7d0d819ed29f8a0501c3e8e99930b83ccdbf65e4
hiram
  Mon Apr 12 14:01:50 2021 -0700
genark table definition to relate GC accession to hub url refs #27285

diff --git src/hg/lib/genark.c src/hg/lib/genark.c
new file mode 100644
index 0000000..eef5151
--- /dev/null
+++ src/hg/lib/genark.c
@@ -0,0 +1,243 @@
+/* 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"
+
+
+
+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 -------------------------------- */
+