Index: src/hg/encode/encodePatchTdb/encodePatchTdb.c
===================================================================
RCS file: src/hg/encode/encodePatchTdb/encodePatchTdb.c
diff -N src/hg/encode/encodePatchTdb/encodePatchTdb.c
--- src/hg/encode/encodePatchTdb/encodePatchTdb.c	4 Jan 2010 19:12:21 -0000	1.2
+++ /dev/null	1 Jan 1970 00:00:00 -0000
@@ -1,803 +0,0 @@
-/* encodePatchTdb - Lay a trackDb.ra file from the pipeline gently on top of the trackDb system. */
-#include "common.h"
-#include "linefile.h"
-#include "hash.h"
-#include "localmem.h"
-#include "options.h"
-#include "obscure.h"
-#include "errabort.h"
-#include "dystring.h"
-#include "portable.h"
-#include "ra.h"
-
-static char const rcsid[] = "$Id$";
-
-char *clMode = "add";
-char *clTest = NULL;
-static char *clRoot = "~/kent/src/hg/makeDb/trackDb";	/* Root dir of trackDb system. */
-
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-  "encodePatchTdb - Lay a trackDb.ra file from the pipeline gently on top of the trackDb system\n"
-  "usage:\n"
-  "   encodePatchTdb patchFile.ra fileToChange.ra\n"
-  "Example:\n"
-  "   encodePatchTdb 849/out/trackDb.ra ~/kent/src/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra\n"
-  "options:\n"
-  "   -mode=mode (default %s).  Operate in one of the following modes\n"
-  "         update - if record is new add it at end. If record is old add any new fields at end,\n"
-  "                  and replace any old field values with new ones\n"
-  "         replace - replace existing records rather than doing field by field update.\n"
-  "         add - add new records at end of parent's subtrack list. Complain if record isn't new\n"
-  "               warn if it's a new track rather than just new subtracks\n"
-  "         addTrack - add new track plus subtracks.  Complains if not new\n"
-  "   -test=patchFile - rather than doing patches in place, write patched output to this file\n"
-  "   -root=/path/to/trackDb/root/dir - Sets the root directory of the trackDb.ra directory\n"
-  "         hierarchy to be given path. By default this is ~/kent/src/hg/makeDb/trackDb.\n"
-  "   -org=organism - try to put this at the organism level of the hierarchy instead of bottom\n"
-  , clMode
-  );
-}
-
-static struct optionSpec options[] = {
-   {"mode", OPTION_STRING},
-   {"test", OPTION_STRING},
-   {"root", OPTION_STRING},
-   {NULL, 0},
-};
-
-struct loadInfo
-/* Information from a stanza of a load.ra file. */
-    {
-    struct loadInfo *next;
-    char *name;		/* from tablename. */
-    char *db;		/* from assembly. */
-    char *view;		/* form view. */
-    char *downloadOnly;	/* downloadOnly 0 or 1 */
-    };
-
-struct raTag
-/* A tag in a .ra file. */
-    {
-    struct raTag *next;
-    char *name;		/* Name of tag. */
-    char *val;		/* Value of tag. */
-    char *text;		/* Text - including white space and comments before tag. */
-    };
-
-struct raRecord
-/* A record in a .ra file. */
-    {
-    struct raRecord *next;	/* Next in list. */
-    struct raRecord *parent;	/* Parent if any. */
-    struct raRecord *children;	/* Children - youngest to oldest. */
-    struct raRecord *olderSibling;	/* Parent to older sibling if any. */
-    char *key;			/* First word in track line if any. */
-    struct raTag *tagList;	/* List of tags that make us up. */
-    int startLineIx, endLineIx; /* Start and end in file for error reporting. */
-    struct raFile *file;	/* Pointer to file we are in. */
-    char *endComments;		/* Some comments that may follow record. */
-    struct raRecord *subtracks;	/* Subtracks of this track. */
-    };
-
-struct raFile
-/* A file full of ra's. */
-    {
-    struct raFile *next;	  /* Next (in include list) */
-    char *name;		  	  /* Name of file */
-    struct raRecord *recordList;  /* List of all records in file */
-    char *endSpace;		  /* Text after last record. */
-    struct hash *trackHash;	  /* Hash of records that have keys */
-    };
-
-void recordLocationReport(struct raRecord *rec, FILE *out)
-/* Write out where record ends. */
-{
-fprintf(out, "in stanza from lines %d-%d of %s\n", 
-	rec->startLineIx, rec->endLineIx, rec->file->name);
-}
-
-void recordWarn(struct raRecord *rec, char *format, ...)
