src/hg/utils/tdbQuery/tdbQuery.c 1.15

Index: src/hg/utils/tdbQuery/tdbQuery.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/utils/tdbQuery/tdbQuery.c,v
retrieving revision 1.14
retrieving revision 1.15
diff -b -B -U 4 -r1.14 -r1.15
--- src/hg/utils/tdbQuery/tdbQuery.c	4 Dec 2009 22:15:16 -0000	1.14
+++ src/hg/utils/tdbQuery/tdbQuery.c	5 Dec 2009 02:32:49 -0000	1.15
@@ -3,8 +3,9 @@
 #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 "tdbRecord.h"
@@ -129,9 +130,8 @@
 {
 /* Do checks that tags are all legitimate and with correct types. */
 char tagTypeFile[PATH_LEN];
 safef(tagTypeFile, sizeof(tagTypeFile), "%s/%s", clRoot, "tagTypes.tab");
-uglyf("tagTypeFile %s, clRoot %s\n", tagTypeFile, clRoot);
 struct hash *tagTypeHash = readTagTypeHash(tagTypeFile);
 struct tdbRecord *record;
 for (record = recordList; record != NULL; record = record->next)
     {
@@ -172,8 +172,23 @@
 /* Get list of all "database" directories with any trackDb.ra files two under us. */
 {
 struct dbPath *pathList = NULL, *path;
 struct fileInfo *org, *orgList = listDirX(root, "*", TRUE);
+
+/* If in strict mode avoid looking up databases that aren't in mysql. */
+struct hash *dbStrictHash = NULL;
+if (clStrict)
+    {
+    struct sqlConnection *conn = sqlConnect("mysql");
+    struct slName *db, *dbList = sqlGetAllDatabase(conn);
+    dbStrictHash = hashNew(0);
+    for (db = dbList; db != NULL; db = db->next)
+        hashAdd(dbStrictHash, db->name, NULL);
+    sqlDisconnect(&conn);
+    slFreeList(&dbList);
+    }
+
+
 for (org = orgList; org != NULL; org = org->next)
     {
     if (org->isDir)
         {
@@ -185,17 +200,21 @@
 		char trackDbPath[PATH_LEN];
 		safef(trackDbPath, sizeof(trackDbPath), "%s/trackDb.ra", db->name);
 		if (fileExists(trackDbPath))
 		    {
-		    AllocVar(path);
-		    path->dir = cloneString(db->name);
 		    char *s = strrchr(db->name, '/');
 		    assert(s != NULL);
-		    path->db = cloneString(s+1);
+		    char *fileOnly = s+1;
+		    if (dbStrictHash == NULL || hashLookup(dbStrictHash, fileOnly) != NULL)
+			{
+			AllocVar(path);
+			path->db = cloneString(fileOnly);
+			path->dir = cloneString(db->name);
 		    slAddHead(&pathList, path);
 		    }
 		}
 	    }
+	    }
 	slFreeList(&dbList);
 	}
     }
 slFreeList(&orgList);
@@ -821,18 +840,35 @@
     }
 fprintf(out, "\n");
 }
 
-static boolean tableExistsInSelfOrOffspring(char *db, struct tdbRecord *record)
+
+static boolean tableExistsInSelfOrOffspring(char *db, struct tdbRecord *record, 
+	int level, struct slRef *parent)
 /* Return TRUE if table corresponding to track exists in database db.  If a parent
  * track look for tables in kids too. */
 {
 if ( hTableOrSplitExists(db, record->key))
     return TRUE;
 struct tdbRecord *child;
-for (child = record->children; child != NULL; child = child->next)
+if (level > 5)
+    {
+    struct slRef *ancestor;
+    struct dyString *err = dyStringNew(0);
+    dyStringPrintf(err, "Heirarchy too deep from %s", record->key);
+    for (ancestor=parent; ancestor != NULL; ancestor = ancestor->next)
     {
-    if (tableExistsInSelfOrOffspring(db, child))
+	struct tdbRecord *a = ancestor->val;
+	dyStringPrintf(err, " to %s", a->key);
+	}
+    recordAbort(record, "%s", err->string);
+    }
+struct slRef me;
+me.next = parent;
+me.val = record;
+for (child = record->children; child != NULL; child = child->olderSibling)
+    {
+    if (tableExistsInSelfOrOffspring(db, child, level+1, &me))
         return TRUE;
     }
 return FALSE;
 }
@@ -873,8 +910,9 @@
     verbose(2, "Composed %d records from %s\n", slCount(recordList), db);
     inheritFromParents(recordList, "subTrack", "noInherit", clAlpha, lm);
     recordList = filterOnRelease(recordList, clAlpha);
     verbose(2, "After filterOnRelease %d records\n", slCount(recordList));
+    linkUpParents(recordList, "subTrack", clAlpha);
     checkDupeKeys(recordList, FALSE);
 
     overridePrioritiesAndVisibilities(recordList, p, lm);
 
@@ -905,9 +943,9 @@
 
 
 	if (rqlStatementMatch(rql, record, lm))
 	    {
-	    if (!clStrict || tableExistsInSelfOrOffspring(p->db, record))
+	    if (!clStrict || tableExistsInSelfOrOffspring(p->db, record, 1, NULL))
 		{
 		matchCount += 1;
 		if (doSelect)
 		    {