a3893022e1a44f898ec19e7e1043472685057582 kent Fri Jan 30 14:07:05 2015 -0800 Implementing a raNextTagValWithIndent function. diff --git src/lib/ra.c src/lib/ra.c index efabdf3..03b4478 100644 --- src/lib/ra.c +++ src/lib/ra.c @@ -1,400 +1,415 @@ /* Stuff to parse .ra files. Ra files are simple text databases. * The database is broken into records by blank lines. * Each field takes a line. The name of the field is the first * word in the line. The value of the field is the rest of the line. * * This file is copyright 2002 Jim Kent, but license is hereby * granted for all use - public, private or commercial. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "localmem.h" #include "dystring.h" #include "ra.h" boolean raSkipLeadingEmptyLines(struct lineFile *lf, struct dyString *dy) /* Skip leading empty lines and comments. Returns FALSE at end of file. * Together with raNextTagVal you can construct your own raNextRecord.... * If dy parameter is non-null, then the text parsed gets placed into dy. */ { char *line; /* Skip leading empty lines and comments. */ if (dy) dyStringClear(dy); for (;;) { if (!lineFileNext(lf, &line, NULL)) return FALSE; char *tag = skipLeadingSpaces(line); if (tag[0] == 0 || tag[0] == '#') { if (dy) { dyStringAppend(dy, line); dyStringAppendC(dy, '\n'); } } else break; } lineFileReuse(lf); return TRUE; } -boolean raNextTagVal(struct lineFile *lf, char **retTag, char **retVal, struct dyString *dyRecord) +boolean raNextTagValWithIndent(struct lineFile *lf, char **retTag, char **retVal, struct dyString *dy, + int *retIndent) // Read next line. Return FALSE at end of file or blank line. Otherwise fill in -// *retTag and *retVal and return TRUE. If dy parameter is non-null, then the text parsed -// gets appended to dy. Continuation lines in RA file will be joined to produce tag and val, -// but dy will be filled with the unedited multiple lines containing the continuation chars. +// *retTag and *retVal and *retIndent and return TRUE. If dy parameter is non-null, then +// the text parsed gets appended to dy. Continuation lines in RA file will be joined to produce +// tag and val, but dy will be filled with the unedited multiple lines containing the continuation chars. // NOTE: retTag & retVal, if returned, point to static mem which will be overwritten on next call! { *retTag = NULL; *retVal = NULL; char *line, *raw = NULL; int lineLen,rawLen; // Don't bother with raw if it isn't used. char **pRaw = NULL; int *pRawLen = NULL; -if (dyRecord != NULL) +if (dy != NULL) { pRaw = &raw; pRawLen = &rawLen; } while (lineFileNextFull(lf, &line, &lineLen, pRaw, pRawLen)) // Joins continuation lines { char *clippedText = skipLeadingSpaces(line); if (*clippedText == 0) { - if (dyRecord) + if (dy) lineFileReuse(lf); // Just so don't loose leading space in dy. return FALSE; } + if (retIndent != NULL) + { + int indentLevel = 0; + char *s = line; + while (s < clippedText) + { + char c = *s++; + if (c == '\t') + indentLevel = ((indentLevel+8) & 0xfffffff8); + else + indentLevel += 1; + } + *retIndent = indentLevel; + } // Append whatever line was read from file. - if (dyRecord) + if (dy) { if (raw != NULL) - dyStringAppendN(dyRecord, raw, rawLen); + dyStringAppendN(dy, raw, rawLen); else - dyStringAppendN(dyRecord, line, lineLen); - dyStringAppendC(dyRecord,'\n'); + dyStringAppendN(dy, line, lineLen); + dyStringAppendC(dy,'\n'); } // Skip comments if (*clippedText == '#') { if (startsWith("#EOF", clippedText)) return FALSE; else continue; } *retTag = nextWord(&line); *retVal = trimSpaces(line); return TRUE; } return FALSE; } struct hash *raNextStanza(struct lineFile *lf) // Return a hash containing next record. // Will ignore '#' comments and joins continued lines (ending in '\'). // Returns NULL at end of file. freeHash this when done. // Note this will free the hash keys and values as well, // so you'll have to cloneMem them if you want them for later. { struct hash *hash = NULL; char *key, *val; if (!raSkipLeadingEmptyLines(lf, NULL)) return NULL; while (raNextTagVal(lf, &key, &val, NULL)) { if (hash == NULL) hash = newHash(7); hashAdd(hash, key, lmCloneString(hash->lm, val)); } return hash; } struct slPair *raNextStanzAsPairs(struct lineFile *lf) // Return ra stanza as an slPair list instead of a hash. Handy to preserve the // order. Will ignore '#' comments and joins continued lines (ending in '\'). { struct slPair *list = NULL; char *key, *val; if (!raSkipLeadingEmptyLines(lf, NULL)) return NULL; while (raNextTagVal(lf, &key, &val, NULL)) { slPairAdd(&list, key, cloneString(val)); // key gets cloned by slPairAdd } slReverse(&list); return list; } struct slPair *raNextStanzaLinesAndUntouched(struct lineFile *lf) // Return list of lines starting from current position, up through last line of next stanza. // May return a few blank/comment lines at end with no real stanza. // Will join continuation lines, allocating memory as needed. // returns pairs with name=joined line and if joined, // val will contain raw lines '\'s and linefeeds, else val will be NULL. { struct slPair *pairs = NULL; boolean stanzaStarted = FALSE; char *line, *raw; int lineLen,rawLen; while (lineFileNextFull(lf, &line, &lineLen, &raw, &rawLen)) // Joins continuation lines { char *clippedText = skipLeadingSpaces(line); if (stanzaStarted && clippedText[0] == 0) { lineFileReuse(lf); break; } if (!stanzaStarted && clippedText[0] != 0 && clippedText[0] != '#') stanzaStarted = TRUE; // Comments don't start stanzas and may be followed by blanks slPairAdd(&pairs, line,(raw != NULL ? cloneString(raw) : NULL)); } slReverse(&pairs); return pairs; } struct hash *raFromString(char *string) /* Return hash of key/value pairs from string. * As above freeHash this when done. */ { char *dupe = cloneString(string); char *s = dupe, *lineEnd; struct hash *hash = newHash(7); char *key, *val; for (;;) { s = skipLeadingSpaces(s); if (s == NULL || s[0] == 0) break; lineEnd = strchr(s, '\n'); if (lineEnd != NULL) *lineEnd++ = 0; key = nextWord(&s); val = skipLeadingSpaces(s); s = lineEnd; val = lmCloneString(hash->lm, val); hashAdd(hash, key, val); } freeMem(dupe); return hash; } char *raFoldInOneRetName(struct lineFile *lf, struct hash *hashOfHash) /* Fold in one record from ra file into hashOfHash. * This will add ra's and ra fields to whatever already * exists in the hashOfHash, overriding fields of the * same name if they exist already. */ { char *word, *line, *name; struct hash *ra; struct hashEl *hel; /* Get first nonempty non-comment line and make sure * it contains name. */ if (!lineFileNextFullReal(lf, &line)) return NULL; word = nextWord(&line); if (!sameString(word, "name")) errAbort("Expecting 'name' line %d of %s, got %s", lf->lineIx, lf->fileName, word); name = nextWord(&line); if (name == NULL) errAbort("Short name field line %d of %s", lf->lineIx, lf->fileName); /* Find ra hash associated with name, making up a new * one if need be. */ if ((ra = hashFindVal(hashOfHash, name)) == NULL) { ra = newHash(7); hashAdd(hashOfHash, name, ra); hashAdd(ra, "name", lmCloneString(ra->lm, name)); } /* Fill in fields of ra hash with data up to next * blank line or end of file. */ for (;;) { if (!lineFileNextFull(lf, &line, NULL,NULL,NULL)) // Not using FullReal to detect end of stanza break; line = skipLeadingSpaces(line); if (line[0] == 0) break; // End of stanza detected if (line[0] == '#') continue; word = nextWord(&line); line = skipLeadingSpaces(line); if (line == NULL) line = ""; hel = hashLookup(ra, word); if (hel == NULL) hel = hashAdd(ra, word, lmCloneString(ra->lm, line)); else hel->val = lmCloneString(ra->lm, line); } return hashFindVal(ra, "name"); } boolean raFoldInOne(struct lineFile *lf, struct hash *hashOfHash) { return raFoldInOneRetName(lf, hashOfHash) != NULL; } void raFoldIn(char *fileName, struct hash *hashOfHash) /* Read ra's in file name and fold them into hashOfHash. * This will add ra's and ra fields to whatever already * exists in the hashOfHash, overriding fields of the * same name if they exist already. */ { struct lineFile *lf = lineFileMayOpen(fileName, TRUE); if (lf != NULL) { struct hash *uniqHash = hashNew(0); char *name; while ((name = raFoldInOneRetName(lf, hashOfHash)) != NULL) { if (hashLookup(uniqHash, name)) errAbort("%s duplicated in record ending line %d of %s", name, lf->lineIx, lf->fileName); hashAdd(uniqHash, name, NULL); } lineFileClose(&lf); hashFree(&uniqHash); } } struct hash *raReadSingle(char *fileName) /* Read in first ra record in file and return as hash. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct hash *hash = raNextRecord(lf); lineFileClose(&lf); return hash; } struct hash *raReadAll(char *fileName, char *keyField) /* Return hash that contains all ra records in file keyed * by given field, which must exist. The values of the * hash are themselves hashes. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct hash *bigHash = hashNew(0); struct hash *hash; while ((hash = raNextRecord(lf)) != NULL) { char *key = hashFindVal(hash, keyField); if (key == NULL) errAbort("Couldn't find key field %s line %d of %s", keyField, lf->lineIx, lf->fileName); hashAdd(bigHash, key, hash); } lineFileClose(&lf); return bigHash; } struct hash *raReadWithFilter(char *fileName, char *keyField,char *filterKey,char *filterValue) /* Return hash that contains all filtered ra records in file keyed by given field, which must exist. * The values of the hash are themselves hashes. The filter is a key/value pair that must exist. * Example raReadWithFilter(file,"term","type","antibody"): returns hash of hashes of every term with type=antibody */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct hash *bigHash = hashNew(14); struct hash *hash; while ((hash = raNextRecord(lf)) != NULL) { char *key = hashFindVal(hash, keyField); if (key == NULL) errAbort("Couldn't find key field %s line %d of %s", keyField, lf->lineIx, lf->fileName); if (filterKey != NULL) { char *filter = hashFindVal(hash, filterKey); if (filter == NULL) { hashFree(&hash); continue; } if (filterValue != NULL && differentString(filterValue,filter)) { hashFree(&hash); continue; } } hashAdd(bigHash, key, hash); } lineFileClose(&lf); if (hashNumEntries(bigHash) == 0) hashFree(&bigHash); return bigHash; } struct hash *raReadThreeLevels(char *fileName, char *lowKeyField, char *middleKeyField) /* Return 3 level hash that contains all ra records in file keyed by lowKeyField, which must exist. * and broken into sub hashes based upon middleKeyField that must exist. * Example raReadThreeLevels("cv.ra","term","type"): * returns hash of 'type' hashes of 'term' hashes of every stanza in cv.ra */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); struct hash *topHash = hashNew(0); // Not expecting that many types struct hash *bottomHash; while ((bottomHash = raNextRecord(lf)) != NULL) { char *lowKey = hashFindVal(bottomHash, lowKeyField); if (lowKey == NULL) errAbort("Couldn't find key field %s line %d of %s", lowKeyField, lf->lineIx, lf->fileName); char *middleKey = hashFindVal(bottomHash, middleKeyField); if (middleKey == NULL) errAbort("Couldn't find middle key field %s line %d of %s", middleKeyField, lf->lineIx, lf->fileName); struct hash *middleHash = hashFindVal(topHash, middleKey); if (middleHash == NULL) { middleHash = hashNew(16); // could be quite a few terms per type. hashAdd(topHash, middleKey, middleHash); } hashAdd(middleHash, lowKey, bottomHash); } lineFileClose(&lf); if (hashNumEntries(topHash) == 0) hashFree(&topHash); return topHash; } struct hash *raTagVals(char *fileName, char *tag) /* Return a hash of all values of given tag seen in any stanza of ra file. */ { struct hash *hash = hashNew(0); struct lineFile *lf = lineFileOpen(fileName, TRUE); char *line; while (lineFileNextFullReal(lf, &line)) { char *word = nextWord(&line); if (sameString(word, tag)) { char *val = trimSpaces(line); if (!hashLookup(hash, val)) hashAdd(hash, val, NULL); } } lineFileClose(&lf); return hash; }