src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c 1.2
1.2 2010/01/04 19:12:40 kent
Merging viewInTheMiddle branch.
Index: src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
===================================================================
RCS file: src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
diff -N src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ src/hg/oneShot/tdbRewriteRemoveUnused/tdbRewriteRemoveUnused.c 4 Jan 2010 19:12:40 -0000 1.2
@@ -0,0 +1,571 @@
+/* tdbRewriteRemoveUnused - Remove stanzas that have no table that exists in any existing database.. */
+#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 "hdb.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(
+ "tdbRewriteRemoveUnused - Remove stanzas that have no table that exists in any existing database.\n"
+ "usage:\n"
+ " tdbRewriteRemoveUnused 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. */
+ boolean seenInDb; /* True if associated table exists. */
+ };
+
+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 *level; /* Level this is in. */
+ };
+
+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. */
+ };
+
+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 raLevel *level, 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);
+raFile->level = level;
+dyStringFree(&dy);
+return raFile;
+}
+
+static void recurseThroughIncludes(char *fileName, struct lm *lm,
+ struct hash *circularHash, struct raLevel *level, struct raFile **pFileList)
+/* Recurse through include files. */
+{
+struct raFile *raFile = raFileRead(fileName, level, 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, level, 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. */
+{
+/* Create structure for level. */
+struct raLevel *level;
+lmAllocVar(lm, level);
+char dir[PATH_LEN];
+splitPath(initialFile, dir, NULL, NULL);
+level->name = lmCloneString(lm, dir);
+
+/* Build up list of files by recursion. */
+if (fileExists(initialFile))
+ {
+ struct hash *circularHash = hashNew(0);
+ hashAdd(circularHash, initialFile, NULL);
+ recurseThroughIncludes(initialFile, lm, circularHash, level, &level->fileList);
+ hashFree(&circularHash);
+ slReverse(&level->fileList);
+ }
+
+level->trackHash = hashLevelTracks(level);
+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. */
+{
+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. */
+{
+/* Look up key in hash */
+struct hashEl *firstEl = hashLookup(level->trackHash, key);
+
+/* 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 has no defined release, return first match regardless of release. */
+if (release == NULL && firstEl != NULL)
+ return firstEl->val;
+
+/* Match to records that have no release defined. */
+for (hel = firstEl; hel != NULL; hel = hashLookupNext(hel))
+ {
+ struct raRecord *r = hel->val;
+ struct raTag *releaseTag = raRecordFindTag(r, "release");
+ if (releaseTag == NULL)
+ return r;
+ }
+
+return NULL;
+}
+
+struct raRecord *findRecordInParentFileLevel(struct raLevel *level, struct raRecord *record)
+/* Find record matching release in parent file level. */
+{
+char *release = findRelease(record, level);
+struct raRecord *parentRecord = NULL;
+struct raLevel *parent;
+for (parent = level->parent; parent != NULL; parent = parent->parent)
+ {
+ if ((parentRecord = findRecordAtLevel(parent, record->key, release)) != NULL)
+ break;
+ }
+return parentRecord;
+}
+
+struct raRecord *findRecordInLevelOrLevelsUp(struct raLevel *level, char *key, char *release)
+/* Find record matching key and compatible with release in level or ancestral levels. */
+{
+struct raLevel *generation;
+for (generation = level; generation != NULL; generation = generation->parent)
+ {
+ struct raRecord *record = findRecordAtLevel(generation, key, release);
+ if (record != NULL)
+ return record;
+ }
+return NULL;
+}
+
+void raRecordWriteTags(struct raRecord *r, FILE *f)
+/* Write out tags in record to file, including preceding spaces. */
+{
+/* Write all tags. */
+struct raTag *t;
+for (t = r->tagList; t != NULL; t = t->next)
+ fputs(t->text, f);
+}
+
+boolean tableExistsInAnyDb(struct fileInfo *dbList, struct raRecord *r)
+/* Return TRUE if record exists in any database on list. */
+{
+struct fileInfo *db;
+for (db = dbList; db != NULL; db = db->next)
+ {
+ if (hTableOrSplitExists(db->name, r->key))
+ return TRUE;
+ }
+return FALSE;
+}
+
+void rewriteTrack(struct raLevel *level, struct raFile *file,
+ struct raRecord *r, FILE *f, struct lm *lm)
+/* Write one track record. */
+{
+if (r->seenInDb)
+ {
+ raRecordWriteTags(r, f);
+ }
+}
+
+void rewriteFile(struct raLevel *level, struct raFile *file, char *outName,
+ struct lm *lm)
+/* Rewrite file to outName, consulting symbols in parent. */
+{
+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"))
+ {
+ rewriteTrack(level, file, r, f, lm);
+ }
+ else
+ {
+ 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 markSelfAndParentsAtAllLevels(struct raRecord *r, struct raLevel *startLevel)
+/* Set seenInDb field. See if track has a parent (supertrack or subtrack system).