-/* Issue a warning message. */
-{
-va_list args;
-va_start(args, format);
-vaWarn(format, args);
-va_end(args);
-recordLocationReport(rec, stderr);
-}
-
-void recordAbort(struct raRecord *rec, char *format, ...)
-/* Issue a warning message. */
-{
-va_list args;
-va_start(args, format);
-vaWarn(format, args);
-va_end(args);
-recordLocationReport(rec, stderr);
-noWarnAbort();
-}
-
-struct raTag *raRecordFindTag(struct raRecord *r, char *name)
-/* Find tag of given name.  Return NULL if not found. */
-{
-struct raTag *tag;
-for (tag = r->tagList; tag != NULL; tag = tag->next)
-    if (sameString(tag->name, name))
-        break;
-return tag;
-}
-
-char *raRecordFindTagVal(struct raRecord *r, char *name)
-/* Return value of tag of given name, or NULL if not found. */
-{
-struct raTag *tag = raRecordFindTag(r, name);
-return (tag == NULL ? NULL : tag->val);
-}
-
-struct raTag *raRecordMustFindTag(struct raRecord *r, char *name)
-/* Find given tag, abort with message if not found. */
-{
-struct raTag *tag = raRecordFindTag(r, name);
-if (tag == NULL)
-    recordAbort(r, "missing required tag %s", name);
-return tag;
-}
-
-char *raRecordMustFindTagVal(struct raRecord *r, char *name)
-/* Find value of given tag.  Abort if it doesn't exist. */
-{
-struct raTag *tag = raRecordMustFindTag(r, name);
-return tag->val;
-}
-
-struct loadInfo *loadInfoReadRa(char *fileName)
-/* Read ra file and turn it into a list of loadInfo. */
-{
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-struct loadInfo *list = NULL, *el;
-while (raSkipLeadingEmptyLines(lf, NULL))
-    {
-    char *tag, *val;
-    AllocVar(el);
-    while (raNextTagVal(lf, &tag, &val, NULL))
-        {
-	if (sameString(tag, "tablename"))
-	    el->name = cloneString(val);
-	else if (sameString(tag, "assembly"))
-	    el->db = cloneString(val);
-	else if (sameString(tag, "view"))
-	    el->view = cloneString(val);
-	else if (sameString(tag, "downloadOnly"))
-	    el->downloadOnly = cloneString(val);
-	}
-    if (el->name == NULL)
-        errAbort("missing tablename line %d of %s", lf->lineIx, lf->fileName);
-    if (el->db == NULL)
-        errAbort("missing assembly line %d of %s", lf->lineIx, lf->fileName);
-    if (el->downloadOnly == NULL)
-        errAbort("missing downloadOnly line %d of %s", lf->lineIx,lf->fileName);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-static struct raRecord *readRecordsFromFile(struct raFile *file, struct dyString *dy)
-/* Read all the records in a file and return as a list.  The dy parameter returns the
- * last bits of the file (after the last record). */
-{
-char *fileName = file->name;
-struct raRecord *r, *rList = NULL;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-while (raSkipLeadingEmptyLines(lf, dy))
-    {
-    /* Create a tag structure in local memory. */
-    AllocVar(r);
-    r->startLineIx = lf->lineIx;
-    char *name, *val;
-    while (raNextTagVal(lf, &name, &val, dy))
-        {
-	struct raTag *tag;
-	AllocVar(tag);
-	tag->name = cloneString( name);
-	tag->val = cloneString( val);
-	tag->text = cloneString( dy->string);
-	if (sameString(name, "track"))
-	    r->key = cloneFirstWord(tag->val);
-	slAddHead(&r->tagList, tag);
-	dyStringClear(dy);
-	}
-    if (dy->stringSize > 0)
