src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c 1.10

Index: src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 1000000 -r1.9 -r1.10
--- src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c	18 May 2009 21:38:07 -0000	1.9
+++ src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c	19 May 2009 23:54:31 -0000	1.10
@@ -1,198 +1,217 @@
 /* refreshNamedSessionCustomTracks -- cron robot for keeping alive custom 
  * tracks that are referenced by saved sessions. */
 
 #include "common.h"
 #include "options.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "hdb.h"
 #include "customTrack.h"
 #include "customFactory.h"
 #include "hui.h"
 
 static char const rcsid[] = "$Id$";
 
 #define savedSessionTable "namedSessionDb"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "refreshNamedSessionCustomTracks -- scan central database's %s\n"
   "    contents for custom tracks and touch any that are found, to prevent\n"
   "    them from being removed by the custom track cleanup process.\n"
   "usage:\n"
   "    refreshNamedSessionCustomTracks hgcentral[test,beta]\n"
   "This is intended to be run as a nightly cron job for each central db.\n"
   "The ~/.hg.conf file (or $HGDB_CONF) must specify the same central db\n"
   "as the command line.  [The command line arg exists only to suppress this\n"
   "message].\n"
   "\n",
   savedSessionTable
   );
 }
 
 /* Options: */
 static struct optionSpec options[] = {
     {"hardcore", OPTION_BOOLEAN}, /* Intentionally omitted from usage(). */
     {NULL, 0},
 };
 
 char *scanSettingsForCT(char *userName, char *sessionName, char *contents,
 			int *pLiveCount, int *pExpiredCount)
 /* Parse the CGI-encoded session contents into {var,val} pairs and search
  * for custom tracks.  If found, refresh the custom track.  Parsing code 
  * taken from cartParseOverHash. 
  * If any nonexistent custom track files are found, return a SQL update
  * command that will remove those from this session.  We can't just do 
  * the update here because that messes up the caller's query. */
 {
 int contentLength = strlen(contents);
 struct dyString *newContents = dyStringNew(contentLength+1);
 struct dyString *oneSetting = dyStringNew(contentLength / 4);
 char *updateIfAny = NULL;
 char *contentsToChop = cloneString(contents);
 char *namePt = contentsToChop;
 verbose(3, "Scanning %s %s\n", userName, sessionName);
 while (isNotEmpty(namePt))
     {
     char *dataPt = strchr(namePt, '=');
     char *nextNamePt;
     if (dataPt == NULL)
 	errAbort("Mangled session content string %s", namePt);
     *dataPt++ = 0;
     nextNamePt = strchr(dataPt, '&');
     if (nextNamePt != NULL)
 	*nextNamePt++ = 0;
     dyStringClear(oneSetting);
     dyStringPrintf(oneSetting, "%s=%s%s",
 		   namePt, dataPt, (nextNamePt ? "&" : ""));
     if (startsWith(CT_FILE_VAR_PREFIX, namePt))
 	{
 	boolean thisGotLiveCT = FALSE, thisGotExpiredCT = FALSE;
 	cgiDecode(dataPt, dataPt, strlen(dataPt));
 	verbose(3, "Found variable %s = %s\n", namePt, dataPt);
 	/* If the file does not exist, omit this setting from newContents so 
 	 * it doesn't get copied from session to session.  If it does exist,
 	 * leave it up to customFactoryTestExistence to parse the file for 
 	 * possible customTrash table references, some of which may exist 
 	 * and some not. */
 	if (! fileExists(dataPt))
 	    {
 	    verbose(3, "Removing %s from %s %s\n", oneSetting->string,
 		    userName, sessionName);
 	    thisGotExpiredCT = TRUE;
 	    }
 	else
 	    {
 	    char *db = namePt + strlen(CT_FILE_VAR_PREFIX);
 	    dyStringAppend(newContents, oneSetting->string);
 	    customFactoryTestExistence(db, dataPt,
 				       &thisGotLiveCT, &thisGotExpiredCT);
 	    }
 	if (thisGotLiveCT && pLiveCount != NULL)
 	    (*pLiveCount)++;
 	if (thisGotExpiredCT && pExpiredCount != NULL)
 	    (*pExpiredCount)++;
 	if (thisGotExpiredCT)
 	    {
 	    if (verboseLevel() >= 3)
 		verbose(3, "Found expired custom track in %s %s: %s\n",
 			userName, sessionName, dataPt);
 	    else
 		verbose(2, "Found expired custom track: %s\n", dataPt);
 	    }
 	if (thisGotLiveCT)
 	    verbose(4, "Found live custom track: %s\n", dataPt);
 	}
     else
 	dyStringAppend(newContents, oneSetting->string);
     namePt = nextNamePt;
     }
 if (newContents->stringSize != contentLength)
     {
     struct dyString *update = dyStringNew(contentLength*2);
     if (newContents->stringSize > contentLength)
 	errAbort("Uh, why is newContents (%d) longer than original (%d)??",
 		 newContents->stringSize, contentLength);
     dyStringPrintf(update, "UPDATE %s set contents='", savedSessionTable);
     dyStringAppendN(update, newContents->string, newContents->stringSize);
     dyStringPrintf(update, "', lastUse=now(), useCount=useCount+1 "
 		   "where userName=\"%s\" and sessionName=\"%s\";",
 		   userName, sessionName);
     verbose(3, "Removing one or more dead CT file settings from %s %s "
 	    "(original length %d, now %d)\n", 
 	    userName, sessionName,
 	    contentLength, newContents->stringSize);
     updateIfAny = dyStringCannibalize(&update);
     }
 dyStringFree(&oneSetting);
 dyStringFree(&newContents);
 freeMem(contentsToChop);
 return updateIfAny;
 }
 
