src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c 1.2

Index: src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c	16 Feb 2010 20:02:14 -0000	1.1
+++ src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c	17 Feb 2010 20:16:44 -0000	1.2
@@ -1,129 +1,148 @@
 /* tdbRewriteSubtrackToParent - Convert subtrack tags to parent tags.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "localmem.h"
 #include "dystring.h"
 #include "obscure.h"
 #include "portable.h"
 #include "errabort.h"
 #include "ra.h"
 #include "rql.h"
 
 
 static char const rcsid[] = "$Id$";
 
 static char *clRoot = "~/kent/src/hg/makeDb/trackDb";	/* Root dir of trackDb system. */
 
+char *newTag = "parent";
+char *oldTag = "subTrack";
+
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "tdbRewriteSubtrackToParent - Convert subtrack tags to parent tags.\n"
   "usage:\n"
   "   tdbRewriteSubtrackToParent outDir\n"
   "options:\n"
   "   -root=/path/to/trackDb/root/dir\n"
   "Sets the root directory of the trackDb.ra directory hierarchy to be given path. By default\n"
   "this is ~/kent/src/hg/makeDb/trackDb.\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"root", OPTION_STRING},
    {NULL, 0},
 };
 
+char *firstTagInText(char *text)
+/* Return the location of tag in text - skipping blank and comment lines and white-space */
+{
+char *s = text;
+for (;;)
+    {
+    s = skipLeadingSpaces(s);
+    if (s[0] == '#')
+        {
+	s = strchr(s, '\n');
+	}
+    else
+        break;
+    }
+return s;
+}
 static void rewriteOneFile(char *inFile, char *outFile)
 /* Rewrite file. */
 {
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 FILE *f = mustOpen(outFile, "w");
 struct dyString *dy = dyStringNew(0);
 while (raSkipLeadingEmptyLines(lf, dy))
     {
     char *name, *val;
     while (raNextTagVal(lf, &name, &val, dy))
         {
-	if (sameString("subTrack", name))
+	if (sameString(oldTag, name))
 	    {
 	    char *s = dy->string;
-	    char *e = skipLeadingSpaces(dy->string);
+	    char *e = firstTagInText(dy->string);
 	    mustWrite(f, s, e-s);
-	    fputs("parent", f);
+	    fputs(newTag, f);
 	    s = skipToSpaces(e);
 	    fputs(s, f);
 	    }
 	else
 	    {
 	    fputs(dy->string, f);
 	    }
 	dyStringClear(dy);
 	}
     fputs(dy->string, f);  /* Catches trailing comments in stanza */
     }
 fputs(dy->string, f);		/* Print part of file after last stanza */
 dyStringFree(&dy);
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 static void rewriteInsideSubdir(char *outDir, char *inDir, char *trackFile)
 /* Do some sort of rewrite on one subdirectory. */
 {
 char tIn[PATH_LEN];
 safef(tIn, sizeof(tIn), "%s/%s", inDir, trackFile);
 if (fileExists(tIn))
      {
      char tOut[PATH_LEN];
      safef(tOut, sizeof(tOut), "%s/%s", outDir, trackFile);
      makeDirsOnPath(outDir);
      rewriteOneFile(tIn, tOut);
      }
 }
 
 void doRewrite(char *outDir, char *inDir, char *trackFile)
 /* Do some sort of rewrite on entire system. */
 {
 struct fileInfo *org, *orgList = listDirX(inDir, "*", FALSE);
 rewriteInsideSubdir(outDir, inDir, trackFile);
 for (org = orgList; org != NULL; org = org->next)
     {
     if (org->isDir)
 	{
 	char inOrgDir[PATH_LEN], outOrgDir[PATH_LEN];
 	safef(inOrgDir, sizeof(inOrgDir), "%s/%s", inDir, org->name);
 	safef(outOrgDir, sizeof(outOrgDir), "%s/%s", outDir, org->name);
 	rewriteInsideSubdir(outOrgDir, inOrgDir, trackFile);
 	struct fileInfo *db, *dbList = listDirX(inOrgDir, "*", FALSE);
 	for (db = dbList; db != NULL; db = db->next)
 	    {
 	    if (db->isDir)
 	        {
 		char inDbDir[PATH_LEN], outDbDir[PATH_LEN];
 		safef(inDbDir, sizeof(inDbDir), "%s/%s", inOrgDir, db->name);
 		safef(outDbDir, sizeof(outDbDir), "%s/%s", outOrgDir, db->name);
 		rewriteInsideSubdir(outDbDir, inDbDir, trackFile);
 		}
 	    }
 	}
     }
 }
 
 void tdbRewriteSubtrackToParent(char *outDir)
 /* tdbRewriteSubtrackToParent - Convert subtrack tags to parent tags.. */
 {
 doRewrite(outDir, clRoot, "trackDb.ra");
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 clRoot = simplifyPathToDir(optionVal("root", clRoot));
 if (argc != 2)
     usage();
 tdbRewriteSubtrackToParent(argv[1]);
 return 0;
 }