src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 1.2
1.2 2009/12/08 23:39:11 kent
Getting rid of debugging statements.
Index: src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 1000000 -r1.1 -r1.2
--- src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 8 Dec 2009 23:38:23 -0000 1.1
+++ src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 8 Dec 2009 23:39:11 -0000 1.2
@@ -1,501 +1,485 @@
/* tdbRewriteAddReplaces - Add replace after tags that are replacing rather than being new or overriding parent dir.. */
#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"
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(
"tdbRewriteAddReplaces - Add replace after tags that are replacing rather than being new or overriding parent dir.\n"
"usage:\n"
" tdbRewriteAddReplaces 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},
};
#define glKeyField "track" /* The field that has the record ID */
#define glParentField "subTrack" /* The field that points to the parent. */
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. */
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 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 raLevel
/* A level of ra files. List of files with includes starting from trackDb.ra at given
* directory level. */
{
struct raLevel *parent; /* Parent level */
char *name; /* Level name - directory */
struct raFile *fileList; /* List of files at this level. */
struct hash *trackHash; /* Hash of all track records in level. */
};
#ifdef SOON
static void raTagWrite(struct raTag *tag, FILE *f)
/* Write tag to file */
{
fputs(tag->text, f);
}
#endif
int raTagCmp(const void *va, const void *vb)
/* Compare two raTags. */
{
const struct raTag *a = *((struct raTag **)va);
const struct raTag *b = *((struct raTag **)vb);
return strcmp(a->name, b->name);
}
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 *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 struct raRecord *readRecordsFromFile(struct raFile *file, struct dyString *dy, struct lm *lm)
/* 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. */
lmAllocVar(lm, r);
r->startLineIx = lf->lineIx;
char *name, *val;
while (raNextTagVal(lf, &name, &val, dy))
{
struct raTag *tag;
lmAllocVar(lm, tag);
tag->name = lmCloneString(lm, name);
tag->val = lmCloneString(lm, val);
tag->text = lmCloneString(lm, dy->string);
if (sameString(name, glKeyField))
r->key = lmCloneFirstWord(lm, tag->val);
slAddHead(&r->tagList, tag);
dyStringClear(dy);
}
if (dy->stringSize > 0)
{
r->endComments = lmCloneString(lm, 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, struct lm *lm)
/* Read in file */
{
struct dyString *dy = dyStringNew(0);
struct raFile *raFile;
lmAllocVar(lm, raFile);
raFile->name = lmCloneString(lm, fileName);
raFile->recordList = readRecordsFromFile(raFile, dy, lm);
raFile->endSpace = lmCloneString(lm, dy->string);
dyStringFree(&dy);
return raFile;
}
static void recurseThroughIncludes(char *fileName, struct lm *lm,
struct hash *circularHash, struct raFile **pFileList)
/* Recurse through include files. */
{
struct raFile *raFile = raFileRead(fileName, lm);
slAddHead(pFileList, raFile);
struct raRecord *r;
for (r = raFile->recordList; r != NULL; r = r->next)
{
struct raTag *tag = r->tagList;
if (sameString(tag->name, "include"))
{
for (; tag != NULL; tag = tag->next)
{
if (!sameString(tag->name, "include"))
recordAbort(r, "Non-include tag %s in an include stanza", tag->name);
char *relPath = tag->val;
char dir[PATH_LEN];
splitPath(fileName, dir, NULL, NULL);
char includeName[PATH_LEN];
safef(includeName, sizeof(includeName), "%s%s", dir, relPath);
if (hashLookup(circularHash, includeName))
recordAbort(r, "Including file %s in an infinite loop", includeName);
recurseThroughIncludes(includeName, lm, circularHash, pFileList);
}
}
}
}
struct hash *hashLevelTracks(struct raLevel *level)
/* Return hash of all track in level. May include multiple copies of same track