-        {
-	r->endComments = cloneString( dy->string);
-	}
-    slReverse(&r->tagList);
-    r->endLineIx = lf->lineIx;
-    r->file = file;
-    slAddHead(&rList, r);
-    }
-lineFileClose(&lf);
-slReverse(&rList);
-return rList;
-}
-
-struct raFile *raFileRead(char *fileName)
-/* Read in file */
-{
-struct dyString *dy = dyStringNew(0);
-struct raFile *raFile;
-AllocVar(raFile);
-raFile->name = cloneString( fileName);
-raFile->recordList = readRecordsFromFile(raFile, dy);
-raFile->endSpace = cloneString( dy->string);
-
-/* Hash up tracks. */
-struct hash *hash = raFile->trackHash = newHash(0);
-struct raRecord *r;
-for (r = raFile->recordList; r != NULL; r = r->next)
-    {
-    if (r->key != NULL)
-	hashAdd(hash, r->key, r);
-    }
-
-/* Clean up and go home. */
-dyStringFree(&dy);
-return raFile;
-}
-
-char *findDb(struct loadInfo *loadList, char *loadRa)
-/* Find the db common to the list.  Abort if mixing dbs. */
-{
-struct loadInfo *loadInfo;
-char *db = loadList->db;
-for (loadInfo = loadList->next; loadInfo != NULL; loadInfo = loadInfo->next)
-    {
-    if (!sameString(db, loadInfo->db))
-        errAbort("Multiple databases in %s: %s and %s, can't handle this.", 
-		loadRa, db, loadInfo->db);
-    }
-return db;
-}
-
-boolean compositeFirst(struct raRecord *raList)
-/* Return first record if it's composite.  Insure there are no other composites.
- * return NULL if first record is not composite. */
-{
-struct raRecord *r;
-struct raTag *compositeTag = raRecordFindTag(raList, "compositeTrack");
-if (compositeTag != NULL)
-    if (!sameString(compositeTag->val, "on"))
-        recordAbort(raList, "Expecting 'on' for compositeTrack value, got '%s'", compositeTag->val);
-for (r = raList->next; r != NULL; r = r->next)
-    {
-    struct raTag *tag = raRecordFindTag(r, "compositeTrack");
-    if (tag != NULL)
-        recordAbort(r, "The compositeTrack tag is only allowed on the first stanza\n");
-    }
-return compositeTag != NULL;
-}
-
-static void checkSubsAreForParent(char *parentName, struct raRecord *subList)
-/* Check that all subtracks in list have parent as subtrack. */
-{
-struct raRecord *sub;
-for (sub = subList; sub != NULL; sub = sub->next)
-    {
-    char *subParent = cloneFirstWord(raRecordMustFindTagVal(sub, "subTrack"));
-    if (!sameString(parentName, subParent))
-        recordAbort(sub, "%s has subTrack %s, expecting subtrack %s", 
-		sub->key, subParent, parentName);
-    }
-}
-
-boolean hasViewSubtracks(struct raRecord *parent)
-/*  Return TRUE if parent has view subtracks. */
-{
-struct raRecord *sub;
-for (sub = parent->children; sub != NULL; sub = sub->next)
-    if (raRecordFindTag(sub, "view"))
-        return TRUE;
-return FALSE;
-}
-
-struct raRecord *rFindView(struct raRecord *r, char *view)
-/* Find view of given name at r or under. */
-{
-char *thisView = raRecordFindTagVal(r, "view");
-if (thisView != NULL && sameString(thisView, view))
-    return r;
-struct raRecord *sub;
-for (sub = r->subtracks; sub != NULL; sub = sub->next)
-    {
-    struct raRecord *viewRecord = rFindView(sub, view);
-    if (viewRecord != NULL)
-        return viewRecord;
-    }
-return NULL;
-}
-
-char *getOneOutOfThisEqualsThat(char *thisEqThat, char *name)
