d947dcc75b04fd0dc921c0eb02ed988d7b4819f0
braney
  Mon Jun 30 16:00:56 2025 -0700
let genark hubs appear in hgConvert if we can figure out their UCSC org

diff --git src/hg/inc/genark.h src/hg/inc/genark.h
index 25876f7c5f7..16587cee49e 100644
--- src/hg/inc/genark.h
+++ src/hg/inc/genark.h
@@ -1,126 +1,134 @@
 /* genark.h was originally generated by the autoSql program, which also 
  * generated genark.c and genark.sql.  This header links the database and
  * the RAM representation of objects. */
 
 #ifndef GENARK_H
 #define GENARK_H
 
 #include "jksql.h"
 #define GENARK_NUM_COLS 8
 
 #define defaultGenarkTableName "genark"
 /* Name of table that maintains the names of hubs we'll automatically attach if referenced. */
 
 #define genarkTableConfVariable    "hub.genArkTableName"
 /* the name of the hg.conf variable to use something other than the default */
 
 
 extern char *genarkCommaSepFieldNames;
 
 struct genark
 /* index to UCSC assembly hubs */
     {
     struct genark *next;  /* Next in singly linked list. */
     char *gcAccession;	/* GC[AF] accssion identifier, e.g.: GCF_000001405.39 */
     char *hubUrl;	/* path name to hub.txt: GCF/000/001/405/GCF_000001405.39/hub.txt */
     char *asmName;	/* assembly name: GRCh38.p13 */
     char *scientificName;	/* scientific name: Homo sapiens */
     char *commonName;	/* common name: human */
     int taxId;	/* taxon id: 9606 */
     int priority;	/* search priority to order hgGateway results */
     char *clade;	/* clade group in the GenArk system */
     };
 
 void genarkStaticLoad(char **row, struct genark *ret);
 /* Load a row from genark table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 
 struct genark *genarkLoadByQuery(struct sqlConnection *conn, char *query);
 /* Load all genark from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with genarkFreeList(). */
 
 void genarkSaveToDb(struct sqlConnection *conn, struct genark *el, char *tableName, int updateSize);
 /* Save genark as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql. */
 
 struct genark *genarkLoad(char **row);
 /* Load a genark from row fetched with select * from genark
  * from database.  Dispose of this with genarkFree(). */
 
 struct genark *genarkLoadAll(char *fileName);
 /* Load all genark from whitespace-separated file.
  * Dispose of this with genarkFreeList(). */
 
 struct genark *genarkLoadAllByChar(char *fileName, char chopper);
 /* Load all genark from chopper separated file.
  * Dispose of this with genarkFreeList(). */
 
 #define genarkLoadAllByTab(a) genarkLoadAllByChar(a, '\t');
 /* Load all genark from tab separated file.
  * Dispose of this with genarkFreeList(). */
 
 struct genark *genarkCommaIn(char **pS, struct genark *ret);
 /* Create a genark out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new genark */
 
 void genarkFree(struct genark **pEl);
 /* Free a single dynamically allocated genark such as created
  * with genarkLoad(). */
 
 void genarkFreeList(struct genark **pList);
 /* Free a list of dynamically allocated genark's */
 
 void genarkOutput(struct genark *el, FILE *f, char sep, char lastSep);
 /* Print out genark.  Separate fields with sep. Follow last field with lastSep. */
 
 #define genarkTabOut(el,f) genarkOutput(el,f,'\t','\n');
 /* Print out genark as a line in a tab-separated file. */
 
 #define genarkCommaOut(el,f) genarkOutput(el,f,',',',');
 /* Print out genark as a comma separated list including final comma. */
 
 void genarkJsonOutput(struct genark *el, FILE *f);
 /* Print out genark in JSON format. */
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 char *genarkUrl(char *accession);
 /* Return the URL to the genark assembly with this accession if present,
  * otherwise return NULL
  * */
 
 char *genArkPath(char *genome);
 /* given a GenArk hub genome name, e.g. GCA_021951015.1 return the path:
  *               GCA/021/951/015
  * prefix that with desired server URL: https://hgdownload.soe.ucsc.edu/hubs/
  *   if desired.  Or suffix add /hub.txt to get the hub.txt URL
  *   The path returned does not depend upon this GCx_ naming scheme,
  *   it simply uses the hub URL as returned from genarkUrl(genome) and
  *   returns the middle part without the https://... prefix
  */
 
 char *genarkTableName();
 /* return the genark table name from the environment, 
  * or hg.conf, or use the default.  Cache the result */
 
 /* temporary function while the genark table is in transistion with
  * new coluns being added, July 2024.  Allows compatibility with existing
  * genark table.
  */
 int genArkColumnCount();
 /* return number of columns in genark table */
 
 boolean isGenArk(char *genome);
 /* given a genome name, see if it is in the genark table to determine
  *  yes/no this is a genark genome assembly
  */
 
+struct dbDb *genarkLiftOverDbs(char *listOfAccs);
+/* return list of dbDb structures for the genark genomes that match listOfAccs */
+
+struct dbDb *genarkLiftOverDb(char *acc);
+/* return dbDb structure for GC* acc */
+
+struct hash *genarkGetOrgHash();
+/* read table that maps gcAccession to UCSC org. */
 #endif /* GENARK_H */