* with different releases. */
{
struct hash *hash = hashNew(0);
struct raFile *file;
for (file = level->fileList; file != NULL; file = file->next)
{
struct raRecord *r;
for (r = file->recordList; r != NULL; r = r->next)
{
if (r->key != NULL)
hashAdd(hash, r->key, r);
}
}
return hash;
}
struct raLevel *raLevelRead(char *initialFile, struct lm *lm)
/* Read initialFile and all files that are included by it. */
{
/* Build up list of files by recursion. */
struct raFile *fileList = NULL;
if (fileExists(initialFile))
{
struct hash *circularHash = hashNew(0);
hashAdd(circularHash, initialFile, NULL);
recurseThroughIncludes(initialFile, lm, circularHash, &fileList);
hashFree(&circularHash);
slReverse(&fileList);
}
/* Wrap a level around it. */
struct raLevel *level;
lmAllocVar(lm, level);
level->fileList = fileList;
level->trackHash = hashLevelTracks(level);
char dir[PATH_LEN];
splitPath(initialFile, dir, NULL, NULL);
level->name = lmCloneString(lm, dir);
return level;
}
struct raRecord *findClosestParent(struct raLevel *level, struct raRecord *record, char *parentKey)
/* Look up key in level hash, and return the one that is closest to self, but before self
* in the same file. This disregards release. It is in fact used to do the
* inheritance of releases. */
{
struct raRecord *closestParent = NULL;
int closestDistance = BIGNUM;
struct hashEl *hel;
for (hel = hashLookup(level->trackHash, parentKey); hel != NULL; hel = hashLookupNext(hel))
{
struct raRecord *parent = hel->val;
int distance = record->startLineIx - parent->startLineIx;
if (distance < 0)
distance = BIGNUM/4 - distance;
if (record->file != parent->file)
distance = BIGNUM/2;
if (distance < closestDistance)
{
closestDistance = distance;
closestParent = parent;
}
}
return closestParent;
}
char *findRelease(struct raRecord *record, struct raLevel *level)
/* Find release tag in self or parent track at this level. */
{
-boolean uglyOne = sameString(record->key, "encodeAffyChIpHl60PvalBrg1Hr00");
-if (uglyOne) uglyf("findRelease for %s\n", record->key);
while (record != NULL)
{
struct raTag *releaseTag = raRecordFindTag(record, "release");
if (releaseTag != NULL)
return releaseTag->val;
struct raTag *parentTag = raRecordFindTag(record, glParentField);
if (parentTag != NULL)
record = findClosestParent(level, record, parentTag->val);
else
record = NULL;
}
return NULL;
}
struct raRecord *findRecordAtLevel(struct raLevel *level, char *key, char *release)
/* Find record of given key and release in level. */
{
-boolean uglyOne = sameString(key, "encodeAffyChIpHl60PvalBrg1Hr00");
-if (uglyOne) uglyf("findRecordAtLevel %s %s %s\n", level->name, key, release);
/* Look up key in hash */
struct hashEl *firstEl = hashLookup(level->trackHash, key);
-if (uglyOne) uglyf("firstEl %p\n", firstEl);
/* Loop through and return any ones that match on both key (implicit in hash find) and
* in release. */
struct hashEl *hel;
for (hel = firstEl; hel != NULL; hel = hashLookupNext(hel))
{
struct raRecord *r = hel->val;
struct raTag *releaseTag = raRecordFindTag(r, "release");
char *rRelease = (releaseTag == NULL ? NULL : releaseTag->val);
if (sameOk(release, rRelease))
return r;
}
/* If given record hash no defined release, return first match regardless of release. */
if (release == NULL && firstEl != NULL)
return firstEl->val;
return NULL;
}
struct raRecord *findRecordInParentFileLevel(struct raLevel *level, struct raRecord *record)
/* Find record matching release in parent file level. */
{
-boolean uglyOne = sameString(record->key, "encodeAffyChIpHl60PvalBrg1Hr00");
-if (uglyOne) uglyf("findRecordInParentFileLevel %s %s\n", level->name, record->key);
char *release = findRelease(record, level);
-if (uglyOne) uglyf("release for %s in %s is %s\n", record->key, record->file->name, release);
struct raRecord *parentRecord = NULL;
struct raLevel *parent;
for (parent = level->parent; parent != NULL; parent = parent->parent)
{
