6696987406845625c252a13b690e0c4d7d9e59fa
max
  Thu Mar 26 06:48:48 2015 -0700
This is a go at libifing the CGI startup code. For all CGIs, we need to
call a few basic setup funtions, like UDC config and CGI apoptosis.
(For most CGIs also bottleneck). Instead of adding it to all of our
30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
at least one of these functions. This commit removes the existing
copy/pasted code from a few CGIs and replaces it with one call.
Adding this to the cart-setup means that (like before), UDC is
setup even for small JSON calls and a process is spawned to watch
the CGI and kill it ("Apoptosis"). Any comments on whether this should
be implemented differently are appreciated. I have not added bottleneck
to this function right now as apparently we're calling bottleneck only
from some of our CGIs.

diff --git src/hg/lib/hCommon.c src/hg/lib/hCommon.c
index 04354c2..a8202c6 100644
--- src/hg/lib/hCommon.c
+++ src/hg/lib/hCommon.c
@@ -1,384 +1,413 @@
 /* hCommon.c - routines used by many files in hgap project. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hCommon.h"
 #include "chromInfo.h"
 #include "portable.h"
 #include "hgConfig.h"
 #include "errAbort.h"
+#include "cgiApoptosis.h"
+#include "udc.h"
+#include "knetUdc.h"
+#include "hui.h"
+#include "cart.h"
 
 
 static char *_hgcName = "../cgi-bin/hgc";	/* Path to click processing program. */
 static char *_hgTracksName = "../cgi-bin/hgTracks"; /* Path back to genome browser. */
 static char *_hgTrackUiName = "../cgi-bin/hgTrackUi"; /* Path to extended ui program. */
 static char *_hgFileUiName = "../cgi-bin/hgFileUi";   /* Path to downloladable files CGI. */
 static char *_hgTextName = "../cgi-bin/hgText"; /* Path back to the text browser. */
 static char *_hgTablesName = "../cgi-bin/hgTables"; /* Path back to the table browser. */
 static char *_hgVaiName = "../cgi-bin/hgVai"; /* Path back to the variant annotation integrator. */
 static char *_hgCustomName = "../cgi-bin/hgCustom"; /* Path back to the custom tracks manager. */
 static char *_hgHubConnectName = "../cgi-bin/hgHubConnect"; /* Path back to the track hub manager. */
 static char *_hgSessionName = "../cgi-bin/hgSession";	/* Path to session manager. */
 static char *_hgPalName = "../cgi-bin/hgPal"; /* Path back to the protein aligner */
 static char *_hgVarAnnogratorName = "../cgi-bin/hgVarAnnogrator"; /* Path to variant annot intgr */
 static char *_hgIntegratorName = "../cgi-bin/hgIntegrator"; /* Path to annotation intgrator */
 
 char *hgPalName()
 /* Relative URL to click processing program. */
 {
 return _hgPalName;
 }
 
 char *hgcName()
 /* Relative URL to click processing program. */
 {
 return _hgcName;
 }
 
 char *hgTracksName()
 /* Relative URL to browser. */
 {
 return _hgTracksName;
 }
 
 char *hgTrackUiName()
 /* Relative URL to extended track UI. */
 {
 return _hgTrackUiName;
 }
 
 char *hgFileUiName()
 /* Relative URL to downloladable files UI. */
 {
 return _hgFileUiName;
 }
 
 char *hgTextName()
 /* Relative URL to old table browser. */
 {
 return _hgTextName;
 }
 
 char *hgTablesName()
 /* Relative URL to table browser. */
 {
 return _hgTablesName;
 }
 
 char *hgVaiName()
 /* Relative URL to variant annotation integrator. */
 {
 return _hgVaiName;
 }
 
 char *hgCustomName()
 /* Relative URL to custom tracks manager. */
 {
 return _hgCustomName;
 }
 
 char *hgHubConnectName()
 /* Relative URL to track hub manager. */
 {
 return _hgHubConnectName;
 }
 
 char *hgSessionName()
 /* Relative URL to session manager. */
 {
 return _hgSessionName;
 }
 
 char *hgVarAnnogratorName()
 /* Relative URL to variant annotation integrator program. */
 {
 return _hgVarAnnogratorName;
 }
 
 char *hgIntegratorName()
 /* Relative URL to annotation integrator program. */
 {
 return _hgIntegratorName;
 }
 
