c49908e3df61eaad9dc356a0e8e17e4547a323a9
angie
  Wed Jan 16 15:03:56 2019 -0800
After processing an uploaded file of user regions, remove its contents from the cart.  Users have uploaded some very large files as identifier lists.

diff --git src/hg/hgTables/userRegions.c src/hg/hgTables/userRegions.c
index 40645c5..617b4a0 100644
--- src/hg/hgTables/userRegions.c
+++ src/hg/hgTables/userRegions.c
@@ -1,227 +1,228 @@
 /* identifiers - handle identifier lists: uploading, pasting,
  * and restricting to just things on the list. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "cheapcgi.h"
 #include "cart.h"
 #include "jksql.h"
 #include "trackDb.h"
 #include "portable.h"
 #include "hgTables.h"
 #include "trashDir.h"
 #include "hui.h"
 #include "obscure.h"
 #include "userRegions.h"
 #include "web.h"
 
 static int maxRegions = 1000;
 static int maxErrors = 100;
 
 void doSetUserRegionsAfterOpen(struct sqlConnection *conn)
 /* Respond to set regions button. */
 {
 char *oldPasted = cartUsualString(cart, hgtaEnteredUserRegions, "");
 char *db = cartOptionalString(cart, hgtaUserRegionsDb);
 if (db && !sameString(db, database))
     oldPasted = "";
 hPrintf("<FORM ACTION=\"%s\" METHOD=%s "
         " ENCTYPE=\"multipart/form-data\" NAME=\"mainForm\">\n", getScriptName(),
         cartUsualString(cart, "formMethod", "POST"));
 cartSaveSession(cart);
 hPrintf("<TABLE><TR><TD ALIGN=LEFT>\n");
 hPrintf("Paste regions:");
 hPrintf("</TD><TD ALIGN=RIGHT>");
 hPrintf("Or upload file: <INPUT TYPE=FILE NAME=\"%s\">&nbsp;<BR>\n",
 	hgtaEnteredUserRegionFile);
 hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
 cgiMakeTextArea(hgtaEnteredUserRegions, oldPasted, 10, 70);
 hPrintf("</TD></TR><TR><TD COLSPAN=2 ALIGN=LEFT>\n");
 cgiMakeButton(hgtaDoSubmitUserRegions, "submit");
 hPrintf("&nbsp;");
 cgiMakeButton(hgtaDoClearSetUserRegionsText, "clear");
 hPrintf("&nbsp;");
 cgiMakeButton(hgtaDoMainPage, "cancel");
 hPrintf("</TD></TR></TABLE>");
 hPrintf("</FORM><BR>\n");
 webIncludeHelpFile("hgTbUserRegionsHelp", FALSE);
 htmlClose();
 }
 
 void doSetUserRegions(struct sqlConnection *conn)
 /* Respond to set regions button. */
 {
 htmlOpen("Enter region definition\n");
 doSetUserRegionsAfterOpen(conn);
 }
 
 static char *limitText(char *text)
 /* read text string and limit to maxRegions actual data lines */
 {
 struct dyString *limitedText = dyStringNew(0);
 /* Even if using FALSE for zTerm, lineFile still does a memmove when it hits the end
  * and thus clobbers the string, so call lineFileOnString on a copy: */
 char copy[strlen(text)+1];
 safecpy(copy, sizeof(copy), text);
 struct lineFile *lf = lineFileOnString("limitText", FALSE, copy);
 char *lineStart = NULL;
 int lineLength = 0;
 int legitimateLineCount = 0;
 while (legitimateLineCount < maxRegions && lineFileNext(lf, &lineStart, &lineLength))
     {
     char *s, c;
     s = skipLeadingSpaces(lineStart);
     c = s[0];
     if (c != 0 && c != '#')
 	++legitimateLineCount;
     dyStringAppendN(limitedText, lineStart, lineLength);
     }
 if ((legitimateLineCount == maxRegions) && lineFileNext(lf, &lineStart, &lineLength))
     warn("WARNING: defined regions limit of %d definitions reached at line %d<BR>\n",
          maxRegions, lf->lineIx-1);
 lineFileClose(&lf);
 return (dyStringCannibalize(&limitedText));
 }
 
 static void cartRemoveUserRegions()
 /* Remove all cart variables related to storage of user regions. */
 {
 cartRemove(cart, hgtaEnteredUserRegions);
 cartRemove(cart, hgtaEnteredUserRegionFile);
 cartRemove(cart, hgtaUserRegionsFile);
 cartRemove(cart, hgtaUserRegionsDb);
 cartRemove(cart, hgtaRegionType);
 }
 
 void doSubmitUserRegions(struct sqlConnection *conn)
 /* Process submit in set regions page. */
 {
 char *idText = trimSpaces(cartString(cart, hgtaEnteredUserRegions));
 char *userRegionFile = trimSpaces(cartString(cart, hgtaEnteredUserRegionFile));
 
 htmlOpen("Table Browser (Region definitions)");
 