-/* Get value on right side of name= in a name=value list. */
-{
-/* Not an efficient implementation, should be ok though. */
-struct hash *hash = hashThisEqThatLine(thisEqThat, 0, FALSE);
-char *val = cloneString(hashFindVal(hash, name));
-freeHashAndVals(&hash);
-return val;
-}
-
-char *findViewOfSub(struct raRecord *sub)
-/* Find view that subtrack belongs to - parsing it out of subTrack. */
-{
-char *subGroups = raRecordFindTagVal(sub, "subGroups");
-if (subGroups == NULL)
-    return NULL;
-char *viewName = getOneOutOfThisEqualsThat(subGroups, "view");
-return viewName;
-}
-
-struct raRecord *findRecordCompatibleWithRelease(struct raFile *file, char *release, char *key)
-/* Look in file for record with given key that is compatible with release.  Compatible means
- * that either the releases are the same, or one or the other is NULL. */
-{
-struct hashEl *hel;
-for (hel = hashLookup(file->trackHash, key); hel != NULL; hel = hashLookupNext(hel))
-    {
-    struct raRecord *r = hel->val;
-    struct raTag *tag = raRecordFindTag(r, "release");
-    if (tag == NULL || release == NULL || sameString(tag->val, release))
-        return r;
-    }
-return NULL;
-}
-
-static void linkUpParents(struct raFile *file)
-/* Link up records according to parent/child relationships. */
-{
-struct raRecord *list = file->recordList;
-
-/* Zero out children, parent, and older sibling fields, since going to recalculate
- * them and need lists to start out empty. */
-struct raRecord *rec;
-for (rec = list; rec != NULL; rec = rec->next)
-    rec->parent = rec->olderSibling = rec->children = NULL;
-
-/* Scan through linking up parents. */
-for (rec = list; rec != NULL; rec = rec->next)
-    {
-    char *subTrack = raRecordFindTagVal(rec, "subTrack");
-    if (subTrack != NULL)
-	{
-	char *release = raRecordFindTagVal(rec, "release");
-	char *parentName = cloneFirstWord(subTrack);
-	struct raRecord *parent = findRecordCompatibleWithRelease(file, release, parentName);
-	if (parent == NULL)
-	    recordAbort(rec, "Can't find parent record %s release %s", parentName, release);
-	rec->parent = parent;
-	rec->olderSibling = parent->children;
-	parent->children = rec;
-	}
-    }
-}
-
-char *nonNullRelease(char *release1, char *release2)
-/* Return whichever of the two releases is non-null. */
-{
-if (release1 != NULL)
-    return release1;
-return release2;
-}
-
-
-struct hash *hashOfHashSubGroupNs(struct raRecord *r)
-/* Return a hash keyed by subGroup names (view, cellType, etc).  The hash value is
- * itself a hash, one that contains the name=val pairs on the subGroupN line. */
-{
-struct hash *hashOfHashes = hashNew(0);
-int groupIx;
-for (groupIx=1; ; groupIx++)
-    {
-    char tagName[16];
-    safef(tagName,  sizeof(tagName), "subGroup%d", groupIx);
-    struct raTag *tag = raRecordFindTag(r, tagName);
-    if (tag == NULL)
-        break;
-    char *dupe = cloneString(tag->val);
-    char *line = dupe;
-    char *groupName = nextWord(&line);
-    char *groupLabel = nextWord(&line);
-    if (groupLabel == NULL)
-        recordAbort(r, "malformed %s %s", tag->name, tag->val);
-    struct hash *hash = hashThisEqThatLine(line, r->startLineIx, FALSE);
-    if (hash->elCount < 1)
