4418dae2476e397d9c03c1301e573e2c45b1a58e
hiram
  Fri Feb 10 12:16:43 2023 -0800
adding asmEquivalent functions to this library no redmine

diff --git src/hg/lib/asmEquivalent.c src/hg/lib/asmEquivalent.c
index 64896b4..3971aadd 100644
--- src/hg/lib/asmEquivalent.c
+++ src/hg/lib/asmEquivalent.c
@@ -1,255 +1,307 @@
 /* asmEquivalent.c was originally generated by the autoSql program, which also 
  * generated asmEquivalent.h and asmEquivalent.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 "asmEquivalent.h"
 
+#include "hdb.h"
+
 
 
 char *asmEquivalentCommaSepFieldNames = "source,destination,sourceAuthority,destinationAuthority,matchCount,sourceCount,destinationCount";
 
 /* definitions for sourceAuthority column */
 static char *values_sourceAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL};
 static struct hash *valhash_sourceAuthority = NULL;
 
 /* definitions for destinationAuthority column */
 static char *values_destinationAuthority[] = {"ensembl", "ucsc", "genbank", "refseq", NULL};
 static struct hash *valhash_destinationAuthority = NULL;
 
 void asmEquivalentStaticLoad(char **row, struct asmEquivalent *ret)
 /* Load a row from asmEquivalent table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->source = row[0];
 ret->destination = row[1];
 ret->sourceAuthority = sqlEnumParse(row[2], values_sourceAuthority, &valhash_sourceAuthority);
 ret->destinationAuthority = sqlEnumParse(row[3], values_destinationAuthority, &valhash_destinationAuthority);
 ret->matchCount = sqlLongLong(row[4]);
 ret->sourceCount = sqlLongLong(row[5]);
 ret->destinationCount = sqlLongLong(row[6]);
 }
 
 struct asmEquivalent *asmEquivalentLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all asmEquivalent 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 asmEquivalentFreeList(). */
 {
 struct asmEquivalent *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = asmEquivalentLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void asmEquivalentSaveToDb(struct sqlConnection *conn, struct asmEquivalent *el, char *tableName, int updateSize)
 /* Save asmEquivalent 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',(null),(null),%lld,%lld,%lld)",
+sqlDyStringPrintf(update, "insert into %s values ( '%s','%s',%d,%d,%lld,%lld,%lld)",
 	tableName,  el->source,  el->destination,  el->sourceAuthority,  el->destinationAuthority,  el->matchCount,  el->sourceCount,  el->destinationCount);
 sqlUpdate(conn, update->string);
 dyStringFree(&update);
 }
 
 struct asmEquivalent *asmEquivalentLoad(char **row)
 /* Load a asmEquivalent from row fetched with select * from asmEquivalent
  * from database.  Dispose of this with asmEquivalentFree(). */
 {
 struct asmEquivalent *ret;
 
 AllocVar(ret);
 ret->source = cloneString(row[0]);
 ret->destination = cloneString(row[1]);
 ret->sourceAuthority = sqlEnumParse(row[2], values_sourceAuthority, &valhash_sourceAuthority);
 ret->destinationAuthority = sqlEnumParse(row[3], values_destinationAuthority, &valhash_destinationAuthority);
 ret->matchCount = sqlLongLong(row[4]);
 ret->sourceCount = sqlLongLong(row[5]);
 ret->destinationCount = sqlLongLong(row[6]);
 return ret;
 }
 
 struct asmEquivalent *asmEquivalentLoadAll(char *fileName)
 /* Load all asmEquivalent from a whitespace-separated file.
  * Dispose of this with asmEquivalentFreeList(). */
 {
 struct asmEquivalent *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = asmEquivalentLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct asmEquivalent *asmEquivalentLoadAllByChar(char *fileName, char chopper)
 /* Load all asmEquivalent from a chopper separated file.
  * Dispose of this with asmEquivalentFreeList(). */
 {
 struct asmEquivalent *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = asmEquivalentLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct asmEquivalent *asmEquivalentCommaIn(char **pS, struct asmEquivalent *ret)
 /* Create a asmEquivalent out of a comma separated string.
  * This will fill in ret if non-null, otherwise will
  * return a new asmEquivalent */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->source = sqlStringComma(&s);
 ret->destination = sqlStringComma(&s);
 ret->sourceAuthority = sqlEnumComma(&s, values_sourceAuthority, &valhash_sourceAuthority);
 ret->destinationAuthority = sqlEnumComma(&s, values_destinationAuthority, &valhash_destinationAuthority);
 ret->matchCount = sqlLongLongComma(&s);
 ret->sourceCount = sqlLongLongComma(&s);
 ret->destinationCount = sqlLongLongComma(&s);
 *pS = s;
 return ret;
 }
 
