7e5840e03baf4a7b7c198016c393d0b86f7b72b6
braney
  Tue Nov 16 15:25:19 2021 -0800
allow hgc pages on chains to provide a link to the "other" browser if
the other assembly is an unattached genark assembly hub

diff --git src/hg/lib/genark.c src/hg/lib/genark.c
index eef5151..bd2707d 100644
--- src/hg/lib/genark.c
+++ src/hg/lib/genark.c
@@ -1,243 +1,290 @@
 /* genark.c was originally generated by the autoSql program, which also 
  * generated genark.h and genark.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 "genark.h"
+#include "hgConfig.h"
+#include "hdb.h"
 
 
 
 char *genarkCommaSepFieldNames = "gcAccession,hubUrl,asmName,scientificName,commonName,taxId";
 
 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. */
 {
 
 ret->gcAccession = row[0];
 ret->hubUrl = row[1];
 ret->asmName = row[2];
 ret->scientificName = row[3];
 ret->commonName = row[4];
 ret->taxId = sqlSigned(row[5]);
 }
 
 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(). */
 {
 struct genark *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 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 dyString *update = newDyString(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s','%s','%s','%s','%s',%d)", 
 	tableName,  el->gcAccession,  el->hubUrl,  el->asmName,  el->scientificName,  el->commonName,  el->taxId);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 struct genark *genarkLoad(char **row)
 /* Load a genark from row fetched with select * from genark
  * from database.  Dispose of this with genarkFree(). */
 {
 struct genark *ret;
 
 AllocVar(ret);
 ret->gcAccession = cloneString(row[0]);
 ret->hubUrl = cloneString(row[1]);
 ret->asmName = cloneString(row[2]);
 ret->scientificName = cloneString(row[3]);
 ret->commonName = cloneString(row[4]);
 ret->taxId = sqlSigned(row[5]);
 return ret;
 }
 
 struct genark *genarkLoadAll(char *fileName) 
 /* Load all genark from a whitespace-separated file.
  * Dispose of this with genarkFreeList(). */
 {
 struct genark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileRow(lf, row))
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct genark *genarkLoadAllByChar(char *fileName, char chopper) 
 /* Load all genark from a chopper separated file.
  * Dispose of this with genarkFreeList(). */
 {
 struct genark *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[6];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = genarkLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 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 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->gcAccession = sqlStringComma(&s);
 ret->hubUrl = sqlStringComma(&s);
 ret->asmName = sqlStringComma(&s);
 ret->scientificName = sqlStringComma(&s);
 ret->commonName = sqlStringComma(&s);
 ret->taxId = sqlSignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void genarkFree(struct genark **pEl)
 /* Free a single dynamically allocated genark such as created
  * with genarkLoad(). */
 {
 struct genark *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->gcAccession);
 freeMem(el->hubUrl);
 freeMem(el->asmName);
 freeMem(el->scientificName);
 freeMem(el->commonName);
 freez(pEl);
 }
 
 void genarkFreeList(struct genark **pList)
 /* Free a list of dynamically allocated genark's */
 {
 struct genark *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     genarkFree(&el);
     }
 *pList = NULL;
 }
 
 void genarkOutput(struct genark *el, FILE *f, char sep, char lastSep) 
 /* Print out genark.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->gcAccession);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->asmName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->commonName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->taxId);
 fputc(lastSep,f);
 }
 
 void genarkJsonOutput(struct genark *el, FILE *f) 
 /* Print out genark in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"gcAccession");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->gcAccession);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"hubUrl");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"asmName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->asmName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"scientificName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"commonName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->commonName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"taxId");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%d", el->taxId);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
+char *genarkUrl(char *accession)
+/* Return the URL to the genark assembly with this accession if present,
+ * otherwise return NULL
+ * */
+{
+char *genarkPrefix = cfgOption("genarkHubPrefix");
+
+if (genarkPrefix == NULL)
+    return NULL;
+
+struct sqlConnection *conn = hConnectCentral();
+if (!sqlTableExists(conn, genarkTableName()))
+    return NULL;
+
+char *url = NULL;
+char query[4096];
+char buffer[4096];
+sqlSafef(query, sizeof query, "select hubUrl from %s where gcAccession='%s'", genarkTableName(), accession);
+if (sqlQuickQuery(conn, query, buffer, sizeof buffer))
+    {
+    char buffer2[4096];
+    safef(buffer2, sizeof buffer2, "%s/%s", genarkPrefix, buffer);
+
+    url = cloneString(buffer2);
+    }
+
+hDisconnectCentral(&conn);
+
+return url;
+}
+
+static char *_genarkTableName = NULL;
+
+char *genarkTableName()
+/* return the genark table name from the environment, 
+ * or hg.conf, or use the default.  Cache the result */
+{
+if (_genarkTableName == NULL)
+    _genarkTableName = cfgOptionEnvDefault("HGDB_GENARK_STATUS_TABLE",
+	    genarkTableConfVariable, defaultGenarkTableName);
+
+return _genarkTableName;
+}
+
+