8ecd4ec7a45dc9f84f487d829b648f69c05fa862
hiram
  Wed Aug 28 15:11:22 2024 -0700
adding four columns to the database table for more accurate search refs #32596

diff --git src/hg/lib/assemblyList.c src/hg/lib/assemblyList.c
index a31a38f..0010c69 100644
--- src/hg/lib/assemblyList.c
+++ src/hg/lib/assemblyList.c
@@ -1,344 +1,419 @@
 /* assemblyList.c was originally generated by the autoSql program, which also
  * generated assemblyList.h and assemblyList.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 "hgConfig.h"
 #include "assemblyList.h"
 
-char *assemblyListCommaSepFieldNames = "name,priority,commonName,scientificName,taxId,clade,description,browserExists,hubUrl";
+char *assemblyListCommaSepFieldNames = "name,priority,commonName,scientificName,taxId,clade,description,browserExists,hubUrl,year,refSeqCategory,versionStatus,assemblyLevel";
 
 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. */
 {
 
 ret->name = row[0];
 if (row[1] != NULL)
     {
     ret->priority = needMem(sizeof(*(ret->priority)));
     *(ret->priority) = sqlUnsigned(row[1]);
     }
 else
     {
     ret->priority = NULL;
     }
 ret->commonName = row[2];
 ret->scientificName = row[3];
 if (row[4] != NULL)
     {
     ret->taxId = needMem(sizeof(*(ret->taxId)));
     *(ret->taxId) = sqlUnsigned(row[4]);
     }
 else
     {
     ret->taxId = NULL;
     }
 ret->clade = row[5];
 ret->description = row[6];
 if (row[7] != NULL)
     {
     ret->browserExists = needMem(sizeof(*(ret->browserExists)));
     *(ret->browserExists) = sqlUnsigned(row[7]);
     }
 else
     {
     ret->browserExists = NULL;
     }
 ret->hubUrl = row[8];
+if (row[9] != NULL)
+    {
+    ret->year = needMem(sizeof(*(ret->year)));
+    *(ret->year) = sqlUnsigned(row[9]);
+    }
+else
+    {
+    ret->year = NULL;
+    }
+ret->refSeqCategory = row[10];
+ret->versionStatus = row[11];
+ret->assemblyLevel = row[12];
 }
 
 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(). */
 {
 struct assemblyList *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = assemblyListLoadWithNull(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 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 dyString *update = dyStringNew(updateSize);
-sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,'%s','%s',%u,'%s','%s',%u,'%s')", 
-	tableName,  el->name,  *(el->priority),  el->commonName,  el->scientificName,  *(el->taxId),  el->clade,  el->description,  *(el->browserExists),  el->hubUrl);
+sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,'%s','%s',%u,'%s','%s',%u,'%s',%u,'%s','%s','%s')",
+	tableName,  el->name,  *(el->priority),  el->commonName,  el->scientificName,  *(el->taxId),  el->clade,  el->description,  *(el->browserExists),  el->hubUrl,  *(el->year),  el->refSeqCategory,  el->versionStatus,  el->assemblyLevel);
 sqlUpdate(conn, update->string);
 dyStringFree(&update);
 }
 
 struct assemblyList *assemblyListLoadWithNull(char **row)
 /* Load a assemblyList from row fetched with select * from assemblyList
  * from database.  Dispose of this with assemblyListFree(). */
 {
 struct assemblyList *ret;
 
 AllocVar(ret);
 ret->name = cloneString(row[0]);
 if (row[1] != NULL)
     {
     ret->priority = needMem(sizeof(*(ret->priority)));
     *(ret->priority) = sqlUnsigned(row[1]);
     }
 else
     {
     ret->priority = NULL;
     }
 ret->commonName = cloneString(row[2]);
 ret->scientificName = cloneString(row[3]);
 if (row[4] != NULL)
     {
     ret->taxId = needMem(sizeof(*(ret->taxId)));
     *(ret->taxId) = sqlUnsigned(row[4]);
     }
 else
     {
     ret->taxId = NULL;
     }
 ret->clade = cloneString(row[5]);
 ret->description = cloneString(row[6]);
 if (row[7] != NULL)
     {
     ret->browserExists = needMem(sizeof(*(ret->browserExists)));
     *(ret->browserExists) = sqlUnsigned(row[7]);
     }
 else
     {
     ret->browserExists = NULL;
     }
 ret->hubUrl = cloneString(row[8]);
+if (row[9] != NULL)
+    {
+    ret->year = needMem(sizeof(*(ret->year)));
+    *(ret->year) = sqlUnsigned(row[9]);
+    }
+else
+    {
+    ret->year = NULL;
+    }
+ret->refSeqCategory = cloneString(row[10]);
+ret->versionStatus = cloneString(row[11]);
+ret->assemblyLevel = cloneString(row[12]);
 return ret;
 }
 