- if (uglyOne) uglyf("parent %s\n", parent->name);
if ((parentRecord = findRecordAtLevel(parent, record->key, release)) != NULL)
break;
}
-if (uglyOne) uglyf(" parentRecord = %p\n", parentRecord);
return parentRecord;
}
void rewriteFile(struct raLevel *level, struct raFile *file, char *outName, struct lm *lm)
/* Rewrite file to outName, consulting symbols in parent. */
{
-uglyf("rewriteFile %s\n", outName);
FILE *f = mustOpen(outName, "w");
struct raRecord *r;
for (r = file->recordList; r != NULL; r = r->next)
{
/* Rewrite leading track tag in stanzas. Other tags pass through. */
struct raTag *t = r->tagList;
if (sameString(t->name, "track"))
{
-boolean uglyOne = sameString(r->key, "encodeAffyChIpHl60PvalBrg1Hr00");
-if (uglyOne) uglyf("got you %s\n", r->key);
char *tagStart = firstTagInText(t->text);
mustWrite(f, t->text, tagStart - t->text);
char *dupeVal = cloneString(t->val);
char *words[8];
int wordCount;
wordCount = chopLine(dupeVal, words);
-if (uglyOne) uglyf("wordCount %d\n", wordCount);
if (wordCount > 2)
recordAbort(r, "too many words in track line");
char *key = words[0];
assert(sameString(key, r->key));
char *mergeOp = (wordCount > 1 ? words[1] : NULL);
-if (uglyOne) uglyf("mergeOp %s\n", mergeOp);
struct raRecord *parentRecord = findRecordInParentFileLevel(level, r);
-if (uglyOne) uglyf("parentRecord %p\n", parentRecord);
if (parentRecord != NULL)
{
if (mergeOp == NULL)
mergeOp = "replace";
}
fprintf(f, "%s %s", t->name, key);
if (mergeOp)
fprintf(f, " %s", mergeOp);
fprintf(f, "\n");
freez(&dupeVal);
t = t->next; /* Skip to next field. */
}
for (; t != NULL; t = t->next)
{
fputs(t->text, f);
}
if (r->endComments != NULL)
fputs(r->endComments, f);
}
fputs(file->endSpace, f);
carefulClose(&f);
}
void rewriteLevel(struct raLevel *level, char *outDir, struct lm *lm)
/* Rewrite files in level. */
{
struct raFile *file;
if (level->fileList != NULL)
makeDirsOnPath(outDir);
for (file = level->fileList; file != NULL; file = file->next)
{
char outName[FILENAME_LEN], outExtension[FILEEXT_LEN];
splitPath(file->name, NULL, outName, outExtension);
char outPath[PATH_LEN];
safef(outPath, sizeof(outPath), "%s/%s%s", outDir, outName, outExtension);
rewriteFile(level, file, outPath, lm);
}
}
void doRewrite(char *outDir, char *inDir, char *trackFile)
/* Do some sort of rewrite on entire system. */
{
/* Make list and hash of root dir */
struct lm *rootLm = lmInit(0);
char rootName[PATH_LEN];
safef(rootName, sizeof(rootName), "%s/%s", inDir, trackFile);
struct raLevel *rootLevel = raLevelRead(rootName, rootLm);
rootLevel->trackHash = hashLevelTracks(rootLevel);
/* Make subdirectory list. */
struct fileInfo *org, *orgList = listDirX(inDir, "*", FALSE);
for (org = orgList; org != NULL; org = org->next)
{
if (org->isDir)
{
struct lm *orgLm = lmInit(0);
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);
char inOrgFile[PATH_LEN];
safef(inOrgFile, sizeof(inOrgFile), "%s/%s", inOrgDir, trackFile);
struct raLevel *orgLevel = raLevelRead(inOrgFile, orgLm);
orgLevel->parent = rootLevel;
rewriteLevel(orgLevel, outOrgDir, orgLm);
struct fileInfo *db, *dbList = listDirX(inOrgDir, "*", FALSE);
for (db = dbList; db != NULL; db = db->next)
{
if (db->isDir)
{
struct lm *dbLm = lmInit(0);
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);
char inDbFile[PATH_LEN];
safef(inDbFile, sizeof(inDbFile), "%s/%s", inDbDir, trackFile);
struct raLevel *dbLevel = raLevelRead(inDbFile, dbLm);
dbLevel->parent = orgLevel;
rewriteLevel(dbLevel, outDbDir, dbLm);
hashFree(&dbLevel->trackHash);
lmCleanup(&dbLm);
}
}
hashFree(&orgLevel->trackHash);
lmCleanup(&orgLm);
}
}
hashFree(&rootLevel->trackHash);
lmCleanup(&rootLm);
}
void tdbRewriteAddReplaces(char *outDir)
/* tdbRewriteAddReplaces - Add replace after tags that are replacing rather than being new
* or overriding parent dir.. */
{
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();
tdbRewriteAddReplaces(argv[1]);
return 0;
}