 static void finishCloneName(char *fragName, char *e, char cloneName[128])
 /* Finish conversion from frag to clone or clone.ver name. */
 {
 int size;
 
 if (e == NULL)
     e = fragName + strlen(fragName);
 size = e - fragName;
 if (size >= 128)
     errAbort("name too long %s\n", fragName);
 memcpy(cloneName, fragName, size);
 cloneName[size] = 0;
 }
 
 void fragToCloneName(char *fragName, char cloneName[128])
 /* Convert fragment name to clone name. */
 {
 char *e = strchr(fragName, '.');
 finishCloneName(fragName, e, cloneName);
 }
 
 void fragToCloneVerName(char *fragName, char cloneVerName[128])
 /* Convert fragment name to clone.version name. */
 {
 char *e = strchr(fragName, '.');
 if (e == NULL)
     errAbort("No . in fragName %s", fragName);
 e = strchr(e, '_');
 finishCloneName(fragName, e, cloneVerName);
 }
 
 void recNameToFileName(char *dir, char *recName, char *fileName, char *suffix)
 /* Convert UCSC style fragment name to name of file for a clone. */
 {
 char *e;
 char *d = fileName;
 int size;
 
 
 /* Start file name with directory if any. */
 if (dir != NULL)
     {
     size = strlen(dir);
     memcpy(d, dir, size);
     d += size;
     if (dir[size-1] != '/')
 	*d++ = '/';
     }
 if (*recName == '>')
     ++recName;
 recName = skipLeadingSpaces(recName);
 e = strchr(recName, '.');
 if (e == NULL)
     e = skipToSpaces(recName);
 if (e == NULL)
     e = recName + strlen(recName);
 size = e - recName;
 memcpy(d, recName, size);
 d += size;
 strcpy(d, suffix);
 }
 
 void faRecNameToQacFileName(char *dir, char *recName, char *fileName)
 /* Convert fa record name to file name. */
 {
 recNameToFileName(dir, recName, fileName, ".qac");
 }
 
 void faRecNameToFaFileName(char *dir, char *recName, char *fileName)
 /* Convert fa record name to file name. */
 {
 recNameToFileName(dir, recName, fileName, ".fa");
 }
 
 void gsToUcsc(char *gsName, char *ucscName)
 /* Convert from
  *    AC020585.5~1.2 Fragment 2 of 29 (AC020585.5:1..1195)
  * to
  *    AC020585.5_1_2
  */
 {
 char *s, *e, *d;
 int size;
 
 /* Copy in accession and version. */
 d = ucscName;
 s = gsName;
 e = strchr(s, '~');
 if (e == NULL)
     errAbort("Expecting . in %s", gsName);
 size = e - s;
 memcpy(d, s, size);
 d += size;
 
 /* Skip over tilde and replace it with _ */
 s = e+1;
 *d++ = '_';
 
 e = skipToSpaces(s);
 if (e == NULL)
     e = s + strlen(s);
 size = e - s;
 memcpy(d, s, size);
 d[size] = 0;
 subChar(d, '.', '_');
 return;
 }
 
 char *skipChr(char *s)
 /* Skip leading 'chr' in string (to get the actual chromosome part). */
 {
 if (startsWith("chr", s))
     s += 3;
 else if (startsWith("scaffold_", s))
     s += 9;
 else if (startsWith("Scaffold_", s))
     s += 9;
 return s;
 }
 
 int chromToInt(char *s)
 /* converts a chrom name chrXX into an integer from 1 to 54.
     X = 23 Y = 24 Un = 25 M = 26 random = chr + 26;*/
 {
 char *u;
 int ret = 0;
 char str[64];
 
 if (!startsWith("chr", s))
     {
     return 0;
     }
 s += 3;
 safef(str, sizeof(str), "%s", s);
 u = strchr(str,'_');
 if (u != NULL)
     {
     ret = 26;
     *u = '\0';
     }
 switch (str[0])
     {
     case 'X':
         ret += 23;
         break;
     case 'Y':
         ret += 24;
         break;
     case 'U':
         ret += 25;
         break;
     case 'M':
         ret += 26;
         break;
     default:
         ret += atoi(s);
     }
 return ret;
 }
 boolean hIsGisaidServer()
 /* Gisaid is not used anymore */
 {
 return FALSE;
 }
 
