0564395ec363631f2ff8d295da6f6b50f873fda4
braney
  Mon Jan 24 17:01:53 2022 -0800
more chromAlias work:  some name changes and support for the new genark
chromAlias format

diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c
index c5c2a59..d123ccd 100644
--- src/hg/lib/chromAlias.c
+++ src/hg/lib/chromAlias.c
@@ -1,252 +1,362 @@
 /* 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 *nameHash;
+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;
 }
 
-void chromAliasSetup(char *database)
-/* Read in the chromAlias file/table for this database. */
+static void readOldAlias(struct lineFile *lf)
+/* Don't assume the table is fully populated, and dummy up a value for source. */
 {
-if (!checkDatabase(database))
+char *words[1024];	/* process lines, no more than 1,024 words on a line */
+char *line;
+int size;
+printf("<BR>readOldAlias<BR>\n");
+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);
+
+if (line[0] == '#')
+    readFieldedTable(lf);
+else
+    readOldAlias(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.nameHash = 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.nameHash, new->chrom, new->alias);
+    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 (!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. */
 {
-if (!checkDatabase(database))
-    return NULL;
+chromAliasSetup(database);
 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. */
 {
-if (!checkDatabase(database))
-    return NULL;
+chromAliasSetup(database);
 return chromHashes.reverseHash;
 }
 
-struct hash *chromAliasGetHash(char *database)
+struct hash *chromAliasAliasToChromHash(char *database)
 /* Get the hash that maps chrom names to their aliases. */
 {
-if (!checkDatabase(database))
-    return NULL;
+chromAliasSetup(database);
+return chromHashes.aliasToChromHash;
+}
 
-return chromHashes.nameHash;
+struct hash *chromAliasChromToAliasHash(char *database)
+/* Get the hash that maps chrom names to their aliases. */
+{
+chromAliasSetup(database);
+return chromHashes.chromToAliasHash;
 }