1f954876a8847da234e0c89b3b43390b40c6ca4e
chmalee
  Tue Feb 25 10:45:31 2025 -0800
Special handle the parentDir setting during uploads by cgi-encoding the components of parentDir but leaving the slash characters in place. This allows hubtools uploads to preserve the filesystem layout on the host on our end, but prevent writing of files outside of the users hubspace directory. Any '..' characters in the parentDir are simply ignored. This commit also fixes some other hubtools related UI bugs, like preventing infinite recursion when doing a row select, displaying file names unencoded, and fixing a bug when deleting subdirectories, refs #31058

diff --git src/hg/hgHubConnect/hooks/hooklib.c src/hg/hgHubConnect/hooks/hooklib.c
index 6b872129160..d88fe7f2ef4 100644
--- src/hg/hgHubConnect/hooks/hooklib.c
+++ src/hg/hgHubConnect/hooks/hooklib.c
@@ -2,40 +2,66 @@
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "wikiLink.h"
 #include "customTrack.h"
 #include "userdata.h"
 #include "jsonQuery.h"
 #include "jsHelper.h"
 #include "errCatch.h"
 #include "obscure.h"
+#include "cheapcgi.h"
 #include "hooklib.h"
 
 char *prettyFileSize(long size)
 /* Return a string representing the size of a file */
 {
 char buf[32];
 sprintWithGreekByte(buf, sizeof(buf), size);
 return cloneString(buf);
 }
 
+char *encodePath(char *path)
+/* Return a string where each individual component of a '/' separated
+ * string has been cgiEncoded, but not the '/' chars themselves */
+{
+int maxSeps = 256;
+char *pathArr[maxSeps]; // errAbort if more than maxSeps subdirs
+int numChops = chopString(path, "/", pathArr, maxSeps);
+if (numChops > maxSeps)
+    errAbort("Too many subdirectories. Fix filesystem layout of upload and try again");
+struct dyString *ret = dyStringNew(0);
+int i = 0;
+for (; i < numChops; i++)
+    {
+    // we can ignore .. and . in paths, it is an error if hubtools is creating these names
+    // don't errAbort right now because hubtools does send things like 'hubName/.'
+    // as a parentDir, but that should be fixed soon
+    if (sameString(pathArr[i], ".") || sameString(pathArr[i], ".."))
+        {
+        continue;
+        }
+    dyStringPrintf(ret, "%s/", cgiEncodeFull(pathArr[i]));
+    }
+return dyStringCannibalize(&ret);
+}
+
 void fillOutHttpResponseError()
 {
 fprintf(stderr, "http response error!\n");
 }
 
 void fillOutHttpResponseSuccess()
 {
 fprintf(stderr, "http response success!\n");
 }
 
 struct jsonElement *makeDefaultResponse()
 /* Create the default response json with some fields pre-filled */
 {
 struct hash *defHash = hashNew(0);
 struct jsonElement *response = newJsonObject(defHash);