = NULL;
 boolean gotWarning = FALSE;
 unsigned id = 0;
 
 if (errCatchStart(errCatch))
     tHub = trackHubOpen(url, "1"); // open hub.. it'll get renamed later
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     gotWarning = TRUE;
     warn("%s", errCatch->message->string);
     }
 errCatchFree(&errCatch);
 
 if (gotWarning)
     {
     return 0;
     }
 
 if (hashLookup(tHub->genomeHash, database) != NULL)
     {
     enterHubInStatus(tHub, unlisted);
     }
 else
     {
     warn("requested hub at %s does not have data for %s\n", url, database);
     return 0;
     }
 
 trackHubClose(&tHub);
 
 char *errorMessage = NULL;
 id = getHubId(url, &errorMessage);
 return id;
 }
 
 static unsigned getAndSetHubStatus(char *database, struct cart *cart, char *url, 
     boolean set, boolean unlisted)
 /* look in the hubStatus table for this url, add it if it isn't in there
  * Set the cart variable to turn the hub on if set == TRUE.  
  * Return id from that status table*/
 {
 char *errorMessage = NULL;
 unsigned id;
 
 if ((id = getHubId(url, &errorMessage)) == 0)
     {
     if ((id = fetchHub(database, url, unlisted)) == 0)
 	return id;
     }
 else if (!hubHasDatabase(id, database))
     {
     warn("requested hub at %s does not have data for %s\n", url, database);
     return id;
     }
 
 char hubName[32];
 safef(hubName, sizeof(hubName), "%s%u", hgHubConnectHubVarPrefix, id);
 if (set)
     cartSetString(cart, hubName, "1");
 
 return id;
 }
 
 unsigned hubFindOrAddUrlInStatusTable(char *database, struct cart *cart,
     char *url, char **errorMessage)
 /* find this url in the status table, and return its id and errorMessage (if an errorMessage exists) */
 {
 int id = 0;
 
 *errorMessage = NULL;
 
 if ((id = getHubId(url, errorMessage)) > 0)
     return id;
 
 getAndSetHubStatus(database, cart, url, FALSE, FALSE);
 
 if ((id = getHubId(url, errorMessage)) == 0)
     errAbort("inserted new hubUrl %s, but cannot find it", url);
 
 return id;
 }
 
 unsigned hubCheckForNew(char *database, struct cart *cart)
 /* see if the user just typed in a new hub url, return id if so */
 {
 char *url = cartOptionalString(cart, hgHubDataText);
 
 if (url != NULL)
     {
     trimSpaces(url);
     unsigned id = getAndSetHubStatus(database, cart, url, TRUE, TRUE);
     cartRemove(cart, hgHubDataText);
     return id;
     }
 return 0;
 }
 
 unsigned hubResetError(char *url)
 /* clear the error for this url in the hubStatus table,return the id */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 
 safef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", hubStatusTableName, url);
 unsigned id = sqlQuickNum(conn, query);
 
 if (id == 0)
     errAbort("could not find url %s in status table (%s)\n", 
 	url, hubStatusTableName);
 
 safef(query, sizeof(query), "update %s set errorMessage=\"\" where hubUrl = \"%s\"", hubStatusTableName, url);
 
 sqlUpdate(conn, query);
 hDisconnectCentral(&conn);
 
 return id;
 }
 
 unsigned hubClearStatus(char *url)
 /* drop the information about this url from the hubStatus table */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[512];
 
 safef(query, sizeof(query), "select id from %s where hubUrl = \"%s\"", hubStatusTableName, url);
 unsigned id = sqlQuickNum(conn, query);
 
 if (id == 0)
     errAbort("could not find url %s in status table (%s)\n", 
 	url, hubStatusTableName);
 
 safef(query, sizeof(query), "delete from %s where hubUrl = \"%s\"", hubStatusTableName, url);
 
 sqlUpdate(conn, query);
 hDisconnectCentral(&conn);
 
 return id;
 }
 
 void hubDisconnect(struct cart *cart, char *url)
 /* drop the information about this url from the hubStatus table, and 
  * the cart variable the references this hub */
 {
 /* clear the hubStatus table */
 unsigned id = hubClearStatus(url);
 
 /* remove the cart variable */
 char buffer[1024];
 safef(buffer, sizeof buffer, "hgHubConnect.hub.%d", id);
 cartRemove(cart, buffer);
 }
 
 void hubSetErrorMessage(char *errorMessage, unsigned id)
 /* set the error message in the hubStatus table */
 {
 struct sqlConnection *conn = hConnectCentral();
 char query[4096];
 
 if (errorMessage != NULL)
     {
     // make sure there is no newline at the end.  This should be unneccesary
     // but there are many, many places where newlines are added in calls
     // to warn and errAbort
     char buffer[4096];
-    strcpy(buffer, errorMessage);
+    safef(buffer, sizeof buffer, errorMessage);
     while (lastChar(buffer) == '\n')
 	buffer[strlen(buffer) - 1] = '\0';
     safef(query, sizeof(query),
 	"update %s set errorMessage=\"%s\", lastNotOkTime=now() where id=%d",
 	hubStatusTableName, buffer, id);
     }
 else
     {
     safef(query, sizeof(query),
 	"update %s set errorMessage=\"\", lastOkTime=now() where id=%d",
 	hubStatusTableName, id);
     }
 sqlUpdate(conn, query);
 hDisconnectCentral(&conn);
 }