-        recordAbort(r, "%s with no this=that", tag->name);
-    hashAdd(hashOfHashes, groupName, hash);
-    freez(&dupe);
-    }
-return hashOfHashes;
-}
-
-void validateParentSub(struct raRecord *parent, struct raRecord *sub)
-/* Make sure that it is kosher that sub belongs to parent.  Mostly check
- * that subGroup1, subGroup2, etc in parent work with subGroups of sub. */
-{
-char *subGroups = raRecordMustFindTagVal(sub, "subGroups");
-struct hash *myGroups = hashThisEqThatLine(subGroups, sub->startLineIx, FALSE);
-struct hash *parentGroups = hashOfHashSubGroupNs(parent);
-struct hashEl *myGroupList = hashElListHash(myGroups);
-struct hashEl *myGroupEl;
-for (myGroupEl = myGroupList; myGroupEl != NULL; myGroupEl = myGroupEl->next)
-    {
-    char *myName = myGroupEl->name;
-    char *myVal = myGroupEl->val;
-    struct hash *parentGroup = hashFindVal(parentGroups, myName);
-    if (parentGroup == NULL)
-        recordAbort(sub, "Parent %s doesn't have a subGroup %s", parent->key, myName);
-    char *groupName = hashFindVal(parentGroup, myVal);
-    if (groupName == NULL)
-        recordAbort(sub, "Parent %s doesn't have a %s %s", parent->key, myName, myVal);
-    verbose(2, "%s %s %s found in %s\n", sub->key, myName, myVal, parent->key);
-    }
-}
-
-void validateParentViewSub(struct raRecord *parent, struct raRecord *view, struct raRecord *sub)
-/* Make sure that it is kosher that sub belongs to parent and view.  */
-{
-validateParentSub(parent, sub);
-}
-
-
-void patchIntoEndOfView(struct raRecord *sub, struct raRecord *view)
-/* Assuming view is in a file,  chase down later records in file until come to
- * first one that does not have view as a parent.  Insert sub right before that. */
-{
-struct raRecord *viewChild = NULL;
-struct raRecord *r;
-for (r = view->next; r != NULL; r = r->next)
-    {
-    if (r->parent == view)
-        viewChild = r;
-    else
-        break;
-    }
-struct raRecord *recordBefore = (viewChild != NULL ? viewChild : view);
-sub->next = recordBefore->next;
-recordBefore->next = sub;
-}
-
-void patchInSubtrack(struct raRecord *parent, struct raRecord *sub)
-/* Patch sub into the correct view of parent */
-{
-if (hasViewSubtracks(parent))
-    {
-    char *viewOfSub = findViewOfSub(sub);
-    if (viewOfSub == NULL)
-        recordAbort(sub, "Can only handle subtracks with view in subGroups");
-    char viewTrackName[PATH_LEN];
-    safef(viewTrackName, sizeof(viewTrackName), "%sView%s", parent->key, viewOfSub);
-    char *parentRelease = raRecordFindTagVal(parent, "release");
-    char *subRelease = raRecordFindTagVal(sub, "release");
-    char *release = nonNullRelease(parentRelease, subRelease);
-    struct raRecord *view = findRecordCompatibleWithRelease(parent->file, release, viewTrackName);
-    struct raRecord *oldSub = findRecordCompatibleWithRelease(parent->file, release, sub->key);
-    if (oldSub)
-	{
-        if (sameString(clMode, "update")  || sameString(clMode, "replace"))
-	    {
-	    uglyAbort("Unfortunately really don't know how to update or replace");
-	    }
-	else
-	    recordAbort(sub, "record %s already exists - use mode update or replace",
-	    	sub->key);
-	}
-    validateParentViewSub(parent, view, sub);
-    patchIntoEndOfView(sub, view);