 void asmEquivalentFree(struct asmEquivalent **pEl)
 /* Free a single dynamically allocated asmEquivalent such as created
  * with asmEquivalentLoad(). */
 {
 struct asmEquivalent *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->source);
 freeMem(el->destination);
 freez(pEl);
 }
 
 void asmEquivalentFreeList(struct asmEquivalent **pList)
 /* Free a list of dynamically allocated asmEquivalent's */
 {
 struct asmEquivalent *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     asmEquivalentFree(&el);
     }
 *pList = NULL;
 }
 
 void asmEquivalentOutput(struct asmEquivalent *el, FILE *f, char sep, char lastSep)
 /* Print out asmEquivalent.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->source);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->destination);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->sourceAuthority, values_sourceAuthority);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 sqlEnumPrint(f, el->destinationAuthority, values_destinationAuthority);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%lld", el->matchCount);
 fputc(sep,f);
 fprintf(f, "%lld", el->sourceCount);
 fputc(sep,f);
 fprintf(f, "%lld", el->destinationCount);
 fputc(lastSep,f);
 }
 
 void asmEquivalentJsonOutput(struct asmEquivalent *el, FILE *f)
 /* Print out asmEquivalent in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"source");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->source);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"destination");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->destination);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"sourceAuthority");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 sqlEnumPrint(f, el->sourceAuthority, values_sourceAuthority);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"destinationAuthority");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 sqlEnumPrint(f, el->destinationAuthority, values_destinationAuthority);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"matchCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->matchCount);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"sourceCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->sourceCount);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"destinationCount");
 fputc('"',f);
 fputc(':',f);
 fprintf(f, "%lld", el->destinationCount);
 fputc('}',f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
+char *asmEquivalentUcscToNCBI(char *ucscName)
+/* check if there is a RefSeq/GenBank equivalent to this UCSC assembly name.
+ *    If RefSeq exists, return that first, else if GenBank than return that.
+ * No checking of sequence match counts in this first implementation,
+ *    therefore, could be a fuzzy match, and since it is returning only the
+ *    first one, it might not be the best match.  Could add more specifics
+ *    later to get better match.
+ */
+{
+char *ret = NULL;
+if (ucscName == NULL)
+    return ret;
+
+struct sqlConnection *conn = hAllocConn("hgFixed");
+if (!conn)
+    return ret;
+
+if (!sqlTableExists(conn, "asmEquivalent"))
+    {
+    hFreeConn(&conn);
+    return ret;
+    }
+
+char buffer[4096];
+
+sqlSafef(buffer, sizeof buffer, "SELECT destination FROM asmEquivalent WHERE sourceAuthority='ucsc' AND destinationAuthority='refseq' AND source='%s' LIMIT 1", ucscName);
+char *sqlAnswer = sqlQuickString(conn, buffer);
+if (isEmpty(sqlAnswer))
+    {
+    sqlSafef(buffer, sizeof buffer, "SELECT destination FROM asmEquivalent WHERE sourceAuthority='ucsc' AND destinationAuthority='genbank' AND source='%s' LIMIT 1", ucscName);
+    sqlAnswer = sqlQuickString(conn, buffer);
+    }
+hFreeConn(&conn);
+
+/* if there is a result, for example: GCA_000001405.28_GRCh38.p13
+ *    want to return only: GCA_000001405.28
+ */
+if (isNotEmpty(sqlAnswer))
+    {
+    char *words[3];
+    int wordCount = 0;
+    wordCount = chopString(sqlAnswer, "_", words, ArraySize(words));
+    if (3 != wordCount)	/* something wrong with this answer */
+       return ret;
+    safef(buffer, sizeof(buffer), "%s_%s", words[0], words[1]);
+    ret = cloneString(buffer);
+    }
+
+return ret;
+}