src/hg/encode/encodePatchTdb/encodePatchTdb.c 1.3
1.3 2010/01/05 04:59:58 kent
Making it ignore parent track in patch.ra. Also making subTrack point to view instead of parent. Making indentation work.
Index: src/hg/encode/encodePatchTdb/encodePatchTdb.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/encode/encodePatchTdb/encodePatchTdb.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/encode/encodePatchTdb/encodePatchTdb.c 4 Jan 2010 19:12:21 -0000 1.2
+++ src/hg/encode/encodePatchTdb/encodePatchTdb.c 5 Jan 2010 04:59:58 -0000 1.3
@@ -1,803 +1,673 @@
/* 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},
};
+boolean glReplace; // If TRUE then do a replacement operation.
+
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;
}
+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;
+}
+
+void substituteParentText(struct raRecord *parent, struct raRecord *view,
+ struct raRecord *sub)
+/* Convert subtrack parent with subtrack view. */
+{
+struct raTag *t = raRecordMustFindTag(sub, "subTrack");
+struct dyString *dy = dyStringNew(0);
+char *s = firstTagInText(t->text);
+dyStringAppendN(dy, t->text, s - t->text);
+dyStringPrintf(dy, "subTrack %s", view->key);
+/* Skip over subTrack and name in original text. */
+int i;
+for (i=0; i<2; ++i)
+ {
+ s = skipLeadingSpaces(s);
+ s = skipToSpaces(s);
+ }
+if (s != NULL)
+ dyStringAppend(dy, s);
+else
+ dyStringAppendC(dy, '\n');
+t->text = dyStringCannibalize(&dy);
+}
+
+void indentTdbText(struct raRecord *r, int indentCount)
+/* Add spaces to start of all text in r. */
+{
+struct raTag *t;
+struct dyString *dy = dyStringNew(0);
+for (t = r->tagList; t != NULL; t = t->next)
+ {
+ char *s, *e;
+ dyStringClear(dy);
+ for (s = t->text; !isEmpty(s); s = e)
+ {
+ int i;
+ e = strchr(s, '\n');
+ if (e == s) // empty line, keep empty
+ {
+ dyStringAppendC(dy, '\n');
+ e += 1;
+ }
+ else
+ {
+ // Indent some extra.
+ for (i=0; i<indentCount; ++i)
+ dyStringAppendC(dy, ' ');
+ if (e == NULL)
+ {
+ dyStringAppend(dy, s);
+ }
+ else
+ {
+ dyStringAppendN(dy, s, e-s+1);
+ e += 1;
+ }
+ }
+ }
+ t->text = cloneString(dy->string);
+ }
+dyStringFree(&dy);
+}
+
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"))
+ if (glReplace)
{
uglyAbort("Unfortunately really don't know how to update or replace");
}
else
- recordAbort(sub, "record %s already exists - use mode update or replace",
+ recordAbort(sub, "record %s already exists - use mode=replace",
sub->key);
}
validateParentViewSub(parent, view, sub);
+ substituteParentText(parent, view, sub);
+ indentTdbText(sub, 4);
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;
+struct raRecord *subList;
if (hasTrack)
{
parentName = patchList->key;
- checkSubsAreForParent(parentName, patchList->next);
+ subList = patchList->next;
}
else
{
parentName = cloneFirstWord(raRecordMustFindTagVal(patchList, "subTrack"));
- checkSubsAreForParent(parentName, patchList);
+ subList = patchList;
}
+checkSubsAreForParent(parentName, subList);
/* 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",
+if (!tdbParent)
+ errAbort("Can't find composite track %s compatible with alpha mode in %s",
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);
- }
+patchInSubtracks(tdbParent, subList);
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);
+if (sameString(clMode, "add"))
+ glReplace = FALSE;
+else if (sameString(clMode, "replace"))
+ glReplace = TRUE;
+else
+ errAbort("unrecognized mode %s", clMode);
encodePatchTdb(argv[1], argv[2]);
return 0;
}