src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c 1.1

Index: src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
===================================================================
RCS file: src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
diff -N src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/oneShot/tdbRewriteSubtrackToParent/tdbRewriteSubtrackToParent.c	16 Feb 2010 20:02:14 -0000	1.1
@@ -0,0 +1,129 @@
+/* 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. */
+
+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},
+};
+
+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))
+	    {
+	    char *s = dy->string;
+	    char *e = skipLeadingSpaces(dy->string);
+	    mustWrite(f, s, e-s);
+	    fputs("parent", 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;
+}