-    }
-else
-    {
-    recordAbort(parent, "Can only handle parents with views for now.");
-    }
-}
-
-void patchInSubtracks(struct raRecord *tdbParent, struct raRecord *patchList)
-/* Move records in patchList to correct position in tdbParent. */
-{
-struct raRecord *patch, *nextPatch;
-for (patch = patchList; patch != NULL; patch = nextPatch)
-    {
-    nextPatch = patch->next;	/* Since patchInSubtrack will alter this. */
-    patchInSubtrack(tdbParent, patch);
-    }
-}
-
-struct raTag *findViewSubGroup(struct raRecord *r)
-/* Find tag that is one of the subGroup tags with first word view.  May return NULL. */
-{
-int i;
-for (i=1; ; ++i)
-    {
-    char tagName[16];
-    safef(tagName, sizeof(tagName), "subGroup%d", i);
-    struct raTag *tag = raRecordFindTag(r, tagName);
-    if (tag == NULL)
-        return NULL;
-    if (startsWithWord("view", tag->val))
-        return tag;
-    }
-}
-
-struct raRecord *makeParentPlusViewSubsFromComplexRecord(struct raRecord *complexRecord)
-/* Convert one complex parent record from the settings-by-view era to parent record plus views. */
-{
-struct lm *lm = lmInit(0);
-/* Get list of views from subGroup1 or subGroup2 tag. */
-struct raTag *viewSubGroupTag = findViewSubGroup(complexRecord);
-if (viewSubGroupTag == NULL)
-    recordAbort(complexRecord, "Can't find view subGroup#");
-char *line = lmCloneString(lm, viewSubGroupTag->val);
-/*  line looks something like: 
- *       view Views FiltTransfrags=Filtered_Transfrags Transfrags=Raw_Transfrags */
-char *viewWord = nextWord(&line);
-assert(sameString(viewWord, "view"));
-nextWord(&line);	// Just skip over name to label views with
-struct slPair *viewList = NULL;
-char *thisEqThat;
-while ((thisEqThat = nextWord(&line)) != NULL)
-    {
-    char *eq = strchr(thisEqThat, '=');
-    if (eq == NULL)
-        recordAbort(complexRecord, "expecting this=that got %s in %s tag", 
-		eq, viewSubGroupTag->name);
-    *eq = 0;
-    slPairAdd(&viewList, thisEqThat, lmCloneString(lm, eq+1));
-    }
-slReverse(&viewList);
-
-
-/* Get pointers to settingsByView and visibilityViewDefaults tags, and take them off of list. */
-struct raTag *settingsByViewTag = raRecordFindTag(complexRecord, "settingsByView");
-struct raTag *visibilityViewDefaultsTag = raRecordFindTag(complexRecord, "visibilityViewDefaults");
-struct raTag *tagList = NULL, *t, *next;
-for (t = complexRecord->tagList; t != NULL; t = next)
-    {
-    next = t->next;
-    if (t != settingsByViewTag && t != visibilityViewDefaultsTag)
-        slAddHead(&tagList, t);
-    }
-slReverse(&tagList);
-complexRecord->tagList = tagList;
-
-/* Parse out visibilityViewDefaults. */
-struct hash *visHash = NULL;
-struct raTag *visTag = raRecordFindTag(complexRecord, "visibilityViewDefaults");
-if (visTag != NULL)
-    {
-    char *dupe = lmCloneString(lm, visTag->val);
-    visHash = hashThisEqThatLine(dupe, complexRecord->startLineIx, FALSE);
-    }
-
-/* Parse out settingsByView. */
-struct raTag *settingsTag = raRecordFindTag(complexRecord, "settingsByView");
-struct hash  *settingsHash = hashNew(4);
-if (settingsTag != NULL)
-    {
-    char *dupe = lmCloneString(lm, settingsTag->val);
-    char *line = dupe;
-    char *viewName;