+ * in which case will call self to do same on parent. */
+{
+r->seenInDb = TRUE;
+
+/* Get sub tab. */
+struct raTag *subTag = raRecordFindTag(r, "subTrack");
+
+/* Get super tag if it points to a parent. */
+struct raTag *superTag = raRecordFindTag(r, "superTrack");
+if (superTag && sameWord(superTag->val, "on"))
+ superTag = NULL;
+
+/* If have one or the other then parse out name and call self on parent (in all releases) */
+if (superTag != NULL || subTag != NULL)
+ {
+ /* Do some error checking and figure out parent's name. */
+ if (superTag != NULL && subTag != NULL)
+ recordAbort(r, "%s has parents in both subTrack and superTrack systems, can't cope.",
+ r->key);
+ struct raTag *parentTag = (superTag != NULL ? superTag : subTag);
+ char *parentName = cloneFirstWord(parentTag->val);
+
+ /* We may have parents at any level above us as well as our own. */
+ struct raLevel *level;
+ for (level = startLevel; level != NULL; level = level->parent)
+ {
+ struct hashEl *hel;
+ /* Might have multiple parents in one level because of releases. A better program
+ * might distinguish between them, but this one just marks them both. */
+ for (hel = hashLookup(level->trackHash, parentName); hel != NULL; hel=hashLookupNext(hel))
+ {
+ struct raRecord *parent = hel->val;
+ if (!parent->seenInDb)
+ markSelfAndParentsAtAllLevels(parent, startLevel);
+ }
+ }
+ }
+}
+
+void rewriteLevel(struct raLevel *level, char *outDir, struct fileInfo *dbList, struct lm *lm)
+/* Rewrite files in level. */
+{
+struct raFile *file;
+if (level->fileList != NULL)
+ makeDirsOnPath(outDir);
+
+/* Make pass that marks used records. */
+for (file = level->fileList; file != NULL; file = file->next)
+ {
+ struct raRecord *r;
+ for (r = file->recordList; r != NULL; r = r->next)
+ {
+ if (r->key)
+ {
+ if (tableExistsInAnyDb(dbList, r))
+ {
+ markSelfAndParentsAtAllLevels(r, level);
+ }
+ }
+ }
+ }
+
+/* Make second pass that writes out used records. */
+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);
+struct fileInfo *allDbList = NULL;
+char rootName[PATH_LEN];
+safef(rootName, sizeof(rootName), "%s/%s", inDir, trackFile);
+struct raLevel *rootLevel = raLevelRead(rootName, rootLm);
+
+/* Make subdirectory list. */
+struct fileInfo *org, *orgList = listDirX(inDir, "*", FALSE);
+uglyf("orgList has %d elements\n", slCount(orgList));
+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;
+ 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);
+ /* Reduce db to a list of one temporarily and call rewrite level. */
+ struct fileInfo *next = db->next;
+ db->next = NULL;
+ dbLevel->parent = orgLevel;
+ rewriteLevel(dbLevel, outDbDir, db, dbLm);
+ db->next = next;
+ hashFree(&dbLevel->trackHash);
+ lmCleanup(&dbLm);
+ }
+ }
+ rewriteLevel(orgLevel, outOrgDir, dbList, orgLm);
+ allDbList = slCat(dbList, allDbList);
+ hashFree(&orgLevel->trackHash);
+ lmCleanup(&orgLm);
+ }
+ }
+rewriteLevel(rootLevel, outDir, allDbList, rootLm);
+hashFree(&rootLevel->trackHash);
+lmCleanup(&rootLm);
+}
+
+
+void tdbRewriteRemoveUnused(char *outDir)
+/* tdbRewriteRemoveUnused - Remove stanzas that have no table that exists in any existing database.. */
+{
+doRewrite(outDir, clRoot, "trackDb.ra");
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 2)
+ usage();
+clRoot = simplifyPathToDir(optionVal("root", clRoot));
+tdbRewriteRemoveUnused(argv[1]);
+return 0;
+}