+struct sessionInfo
+    {
+    struct sessionInfo *next;
+    char userName[256];
+    char sessionName[256];
+    char *contents;
+    };
+
 void refreshNamedSessionCustomTracks(char *centralDbName)
 /* refreshNamedSessionCustomTracks -- cron robot for keeping alive custom 
  * tracks that are referenced by saved sessions. */
 {
 struct sqlConnection *conn = hConnectCentral();
 struct slPair *updateList = NULL, *update;
 char *actualDbName = sqlGetDatabase(conn);
 int liveCount=0, expiredCount=0;
 
 setUdcCacheDir();  /* programs that use udc must call this to initialize cache dir location */
 
 if (!sameString(centralDbName, actualDbName))
     errAbort("Central database specified in hg.conf file is %s but %s "
 	     "was specified on the command line.",
 	     actualDbName, centralDbName);
 else
     verbose(2, "Got connection to %s\n", centralDbName);
 
 if (sqlTableExists(conn, savedSessionTable))
     {
+    struct sessionInfo *sessionList = NULL, *si;
     struct sqlResult *sr = NULL;
     char **row = NULL;
     char query[512];
     safef(query, sizeof(query),
 	  "select userName,sessionName,contents from %s "
 	  "order by userName,sessionName", savedSessionTable);
     sr = sqlGetResult(conn, query);
+    // Slurp results into memory instead of processing row by row,
+    // reducing the chance of lost connection.
     while ((row = sqlNextRow(sr)) != NULL)
 	{
-	char *updateIfAny = scanSettingsForCT(row[0], row[1], row[2],
+	AllocVar(si);
+	safecpy(si->userName, sizeof(si->userName), row[0]);
+	safecpy(si->sessionName, sizeof(si->sessionName), row[1]);
+	si->contents = cloneString(row[2]);
+	slAddHead(&sessionList, si);
+	}
+    sqlFreeResult(&sr);
+    for (si = sessionList;  si != NULL;  si = si->next)
+	{
+	char *updateIfAny = scanSettingsForCT(si->userName, si->sessionName, si->contents,
 					      &liveCount, &expiredCount);
 	if (updateIfAny)
 	    {
 	    AllocVar(update);
 	    update->name = updateIfAny;
 	    slAddHead(&updateList, update);
 	    }
 	}
-    sqlFreeResult(&sr);
     }
 
 /* Now that we're done reading from savedSessionTable, we can modify it: */
 if (optionExists("hardcore"))
     {
     for (update = updateList;  update != NULL;  update = update->next)
 	sqlUpdate(conn, update->name);
     }
 hDisconnectCentral(&conn);
 verbose(1, "Found %d live and %d expired custom tracks in %s.\n",
 	liveCount, expiredCount, centralDbName);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 2)
     usage();
 setCurrentDir(CGI_BIN);
 refreshNamedSessionCustomTracks(argv[1]);
 return 0;
 }