-    while ((viewName = nextWord(&line)) != NULL)
-	{
-	char *settings = strchr(viewName, ':');
-	if (settings == NULL)
-	    recordAbort(complexRecord, "missing colon in settingsByView '%s'", viewName);
-	struct slPair *el, *list = NULL;
-	*settings++ = 0;
-	if (!slPairFind(viewList, viewName))
-	    recordAbort(complexRecord, "View '%s' in settingsByView is not defined in subGroup",
-	    	viewName);
-	char *words[32];
-	int cnt,ix;
-	cnt = chopByChar(settings,',',words,ArraySize(words));
-	for (ix=0; ix<cnt; ix++)
-	    {
-	    char *name = words[ix];
-	    char *val = strchr(name, '=');
-	    if (val == NULL)
-		recordAbort(complexRecord, "Missing equals in settingsByView on %s", name);
-	    *val++ = 0;
-
-	    AllocVar(el);
-	    el->name = cloneString(name);
-	    el->val = cloneString(val);
-	    slAddHead(&list,el);
-	    }
-	slReverse(&list);
-	hashAdd(settingsHash, viewName, list);
-	}
-    }
-
-#ifdef SOON
-/* Go through each view and write it, and then the children who are in that view. */
-struct slPair *view;
-for (view = viewList; view != NULL; view = view->next)
-    {
-    char viewTrackName[256];
-    safef(viewTrackName, sizeof(viewTrackName), "%sView%s", complexRecord->key, view->name);
-    fprintf(f, "\n");	/* Blank line to open view. */
-    fprintf(f, "    track %s\n", viewTrackName);
-    char *shortLabel = lmCloneString(lm, view->val);
-    subChar(shortLabel, '_', ' ');
-    fprintf(f, "    shortLabel %s\n", shortLabel);
-    fprintf(f, "    view %s\n", view->name);
-    char *vis = NULL;
-    if (visHash != NULL)
-         vis = hashFindVal(visHash, view->name);
-    if (vis != NULL)
-	{
-	int len = strlen(vis);
-	boolean gotPlus = (lastChar(vis) == '+');
-	if (gotPlus)
-	    len -= 1;
-	char visOnly[len+1];
-	memcpy(visOnly, vis, len);
-	visOnly[len] = 0;
-	fprintf(f, "    visibility %s\n", visOnly);
-	if (gotPlus)
-	    fprintf(f, "    viewUi on\n");
-	}
-    fprintf(f, "    subTrack %s\n", complexRecord->key);
-    struct slPair *settingList = hashFindVal(settingsHash, view->name);
-    struct slPair *setting;
-    for (setting = settingList; setting != NULL; setting = setting->next)
-	fprintf(f, "    %s %s\n", setting->name, (char*)setting->val);
-
-    /* Scan for children that are in this view. */
-    struct raRecord *r;
-    for (r = file->recordList; r != NULL; r = r->next)
-	{
-	struct raTag *subTrackTag = raRecordFindTag(r, "subTrack");
-	if (subTrackTag != NULL)
-	    {
-	    if (startsWithWord(complexRecord->key, subTrackTag->val))
-		{
-		struct raTag *subGroupsTag = raRecordFindTag(r, "subGroups");
-		if (subGroupsTag != NULL)
-		    {
-		    struct hash *hash = hashThisEqThatLine(subGroupsTag->val, 
-			    r->startLineIx, FALSE);
-		    char *viewName = hashFindVal(hash, "view");
-		    if (viewName != NULL && sameString(viewName, view->name))
-			{
-			writeRecordAsSubOfView(r, f, viewTrackName);
-			}
-		    hashFree(&hash);
-		    }
-		}
-	    }
-	}
-    }
-#endif /* SOON */
-return NULL;  // uglyf
-}
-
-
-void patchInTrack(struct raFile *tdbFile, struct raRecord *patchList)
-/* Move records in patch to appropriate place in file.   Have to make up view subtracks. */
-{
-struct raFile *patchFile = patchList->file;
-linkUpParents(patchFile);
