cce51ca0744763b5d358c73cf6190d7a6ea29399 braney Sun Jan 30 07:38:58 2022 -0800 oops ... added an errant lineFileClose on the last checkin diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c index b4e66b6..79cc541 100644 --- src/hg/lib/chromAlias.c +++ src/hg/lib/chromAlias.c @@ -1,363 +1,360 @@ /* chromAlias.c was originally generated by the autoSql program, which also * generated chromAlias.h and chromAlias.sql. This module links the database and * the RAM representation of objects. */ #include "common.h" #include "linefile.h" #include "dystring.h" #include "jksql.h" #include "chromAlias.h" #include "hdb.h" #include "trackHub.h" #include "fieldedTable.h" char *chromAliasCommaSepFieldNames = "alias,chrom,source"; void chromAliasStaticLoad(char **row, struct chromAlias *ret) /* Load a row from chromAlias table into ret. The contents of ret will * be replaced at the next call to this function. */ { ret->alias = row[0]; ret->chrom = row[1]; ret->source = row[2]; } struct chromAlias *chromAliasLoad(char **row) /* Load a chromAlias from row fetched with select * from chromAlias * from database. Dispose of this with chromAliasFree(). */ { struct chromAlias *ret; AllocVar(ret); ret->alias = cloneString(row[0]); ret->chrom = cloneString(row[1]); ret->source = cloneString(row[2]); return ret; } struct chromAlias *chromAliasLoadAll(char *fileName) /* Load all chromAlias from a whitespace-separated file. * Dispose of this with chromAliasFreeList(). */ { struct chromAlias *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileRow(lf, row)) { el = chromAliasLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct chromAlias *chromAliasLoadAllByChar(char *fileName, char chopper) /* Load all chromAlias from a chopper separated file. * Dispose of this with chromAliasFreeList(). */ { struct chromAlias *list = NULL, *el; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *row[3]; while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) { el = chromAliasLoad(row); slAddHead(&list, el); } lineFileClose(&lf); slReverse(&list); return list; } struct chromAlias *chromAliasCommaIn(char **pS, struct chromAlias *ret) /* Create a chromAlias out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new chromAlias */ { char *s = *pS; if (ret == NULL) AllocVar(ret); ret->alias = sqlStringComma(&s); ret->chrom = sqlStringComma(&s); ret->source = sqlStringComma(&s); *pS = s; return ret; } void chromAliasFree(struct chromAlias **pEl) /* Free a single dynamically allocated chromAlias such as created * with chromAliasLoad(). */ { struct chromAlias *el; if ((el = *pEl) == NULL) return; freeMem(el->alias); freeMem(el->chrom); freeMem(el->source); freez(pEl); } void chromAliasFreeList(struct chromAlias **pList) /* Free a list of dynamically allocated chromAlias's */ { struct chromAlias *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; chromAliasFree(&el); } *pList = NULL; } void chromAliasOutput(struct chromAlias *el, FILE *f, char sep, char lastSep) /* Print out chromAlias. Separate fields with sep. Follow last field with lastSep. */ { if (sep == ',') fputc('"',f); fprintf(f, "%s", el->alias); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->chrom); if (sep == ',') fputc('"',f); fputc(sep,f); if (sep == ',') fputc('"',f); fprintf(f, "%s", el->source); if (sep == ',') fputc('"',f); fputc(lastSep,f); } void chromAliasJsonOutput(struct chromAlias *el, FILE *f) /* Print out chromAlias in JSON format. */ { fputc('{',f); fputc('"',f); fprintf(f,"alias"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->alias); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"chrom"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->chrom); fputc('"',f); fputc(',',f); fputc('"',f); fprintf(f,"source"); fputc('"',f); fputc(':',f); fputc('"',f); fprintf(f, "%s", el->source); fputc('"',f); fputc('}',f); } /* -------------------------------- End autoSql Generated Code -------------------------------- */ /* our "global" data */ static struct { boolean inited; char *database; struct hash *chromToAliasHash; struct hash *aliasToChromHash; struct hash *forwardHash; struct hash *reverseHash; } chromHashes; static boolean checkDatabase(char *database) /* Make sure we don't see different databases. */ { if (database == NULL) return TRUE; if (chromHashes.database != NULL) { if (!sameString(chromHashes.database, database)) { errAbort("chromAliasSetup: only works for one db. %s was passed in earlier, now %s.", chromHashes.database, database); return FALSE; } return TRUE; } chromHashes.database = cloneString(database); return TRUE; } static