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;
 }