-struct raRecord *r;
-for (r=patchFile->recordList; r != NULL; r = r->next)
-    {
-    if (r->parent)
-        validateParentSub(r->parent, r);
-    char *release = raRecordFindTagVal(r, "release");
-    struct raRecord *oldR = findRecordCompatibleWithRelease(tdbFile, release, r->key);
-    if (oldR)
-        {
-	if (!sameString(clMode, "update") && !sameString(clMode, "replace"))
-	    {
-	    errAbort("track %s already exists in %s.  Use mode=update or mode=replace",
-	    	r->key, tdbFile->name);
-	    }
-	uglyAbort("mode update and replace not yet implemented");
-	}
-    }
-uglyf("At least the subGroups in %s check\n", patchFile->name);
-uglyAbort("patchInTrack not implemented");
-}
-
-void encodePatchTdb(char *patchFileName, char *tdbFileName)
-/* encodePatchTdb - Lay a trackDb.ra file from the pipeline gently on top of the trackDb system. */
-{
-struct raFile *patchFile = raFileRead(patchFileName);
-struct raRecord *patchList = patchFile->recordList;
-int trackCount = slCount(patchList);
-if (trackCount < 1)
-    errAbort("No tracks in %s", patchFileName);
-
-boolean hasTrack = compositeFirst(patchList);
-if (hasTrack && sameString(clMode, "add"))
-    errAbort("%s has a compositeTrack as well as subtracks.  Use mode=addTrack to permit this.",
-        patchFileName);
-
-/* Find parent track name. */
-char *parentName;
-if (hasTrack)
-    {
-    parentName = patchList->key;
-    checkSubsAreForParent(parentName, patchList->next);
-    }
-else
-   {
-   parentName = cloneFirstWord(raRecordMustFindTagVal(patchList, "subTrack"));
-   checkSubsAreForParent(parentName, patchList);
-   }
-
-/* Load file to patch. */
-struct raFile *tdbFile = raFileRead(tdbFileName);
-int oldTdbCount = slCount(tdbFile->recordList);
-if (oldTdbCount < 100)
-    warn("%s only has %d records, I hope you meant to hit a new file\n", tdbFileName, 
-    	oldTdbCount);
-linkUpParents(tdbFile);
-
-struct raRecord *tdbParent = findRecordCompatibleWithRelease(tdbFile, "alpha", parentName);
-if (hasTrack)
-    {
-    if (tdbParent)
-        {
-	if (!sameString(clMode, "update") && !sameString(clMode, "replace"))
-	    {
-	    errAbort("track %s already exists in %s.  Use mode=update or mode=replace",
-	    	parentName, tdbFileName);
-	    }
-	uglyAbort("mode update and replace not yet implemented");
-	}
-    else
-        {
-	patchInTrack(tdbFile, patchList);
-	}
-    }
-else
-    {
-    if (!tdbParent)
-	errAbort("parent track %s doesn't exist in %s", parentName, tdbFileName);
-    patchInSubtracks(tdbParent, patchList);
-    }
-
-char *outName = tdbFileName;
-if (clTest != NULL)
-    outName = clTest;
-
-
-FILE *f = mustOpen(outName, "w");
-struct raRecord *r;
-for (r = tdbFile->recordList; r != NULL; r = r->next)
-    {
-    struct raTag *tag;
-    for (tag = r->tagList; tag != NULL; tag = tag->next)
-        fputs(tag->text, f);
-    if (r->endComments != NULL)
-	fputs(r->endComments, f);
-    }
-fputs(tdbFile->endSpace, f);
-carefulClose(&f);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, options);
-if (argc != 3)
-    usage();
-clRoot = simplifyPathToDir(optionVal("root", clRoot));
-clMode = optionVal("mode", clMode);
-clTest = optionVal("test", clTest);
-encodePatchTdb(argv[1], argv[2]);
-return 0;
-}

