4c1d2a0a761f1afc9da81243357e462ae14c3756
braney
  Thu Dec 15 14:49:26 2022 -0800
add assembly aliasing to hub connection

diff --git src/hg/lib/asmAlias.c src/hg/lib/asmAlias.c
new file mode 100644
index 0000000..4ca38e6
--- /dev/null
+++ src/hg/lib/asmAlias.c
@@ -0,0 +1,185 @@
+/* asmAlias.c was originally generated by the autoSql program, which also 
+ * generated asmAlias.h and asmAlias.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 "hdb.h"
+#include "asmAlias.h"
+
+
+
+char *asmAliasCommaSepFieldNames = "alias,browser";
+
+void asmAliasStaticLoad(char **row, struct asmAlias *ret)
+/* Load a row from asmAlias table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->alias = row[0];
+ret->browser = row[1];
+}
+
+struct asmAlias *asmAliasLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all asmAlias 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 asmAliasFreeList(). */
+{
+struct asmAlias *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = asmAliasLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void asmAliasSaveToDb(struct sqlConnection *conn, struct asmAlias *el, char *tableName, int updateSize)
+/* Save asmAlias 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 = dyStringNew(updateSize);
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s')", 
+	tableName,  el->alias,  el->browser);
+sqlUpdate(conn, update->string);
+dyStringFree(&update);
+}
+
+struct asmAlias *asmAliasLoad(char **row)
+/* Load a asmAlias from row fetched with select * from asmAlias
+ * from database.  Dispose of this with asmAliasFree(). */
+{
+struct asmAlias *ret;
+
+AllocVar(ret);
+ret->alias = cloneString(row[0]);
+ret->browser = cloneString(row[1]);
+return ret;
+}
+
+struct asmAlias *asmAliasLoadAll(char *fileName) 
+/* Load all asmAlias from a whitespace-separated file.
+ * Dispose of this with asmAliasFreeList(). */
+{
+struct asmAlias *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileRow(lf, row))
+    {
+    el = asmAliasLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct asmAlias *asmAliasLoadAllByChar(char *fileName, char chopper) 
+/* Load all asmAlias from a chopper separated file.
+ * Dispose of this with asmAliasFreeList(). */
+{
+struct asmAlias *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[2];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = asmAliasLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct asmAlias *asmAliasCommaIn(char **pS, struct asmAlias *ret)
+/* Create a asmAlias out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new asmAlias */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->alias = sqlStringComma(&s);
+ret->browser = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void asmAliasFree(struct asmAlias **pEl)
+/* Free a single dynamically allocated asmAlias such as created
+ * with asmAliasLoad(). */
+{
+struct asmAlias *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->alias);
+freeMem(el->browser);
+freez(pEl);
+}
+
+void asmAliasFreeList(struct asmAlias **pList)
+/* Free a list of dynamically allocated asmAlias's */
+{
+struct asmAlias *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    asmAliasFree(&el);
+    }
+*pList = NULL;
+}
+
+void asmAliasOutput(struct asmAlias *el, FILE *f, char sep, char lastSep) 
+/* Print out asmAlias.  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->browser);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+char *asmAliasFind(char *alias)
+/* If this assembly is an alias for a db we know about, return it.  Otherwise return what we were sent. */
+{
+if (alias == NULL)
+    return NULL;
+
+char *ret = alias;
+struct sqlConnection *centralConn = hConnectCentral();
+
+if (!sqlTableExists(centralConn, "asmAlias"))
+    return alias;
+
+char buffer[4096];
+
+sqlSafef(buffer, sizeof buffer, "select * from asmAlias where alias='%s' limit 1", alias);
+struct asmAlias *asmAlias = asmAliasLoadByQuery(centralConn, buffer);
+hDisconnectCentral(&centralConn);
+if (asmAlias)
+    ret = asmAlias->browser;
+
+return ret;
+}