 /* presence of fileName text overrides previously existing text area
  *	contents
  */
 if (userRegionFile != NULL && userRegionFile[0] != 0)
     {
     idText = cloneString(userRegionFile);
     cartRemove(cart, hgtaEnteredUserRegions);
     cartRemove(cart, hgtaUserRegionsFile);
     cartSetString(cart, hgtaEnteredUserRegions, idText);
     }
 
 char *lineLimitText = limitText(idText);
 if ( (strlen(lineLimitText) > 0) && (strlen(lineLimitText) != strlen(idText)) )
     {
     idText = lineLimitText;
     cartSetString(cart, hgtaEnteredUserRegions, lineLimitText);
     }
 else
     freeMem(lineLimitText);
 
 boolean success = TRUE;
 if (isNotEmpty(idText))
     {
     int regionCount = 0;
     char *warnText = NULL;
     char *trashFileName = userRegionsParse(database, idText, maxRegions, maxErrors,
                                            &regionCount, &warnText);
     if (isNotEmpty(warnText))
         {
         success = FALSE;
         warn("%s", warnText);
         }
     if (regionCount == 0)
         {
         success = FALSE;
 	warn("No valid regions found in input; see below for formatting instructions");
         }
     cartSetString(cart, hgtaUserRegionsDb, database);
     cartSetString(cart, hgtaUserRegionsFile, trashFileName);
     cartSetString(cart, hgtaRegionType, hgtaRegionTypeUserRegions);
     if (strlen(idText) > 64 * 1024)
          cartRemove(cart, hgtaEnteredUserRegions);
+    cartRemove(cart, hgtaEnteredUserRegionFile);
     }
 else
     {
     cartRemoveUserRegions();
     }
 if (success)
     mainPageAfterOpen(conn);
 else
     doSetUserRegionsAfterOpen(conn);
 htmlClose();
 }
 
 char *userRegionsFileName()
 /* File name defined regions are in, or NULL if no such file. */
 {
 char *fileName = cartOptionalString(cart, hgtaUserRegionsFile);
 char *db = cartOptionalString(cart, hgtaUserRegionsDb);
 if (db && !sameString(database, db))
     return NULL;
 if (fileName == NULL)
     return NULL;
 if (fileExists(fileName))
     return fileName;
 else
     {
     cartRemoveUserRegions();
     return NULL;
     }
 }
 
 struct region *getUserRegions(char *fileName)
 /* Get user defined regions from fileName. */
 {
 struct region *list = NULL, *region;
 struct lineFile *lf;
 char *words[4];
 int wordCount;
 
 lf = lineFileOpen(fileName, TRUE); /* TRUE == replace CR with 0 */
 while (0 != (wordCount = lineFileChopNext(lf, words, ArraySize(words))))
     {
     AllocVar(region);
     region->chrom = cloneString(words[0]);
     region->start = atoi(words[1]);
     region->end = atoi(words[2]);
     if (wordCount > 3)
 	region->name = cloneString(words[3]);
     else
 	region->name = NULL;
     slAddHead(&list, region);
     }
 slReverse(&list);
 lineFileClose(&lf);
 return list;
 }
 
 void doClearSetUserRegionsText(struct sqlConnection *conn)
 /* Respond to clear within user regions enter page. */
 {
 char *fileName = userRegionsFileName();
 if (fileName != NULL)
     remove(fileName);
 cartRemoveUserRegions();
 doSetUserRegions(conn);
 }
 
 void doClearUserRegions(struct sqlConnection *conn)
 /* Respond to clear user regions button. */
 {
 char *fileName = userRegionsFileName();
 
 htmlOpen("Table Browser (Cleared Region List)");
 if (fileName != NULL)
     remove(fileName);
 cartRemoveUserRegions();
 mainPageAfterOpen(conn);
 htmlClose();
 }