 struct assemblyList *assemblyListLoadAll(char *fileName)
 /* Load all assemblyList from a whitespace-separated file.
  * Dispose of this with assemblyListFreeList(). */
 {
 struct assemblyList *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[9];
+char *row[13];
 
 while (lineFileRow(lf, row))
     {
     el = assemblyListLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct assemblyList *assemblyListLoadAllByChar(char *fileName, char chopper)
 /* Load all assemblyList from a chopper separated file.
  * Dispose of this with assemblyListFreeList(). */
 {
 struct assemblyList *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[9];
+char *row[13];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = assemblyListLoadWithNull(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 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 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->name = sqlStringComma(&s);
 ret->priority = needMem(sizeof(unsigned));
 *(ret->priority) = sqlUnsignedComma(&s);
 ret->commonName = sqlStringComma(&s);
 ret->scientificName = sqlStringComma(&s);
 ret->taxId = needMem(sizeof(unsigned));
 *(ret->taxId) = sqlUnsignedComma(&s);
 ret->clade = sqlStringComma(&s);
 ret->description = sqlStringComma(&s);
 ret->browserExists = needMem(sizeof(unsigned));
 *(ret->browserExists) = sqlUnsignedComma(&s);
 ret->hubUrl = sqlStringComma(&s);
+ret->year = needMem(sizeof(unsigned));
+*(ret->year) = sqlUnsignedComma(&s);
+ret->refSeqCategory = sqlStringComma(&s);
+ret->versionStatus = sqlStringComma(&s);
+ret->assemblyLevel = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void assemblyListFree(struct assemblyList **pEl)
 /* Free a single dynamically allocated assemblyList such as created
  * with assemblyListLoad(). */
 {
 struct assemblyList *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->commonName);
 freeMem(el->scientificName);
 freeMem(el->clade);
 freeMem(el->description);
 freeMem(el->hubUrl);
+freeMem(el->refSeqCategory);
+freeMem(el->versionStatus);
+freeMem(el->assemblyLevel);
 freez(pEl);
 }
 
 void assemblyListFreeList(struct assemblyList **pList)
 /* Free a list of dynamically allocated assemblyList's */
 {
 struct assemblyList *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     assemblyListFree(&el);
     }
 *pList = NULL;
 }
 
 void assemblyListOutput(struct assemblyList *el, FILE *f, char sep, char lastSep)
 /* Print out assemblyList.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", *(el->priority));
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->commonName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", *(el->taxId));
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->clade);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", *(el->browserExists));
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->hubUrl);
 if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", *(el->year));
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->refSeqCategory);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->versionStatus);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->assemblyLevel);
+if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void assemblyListJsonOutput(struct assemblyList *el, FILE *f)
 /* Print out assemblyList in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"name");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->name);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"priority");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%u", *(el->priority));
 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,"scientificName");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->scientificName);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"taxId");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%u", *(el->taxId));
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"clade");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->clade);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"description");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->description);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"browserExists");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%u", *(el->browserExists));
 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,"year");
+fputc('"',f);
+fputc(':',f);
+fprintf(f, "%u", *(el->year));
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"refSeqCategory");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->refSeqCategory);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"versionStatus");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->versionStatus);
+fputc('"',f);
+fputc(',',f);
+fputc('"',f);
+fprintf(f,"assemblyLevel");
+fputc('"',f);
+fputc(':',f);
+fputc('"',f);
+fprintf(f, "%s", el->assemblyLevel);
+fputc('"',f);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *_assemblyListTableName = NULL;
 
 char *assemblyListTableName()
 /* return the assemblyList table name from the environment,
  * or hg.conf, or use the default.  Cache the result */
 {
 if (_assemblyListTableName == NULL)
     _assemblyListTableName = cfgOptionEnvDefault("HGDB_ASSEMBLYLIST_STATUS_TABLE",
 	    assemblyListTableConfVariable, defaultAssemblyListTableName);
 
 return _assemblyListTableName;
 }
-