2390b3f3a5623be111160d4f96fc6ea4c197ca4a
hiram
  Fri Jul 19 11:12:57 2024 -0700
assemblyList table definition for gateway search and findGenome API functions refs #33720

diff --git src/hg/inc/assemblyList.h src/hg/inc/assemblyList.h
new file mode 100644
index 0000000..db0ee5f
--- /dev/null
+++ src/hg/inc/assemblyList.h
@@ -0,0 +1,89 @@
+/* assemblyList.h was originally generated by the autoSql program, which also 
+ * generated assemblyList.c and assemblyList.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef ASSEMBLYLIST_H
+#define ASSEMBLYLIST_H
+
+#include "jksql.h"
+#define ASSEMBLYLIST_NUM_COLS 9
+
+extern char *assemblyListCommaSepFieldNames;
+
+struct assemblyList
+/* listing all UCSC genomes, and all NCBI assemblies, with search priority, and status if browser available or can be requested */
+    {
+    struct assemblyList *next;  /* Next in singly linked list. */
+    char *name;	/* UCSC genome: dbDb name or GenArk/NCBI accession */
+    unsigned *priority;	/* assigned search priority */
+    char *commonName;	/* a common name */
+    char *scientificName;	/* binomial scientific name */
+    unsigned *taxId;	/* Entrez taxon ID: www.ncbi.nlm.nih.gov/taxonomy/?term=xxx */
+    char *clade;	/* approximate clade: primates mammals birds fish ... etc ... */
+    char *description;	/* other description text */
+    unsigned char *browserExists;	/* 1 == this assembly is available at UCSC, 0 == can be requested */
+    char *hubUrl;	/* path name to hub.txt: GCF/000/001/405/GCF_000001405.39/hub.txt */
+    };
+
+void assemblyListStaticLoadWithNull(char **row, struct assemblyList *ret);
+/* Load a row from assemblyList table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct assemblyList *assemblyListLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all assemblyList 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 assemblyListFreeList(). */
+
+void assemblyListSaveToDb(struct sqlConnection *conn, struct assemblyList *el, char *tableName, int updateSize);
+/* Save assemblyList 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 assemblyList *assemblyListLoadWithNull(char **row);
+/* Load a assemblyList from row fetched with select * from assemblyList
+ * from database.  Dispose of this with assemblyListFree(). */
+
+struct assemblyList *assemblyListLoadAll(char *fileName);
+/* Load all assemblyList from whitespace-separated file.
+ * Dispose of this with assemblyListFreeList(). */
+
+struct assemblyList *assemblyListLoadAllByChar(char *fileName, char chopper);
+/* Load all assemblyList from chopper separated file.
+ * Dispose of this with assemblyListFreeList(). */
+
+#define assemblyListLoadAllByTab(a) assemblyListLoadAllByChar(a, '\t');
+/* Load all assemblyList from tab separated file.
+ * Dispose of this with assemblyListFreeList(). */
+
+struct assemblyList *assemblyListCommaIn(char **pS, struct assemblyList *ret);
+/* Create a assemblyList out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new assemblyList */
+
+void assemblyListFree(struct assemblyList **pEl);
+/* Free a single dynamically allocated assemblyList such as created
+ * with assemblyListLoad(). */
+
+void assemblyListFreeList(struct assemblyList **pList);
+/* Free a list of dynamically allocated assemblyList's */
+
+void assemblyListOutput(struct assemblyList *el, FILE *f, char sep, char lastSep);
+/* Print out assemblyList.  Separate fields with sep. Follow last field with lastSep. */
+
+#define assemblyListTabOut(el,f) assemblyListOutput(el,f,'\t','\n');
+/* Print out assemblyList as a line in a tab-separated file. */
+
+#define assemblyListCommaOut(el,f) assemblyListOutput(el,f,',',',');
+/* Print out assemblyList as a comma separated list including final comma. */
+
+void assemblyListJsonOutput(struct assemblyList *el, FILE *f);
+/* Print out assemblyList in JSON format. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* ASSEMBLYLIST_H */
+