2e15b699069d147795f3b4bcdf50aa9d099be9ff
max
  Thu Mar 6 02:31:47 2014 -0800
moving the phoneHome business into cgiApoptosis.c/.h to make it callablefrom cart.c. We need to call it from cart.c as otherwise
cgiApoptosisSetup (originally: phoneHome) will be called after mysql
connections are opened. This leads to "mysql server has gone away" if
any CGI is not faster than the child process forked here. The child will
close all mysql connections of the parent process. With the new setup,
the childi is forked before any mysql connections are opened. Ideally
this would be all done in cheapcgi, but cheapcgi is not in the hg/lib
part of the code.

diff --git src/hg/lib/cgiApoptosis.c src/hg/lib/cgiApoptosis.c
new file mode 100644
index 0000000..7ce50b2
--- /dev/null
+++ src/hg/lib/cgiApoptosis.c
@@ -0,0 +1,130 @@
+/* functions to auto-kill CGIs after a certain amount of time has passed */
+
+#include <utime.h>
+#include <signal.h>
+#include "htmlPage.h"
+#include "hgConfig.h"
+#include "sqlNum.h"
+#include "jksql.h"
+#include "hdb.h"
+#include "portable.h"
+#include "cheapcgi.h"
+
+static unsigned long expireSeconds = 0;
+static boolean lazarus = FALSE;
+
+void lazarusLives(unsigned long newExpireSeconds)
+/* Long running process requests more time */
+{
+lazarus = TRUE;
+expireSeconds = newExpireSeconds;
+}
+
+static void cgiApoptosisHandler(int status)
+/* signal handler for SIGALRM for CGI expiration */
+{
+(void)(status); // skip gcc warning "unused variable"
+if (lazarus)
+    {
+    (void) alarm(expireSeconds);    /* CGI timeout */
+    lazarus = FALSE;
+    return;
+    }
+if (expireSeconds > 0)
+    {
+    /* want to see this error message in the apache error_log also */
+    fprintf(stderr, "cgiApoptosis: %lu seconds\n", expireSeconds);
+    /* most of our CGIs post a polite non-fatal message with this errAbort */
+    errAbort("procedures have exceeded timeout: %lu seconds, function has ended.\n", expireSeconds);
+    }
+exit(0);
+}
+
+void cgiApoptosisSetup()
+/* setting up cgi auto killing after x minutes. 
+ * This must be called before any mysql connections have been setup, 
+ * as otherwise the child thread will close all mysql connections for 
+ * the parent. */
+{
+static boolean beenHere = FALSE;
+if (beenHere)  /* one at a time please */
+    return;
+beenHere = TRUE;
+
+char *expireTime = cfgOptionDefault("browser.cgiExpireMinutes", "20");
+unsigned expireMinutes = sqlUnsigned(expireTime);
+expireSeconds = expireMinutes * 60;
+
+char trashFile[PATH_LEN];
+safef(trashFile, sizeof(trashFile), "%s/registration.txt", trashDir());
+
+/* trashFile does not exist during command line execution */
+if(fileExists(trashFile))	/* update access time for trashFile */
+    {
+    struct utimbuf ut;
+    struct stat mystat;
+    ZeroVar(&mystat);
+    if (stat(trashFile,&mystat)==0)
+	{
+	ut.actime = clock1();
+	ut.modtime = mystat.st_mtime;
+	}
+    else
+	{
+	ut.actime = ut.modtime = clock1();
+	}
+    (void) utime(trashFile, &ut);
+    if (expireSeconds > 0)
+	{
+	(void) signal(SIGALRM, cgiApoptosisHandler);
+	(void) alarm(expireSeconds);	/* CGI timeout */
+	}
+    return;
+    }
+
+char *scriptName = cgiScriptName();
+char *ip = getenv("SERVER_ADDR");
+if (scriptName && ip)  /* will not be true from command line execution */
+    {
+    FILE *f = fopen(trashFile, "w");
+    if (f)		/* rigamarole only if we can get a trash file */
+	{
+	time_t now = time(NULL);
+	char *localTime;
+	extern char *tzname[2];
+	struct tm *tm = localtime(&now);
+	localTime = sqlUnixTimeToDate(&now,FALSE); /* FALSE == localtime */
+	fprintf(f, "%s, %s, %s %s, %s\n", scriptName, ip, localTime,
+	    tm->tm_isdst ? tzname[1] : tzname[0], trashFile);
+	fclose(f);
+
+	chmod(trashFile, 0666);
+	pid_t pid0 = fork();
+	if (0 == pid0)	/* in child */
+	    {
+	    close(STDOUT_FILENO); /* do not hang up Apache finish for parent, but apache will still wait */
+	    expireSeconds = 0;	/* no error message from this exit */
+	    (void) signal(SIGALRM, cgiApoptosisHandler);
+	    (void) alarm(6);	/* timeout here in 6 seconds */
+#include "versionInfo.h"
+	    char url[1024];
+            char *browserName = "browser.v";
+
+	    safef(url, sizeof(url), "%s%s%s%s%s%s%s", "http://",
+	"genomewiki.", "ucsc.edu/", "cgi-bin/useCount?", "version=", browserName,
+		CGI_VERSION);
+
+	    /* 6 second alarm will exit this page fetch if it does not work */
+	    (void) htmlPageGetWithCookies(url, NULL); /* ignore return */
+
+            exit(0);
+            }	/* child of fork has done exit(0) normally or via alarm */
+	}		/* trash file open OK */
+    if (expireSeconds > 0)
+	{
+	(void) signal(SIGALRM, cgiApoptosisHandler);
+	(void) alarm(expireSeconds);	/* CGI timeout */
+	}
+    }			/* an actual CGI binary */
+}			/* phoneHome()	*/
+