 boolean hIsGsidServer()
 /* Gsid is not use anymore */
 {
 return FALSE;
 }
 
 boolean validateGisaidUser()
 /* Gsid is not use anymore */
 {
 return FALSE;
 }
 
 boolean hIsCgbServer()
 /* Is this a cancer genome browser server? Change for config variable
  * cgb.server=yes */
 {
 static boolean cgbHost = FALSE;
 static boolean haveChecked = FALSE;
 if (!haveChecked)
     {
     char *serverOpt = cfgOption("cgb.server");
     cgbHost = (serverOpt != NULL) && sameString(serverOpt, "yes");
     haveChecked = TRUE;
     }
 return cgbHost;
 }
 
 void hTableStart()
 /* Output a table with solid borders. */
 /* For some reason BORDER=1 does not work in our web.c nested table scheme.
  * So use web.c's trick of using an enclosing table to provide a border.   */
 {
 puts("<!--hTableStart-->" "\n"
      "<TABLE BGCOLOR=\"#"HG_COL_BORDER"\" BORDER=\"0\" CELLSPACING=\"0\" CELLPADDING=\"1\"><TR><TD>");
 puts("<TABLE BORDER=\"1\" BGCOLOR=\"#"HG_COL_INSIDE"\" CELLSPACING=\"0\">");
 }
 
 void hTableEnd()
 /* Close out table started with hTableStart() */
 {
 puts("</TABLE>");
 puts("</TD></TR></TABLE>");
 puts("<!--hTableEnd-->");
 }
 
 static boolean stackDumpDisabled = FALSE;  // prevent accidental recursion or undesired dumps
 
 static void hDumpStackAbortHandler()
 /* abort handle that prints stack dump then invokes the previous abort
  * handler on the stack. */
 {
 if (!stackDumpDisabled)
     {
     stackDumpDisabled = TRUE;
     popWarnHandler(); // remove us from the stack
     dumpStack("\nStack dump:");
     // continue with next abort handler
     noWarnAbort();
     }
 }
 
 boolean hDumpStackEnabled(void)
 /* is browser.pstack enabled?  */
 {
 return cfgOptionBooleanDefault("browser.dumpStack", FALSE);
 }
 
 void hDumpStackDisallow(void)
 /* prevent any dumping of the stack */
 {
 stackDumpDisabled = TRUE;
 }
 
 void hDumpStackPushAbortHandler(void)
 /* push the stack dump abort handler on the stack if it's enabled.  This should be pushed
  * after the warn handle that will do the actual reporting */
 {
 if (hDumpStackEnabled())
     {
     errAbortDebugnPushPopErr();
     pushAbortHandler(hDumpStackAbortHandler);
     }
 }
 
 void hDumpStackPopAbortHandler(void)
 /* pop the stack dump abort handler from the stack if it's enabled */
 {
 if (hDumpStackEnabled() && !stackDumpDisabled)
     popAbortHandler();
 }
 
 void hVaUserAbort(char *format, va_list args)
 /* errAbort when a `user' error is detected.  This is an error that comes
  * from user input. This disables the logging stack dumps. */
 {
 hDumpStackDisallow();
 vaErrAbort(format, args);
 }
 
 void hUserAbort(char *format, ...)
 /* errAbort when a `user' error is detected.  This is an error that comes
  * from user input. This disables the logging stack dumps. */
 {
 va_list args;
 va_start(args, format);
 hVaUserAbort(format, args);
 va_end(args);
 }
 
 boolean hAllowAllTables(void)
 /* Return TRUE if hg.conf's hgta.disableAllTables doesn't forbid an 'all tables' menu. */
 {
 return !cfgOptionBooleanDefault("hgta.disableAllTables", FALSE);
 }
+
+void hCgiStartSetup(struct cart *cart)
+/* should be called at the start of the CGI */
+/* do the CGI setup operations: CGI apoptosis, UDC setup etc  */
+/* cart parameter can be NULL */
+/* is not in cart.c as it can be called from parts of the code that 
+ * do not need a cart */
+{
+static bool setupDone = FALSE;
+if (setupDone)
+    return;
+setupDone = TRUE;
+
+cgiApoptosisSetup();
+
+knetUdcInstall();
+setUdcCacheDir();
+
+if (cart==NULL)
+    udcSetCacheTimeout(300);
+else
+    setUdcTimeout(cart);
+
+}