src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 1.1
1.1 2009/12/08 23:38:23 kent
Rewriter that adds 'replace' on track lines in subdirectories where are redefining an old track rather than defining a new track at that level.
Index: src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
===================================================================
RCS file: src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
diff -N src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c 8 Dec 2009 23:38:23 -0000 1.1
@@ -0,0 +1,501 @@
+/* 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;
+}