b94993d07e5d0ef24f17a40c9ca7f5b2ddb93701
braney
  Wed May 11 10:50:56 2022 -0700
allow hubs to specify a naming authority for the chromosome that's
displayed by the browser

diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c
index f318542..98f56e0 100644
--- src/hg/lib/chromAlias.c
+++ src/hg/lib/chromAlias.c
@@ -1,410 +1,487 @@
 /* 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 <pthread.h>
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
+#include "cart.h"
 #include "chromAlias.h"
 #include "hdb.h"
 #include "trackHub.h"
 #include "fieldedTable.h"
 #include "bigBed.h"
 #include "bbiAlias.h"
 #include "bPlusTree.h"
+#include "errCatch.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;
 boolean bptInited;
 struct bptIndex *bptList;
 struct bbiFile *bbi;
 struct lm *lm;
+int fieldCount; /* Number of fields. */
+char **fields;  /* Names of fields. */
 struct hash *chromToAliasHash;
 struct hash *aliasToChromHash;
 } chromAliasGlobals;
 
 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;
+        char *native = cloneString(words[0]);
         for ( ; i < wordCount; ++i )
             {
             if (isNotEmpty(words[i]))
                 {
-                char *alias = cloneString(words[i]);
-                char *chrom = cloneString(words[0]);
-                hashAdd(chromAliasGlobals.chromToAliasHash, chrom, alias);
-                hashAdd(chromAliasGlobals.aliasToChromHash, alias, chrom);
+                struct chromAlias *chromAlias;
+                AllocVar(chromAlias);
+                chromAlias->chrom = native;
+                chromAlias->alias = cloneString(words[i]);
+                chromAlias->source = "none";
+
+                hashAdd(chromAliasGlobals.chromToAliasHash, chromAlias->chrom, chromAlias);
+                hashAdd(chromAliasGlobals.aliasToChromHash, chromAlias->alias, chromAlias);
                 }
             }
         }
     }
 }
 
 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); 
+chromAliasGlobals.fieldCount = aliasTable->fieldCount;
+chromAliasGlobals.fields = aliasTable->fields;
+
 struct fieldedRow *row;
 for(row = aliasTable->rowList; row; row = row->next)
     {
-    char *chrom = row->row[0];
+    char *native = row->row[0];
 
     unsigned field;
     for(field=1; field< aliasTable->fieldCount; field++)
         {
         char *alias = row->row[field];
-        hashAdd(chromAliasGlobals.chromToAliasHash, chrom, alias);
-        hashAdd(chromAliasGlobals.aliasToChromHash, alias, chrom);
+        char *source = aliasTable->fields[field];
+
+        struct chromAlias *chromAlias;
+        AllocVar(chromAlias);
+        chromAlias->chrom = native;
+        chromAlias->alias = alias;
+        chromAlias->source = source;
+        hashAdd(chromAliasGlobals.chromToAliasHash, native, chromAlias);
+        hashAdd(chromAliasGlobals.aliasToChromHash, alias, chromAlias);
         }
     }
 }
 
 static char * gbdbBbExists(char *database)
 /* use a gbdb bigBed as our alias file. */
 {
 // not supported at the moment
+/*
+char buffer[4096];
+safef(buffer, sizeof buffer, "/gbdb/%s/chromAlias.bb", database);
+if (fileExists(buffer))
+    return cloneString(buffer);
+    */
 return NULL;
 }
 
 static void chromAliasSetupBb(char *database, char *bbFile)
 /* Look for a chromAlias bigBed file and open it. */
 {
 chromAliasGlobals.bbi = bigBedFileOpen(bbFile);
 chromAliasGlobals.bptList = bbiAliasOpenExtra(chromAliasGlobals.bbi);
 chromAliasGlobals.lm = lmInit(0);
 }
 
 static void chromAliasSetupHub(char *database)
 /* Look for a chromAlias text table and load the hashes with its contents. */
 {
 char *aliasBbFile = trackHubAliasBbFile(database);
 if (aliasBbFile != NULL)
     {
     chromAliasSetupBb(database, aliasBbFile);
     return;
     }
 char *aliasFile = trackHubAliasFile(database);
 if (aliasFile == NULL)
     return;
 
 struct lineFile *lf = udcWrapShortLineFile(aliasFile, NULL, MAX_HUB_TRACKDB_FILE_SIZE);
 
 chromAliasGlobals.chromToAliasHash = hashNew(0);
 chromAliasGlobals.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)
+struct errCatch *errCatch = errCatchNew();
+if (errCatchStart(errCatch))
     readFieldedTable(lf);
-else
+errCatchEnd(errCatch);
+if (errCatch->gotError)
+    {
+    lineFileClose(&lf);
+    lf = udcWrapShortLineFile(aliasFile, NULL, MAX_HUB_TRACKDB_FILE_SIZE);
     readOldAlias(lf);
+    }
+errCatchFree(&errCatch);
 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);
 chromAliasGlobals.chromToAliasHash = hashNew(0);
 chromAliasGlobals.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(chromAliasGlobals.chromToAliasHash, new->chrom, new->alias);
-    hashAdd(chromAliasGlobals.aliasToChromHash, new->alias, new->chrom);
+    hashAdd(chromAliasGlobals.chromToAliasHash, new->chrom, new);
+    hashAdd(chromAliasGlobals.aliasToChromHash, new->alias, new);
     }
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 }
 