void readOldAlias(struct lineFile *lf) /* Don't assume the table is fully populated, and dummy up a value for source. */ { char *words[1024]; /* process lines, no more than 1,024 words on a line */ char *line; int size; while (lineFileNext(lf, &line, &size)) { int wordCount = chopByWhite(line, words, ArraySize(words)); if (wordCount > 1) { int i = 1; for ( ; i < wordCount; ++i ) { if (isNotEmpty(words[i])) { struct chromAlias *ali; AllocVar(ali); ali->alias = cloneString(words[i]); ali->chrom = cloneString(words[0]); ali->source = cloneString("asmHub"); hashAdd(chromHashes.forwardHash, ali->alias, ali); hashAdd(chromHashes.reverseHash, ali->chrom, ali); hashAdd(chromHashes.chromToAliasHash, ali->chrom, ali->alias); hashAdd(chromHashes.aliasToChromHash, ali->alias, ali->chrom); //hashAdd(aliasHash, words[0], ali); } } } } - -lineFileClose(&lf); } static void readFieldedTable(struct lineFile *lf) /* Use the fieldedTable library to read in fully populated chromAlias.txt file. */ { struct fieldedTable *aliasTable = fieldedTableAttach(lf, NULL, 0); struct fieldedRow *row; for(row = aliasTable->rowList; row; row = row->next) { char *chrom = row->row[0]; unsigned field; for(field=1; field< aliasTable->fieldCount; field++) { struct chromAlias *new; AllocVar(new); new->chrom = chrom; new->alias = row->row[field]; new->source = aliasTable->fields[field]; hashAdd(chromHashes.forwardHash, new->alias, new); hashAdd(chromHashes.reverseHash, new->chrom, new); hashAdd(chromHashes.chromToAliasHash, new->chrom, new->alias); hashAdd(chromHashes.aliasToChromHash, new->alias, new->chrom); } } } static void chromAliasSetupHub(char *database) /* Look for a chromAlias text table and load the hashes with its contents. */ { char *aliasFile = trackHubAliasFile(database); if (aliasFile == NULL) return; struct lineFile *lf = udcWrapShortLineFile(aliasFile, NULL, MAX_HUB_TRACKDB_FILE_SIZE); chromHashes.forwardHash = hashNew(0); chromHashes.reverseHash = hashNew(0); chromHashes.chromToAliasHash = hashNew(0); chromHashes.aliasToChromHash = hashNew(0); char *line; if (!lineFileNext(lf, &line, NULL)) errAbort("%s is empty", lf->fileName); lineFileReuse(lf); // for the moment always read the alias file in the "old" way //if (line[0] == '#') if (0) readFieldedTable(lf); else readOldAlias(lf); lineFileClose(&lf); } - static void chromAliasSetupSql(char *database) /* Look for a chromAlias SQL table and load the hashes with its contents. */ { if (!hTableExists(database, "chromAlias")) return; struct sqlConnection *conn = hAllocConn(database); chromHashes.forwardHash = hashNew(0); chromHashes.reverseHash = hashNew(0); chromHashes.chromToAliasHash = hashNew(0); chromHashes.aliasToChromHash = hashNew(0); char query[2048]; sqlSafef(query, sizeof(query), "select * from chromAlias"); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { struct chromAlias *new = chromAliasLoad(row); hashAdd(chromHashes.forwardHash, new->alias, new); hashAdd(chromHashes.reverseHash, new->chrom, new); hashAdd(chromHashes.chromToAliasHash, new->chrom, new->alias); hashAdd(chromHashes.aliasToChromHash, new->alias, new->chrom); } sqlFreeResult(&sr); hFreeConn(&conn); } void chromAliasSetup(char *database) /* Read in the chromAlias file/table for this database. */ { if (database == NULL) return; if (!checkDatabase(database)) return; if (chromHashes.inited) return; chromHashes.inited = TRUE; if (trackHubDatabase(database)) chromAliasSetupHub(database); else chromAliasSetupSql(database); } struct hash *chromAliasMakeLookupTable(char *database) /* Given a database name and a connection to that database, construct a lookup table * that takes chromosome alias names to a matching struct chromAlias. Returns NULL * if the given database does not have a chromAlias table. */ { return chromHashes.forwardHash; } struct hash *chromAliasMakeReverseLookupTable(char *database) /* Given a database name and a connection to that database, construct a lookup table * that takes the actual assembly chromosome names to struct chromAliases. Because a * chromosome name may well have multiple aliases, repeated calls to hashLookupNext * may be required to see them all. Returns NULL if the given database does not have * a chromAlias table. */ { return chromHashes.reverseHash; } struct hash *chromAliasAliasToChromHash(char *database) /* Get the hash that maps chrom names to their aliases. */ { return chromHashes.aliasToChromHash; } struct hash *chromAliasChromToAliasHash(char *database) /* Get the hash that maps chrom names to their aliases. */ { return chromHashes.chromToAliasHash; }