 static pthread_mutex_t ourMutex = PTHREAD_MUTEX_INITIALIZER;
 
 static void getLock()
 /* Create a mutex to make the code thread safe. */
 {
 pthread_mutex_lock( &ourMutex );
 }
 
 static void releaseLock()
 /* Release our mutex. */
 {
 pthread_mutex_unlock( &ourMutex );
 }
 
 void chromAliasSetup(char *database)
 /* Read in the chromAlias file/table for this database. */
 {
 if (database == NULL)
     return;
 
 getLock();
 if (chromAliasGlobals.inited)
     return;
 chromAliasGlobals.inited = TRUE;
 
 char *gbdbFile;
 if (trackHubDatabase(database))
     chromAliasSetupHub(database);
 else if ((gbdbFile = gbdbBbExists(database)) != NULL)
     chromAliasSetupBb(database, gbdbFile);
 else
     chromAliasSetupSql(database);
 releaseLock();
 }
 
 char *findNativeHashes(char *alias)
 /* Find a native sequence given an alias using the hash tables. */
 {
-char *chrom = (char *)hashFindVal(chromAliasGlobals.aliasToChromHash, alias);
-if (isNotEmpty(chrom))
-    return cloneString(chrom);
+struct chromAlias *chromAlias = (struct chromAlias *)hashFindVal(chromAliasGlobals.aliasToChromHash, alias);
+if (chromAlias != NULL)
+    return cloneString(chromAlias->chrom);
 return NULL;
 }
 
 char *chromAliasFindNative(char *alias)
 /* Find the native seqName for a given alias. */
 {
 static struct hash *cachedNative;
 char *chrom;
 
 if (cachedNative == NULL)
     cachedNative = newHash(6);
 
 if ((chrom = hashFindVal(cachedNative, alias)) != NULL)
     return chrom;
 
 getLock();
 if ((chrom = hashFindVal(cachedNative, alias)) == NULL)
     {
     if (chromAliasGlobals.bbi)
         chrom = bbiAliasFindNative(chromAliasGlobals.bbi, chromAliasGlobals.bptList, chromAliasGlobals.lm,  alias);
     else if (chromAliasGlobals.aliasToChromHash)
         chrom = findNativeHashes(alias);
 
-    hashAdd(cachedNative, alias, chrom);
+    hashAdd(cachedNative, alias, cloneString(chrom));
     }
 releaseLock();
 
 return cloneString(chrom);
 }
 
 struct slName *findAliasesHashes(char *seqName)
 /* Find the aliases for a given seqName using the hashes. */
 {
 struct slName *slList = NULL;
 struct hashEl *thisEl = hashLookup(chromAliasGlobals.chromToAliasHash, seqName);
 
 for (;thisEl != NULL; thisEl = hashLookupNext(thisEl))
     {
-    struct slName *name = newSlName((char *)thisEl->val);
+    struct chromAlias *chromAlias = (struct chromAlias *)thisEl->val;
+    struct slName *name = newSlName(chromAlias->alias);
     slAddHead(&slList, name);
     }
 
 return slList;
 }
 
 struct slName *chromAliasFindAliases(char *seqName)
 /* Find the aliases for a given seqName. */
 {
 static struct hash *cachedAliases;
 struct slName *aliases;
 
 if (cachedAliases == NULL)
     cachedAliases = newHash(6);
 
 if ((aliases = hashFindVal(cachedAliases, seqName)) != NULL)
     return aliases;
 
 getLock();
 if ((aliases = hashFindVal(cachedAliases, seqName)) == NULL)
     {
     if (chromAliasGlobals.bbi)
         aliases = bbiAliasFindAliases(chromAliasGlobals.bbi,chromAliasGlobals.lm, seqName);
     else if (chromAliasGlobals.chromToAliasHash)
         aliases = findAliasesHashes(seqName);
 
     hashAdd(cachedAliases, seqName, aliases);
     }
 releaseLock();
 
 return aliases;
 }
+
+char *chromAliasFindSingleAlias(char *seqName, char *authority)
+/* Find the aliases for a given seqName from a given authority. */
+{
+if (authority == NULL)
+    return cloneString(seqName);
+
+
+struct slName *aliases = chromAliasFindAliases(seqName);
+
+if (aliases == NULL)
+    return cloneString(seqName);
+
+unsigned fieldNum = 1;
+for(; fieldNum < chromAliasGlobals.fieldCount; fieldNum++)
+    {
+    if (sameString(authority, chromAliasGlobals.fields[fieldNum]))
+        break;
+    }
+
+if (fieldNum >= chromAliasGlobals.fieldCount)
+    return cloneString(seqName);
+
+
+unsigned count = 1;
+for(; aliases && count < fieldNum; count++,aliases = aliases->next)
+    ;
+if (!isEmpty(aliases->name))
+    return cloneString(aliases->name);
+
+return cloneString(seqName);
+}
+
+char *chromAliasGetDisplayChrom(char *db, struct cart *cart, char *seqName)
+/* Return the sequence name to display based on the database and cart. */
+{
+if (trackHubDatabase(db))
+    {
+    struct trackHubGenome *genome = trackHubGetGenome(db);
+
+    return chromAliasFindSingleAlias(seqName, genome->chromAuthority);
+    }
+
+return seqName;
+}
+