3a63c684fc647b345d52e96147b3344453b3d28a
kate
  Fri Jul 31 10:12:14 2015 -0700
1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats.  3. Extend gtexInfo table.refs #15645

diff --git src/hg/lib/gtexTissueData.c src/hg/lib/gtexTissueData.c
index 4bae523..53caaa3 100644
--- src/hg/lib/gtexTissueData.c
+++ src/hg/lib/gtexTissueData.c
@@ -1,158 +1,187 @@
 /* gtexTissueData.c was originally generated by the autoSql program, which also 
  * generated gtexTissueData.h and gtexTissueData.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 "gtexTissueData.h"
 
 
 
-char *gtexTissueDataCommaSepFieldNames = "geneId,tissueCount,scores";
+char *gtexTissueDataCommaSepFieldNames = "geneId,tissue,min,q1,median,q3,max";
+
+void gtexTissueDataStaticLoad(char **row, struct gtexTissueData *ret)
+/* Load a row from gtexTissueData table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+{
+
+ret->geneId = row[0];
+ret->tissue = row[1];
+ret->min = sqlDouble(row[2]);
+ret->q1 = sqlDouble(row[3]);
+ret->median = sqlDouble(row[4]);
+ret->q3 = sqlDouble(row[5]);
+ret->max = sqlDouble(row[6]);
+}
+
+struct gtexTissueData *gtexTissueDataLoadByQuery(struct sqlConnection *conn, char *query)
+/* Load all gtexTissueData 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 gtexTissueDataFreeList(). */
+{
+struct gtexTissueData *list = NULL, *el;
+struct sqlResult *sr;
+char **row;
+
+sr = sqlGetResult(conn, query);
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    el = gtexTissueDataLoad(row);
+    slAddHead(&list, el);
+    }
+slReverse(&list);
+sqlFreeResult(&sr);
+return list;
+}
+
+void gtexTissueDataSaveToDb(struct sqlConnection *conn, struct gtexTissueData *el, char *tableName, int updateSize)
+/* Save gtexTissueData 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',%g,%g,%g,%g,%g)", 
+	tableName,  el->geneId,  el->tissue,  el->min,  el->q1,  el->median,  el->q3,  el->max);
+sqlUpdate(conn, update->string);
+freeDyString(&update);
+}
 
 struct gtexTissueData *gtexTissueDataLoad(char **row)
 /* Load a gtexTissueData from row fetched with select * from gtexTissueData
  * from database.  Dispose of this with gtexTissueDataFree(). */
 {
 struct gtexTissueData *ret;
 
 AllocVar(ret);
-ret->tissueCount = sqlUnsigned(row[1]);
 ret->geneId = cloneString(row[0]);
-{
-int sizeOne;
-sqlFloatDynamicArray(row[2], &ret->scores, &sizeOne);
-assert(sizeOne == ret->tissueCount);
-}
+ret->tissue = cloneString(row[1]);
+ret->min = sqlDouble(row[2]);
+ret->q1 = sqlDouble(row[3]);
+ret->median = sqlDouble(row[4]);
+ret->q3 = sqlDouble(row[5]);
+ret->max = sqlDouble(row[6]);
 return ret;
 }
 
 struct gtexTissueData *gtexTissueDataLoadAll(char *fileName) 
 /* Load all gtexTissueData from a whitespace-separated file.
  * Dispose of this with gtexTissueDataFreeList(). */
 {
 struct gtexTissueData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[3];
+char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = gtexTissueDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissueData *gtexTissueDataLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexTissueData from a chopper separated file.
  * Dispose of this with gtexTissueDataFreeList(). */
 {
 struct gtexTissueData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[3];
+char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexTissueDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissueData *gtexTissueDataCommaIn(char **pS, struct gtexTissueData *ret)
 /* Create a gtexTissueData out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexTissueData */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->geneId = sqlStringComma(&s);
-ret->tissueCount = sqlUnsignedComma(&s);
-{
-int i;
-s = sqlEatChar(s, '{');
-AllocArray(ret->scores, ret->tissueCount);
-for (i=0; i<ret->tissueCount; ++i)
-    {
-    ret->scores[i] = sqlFloatComma(&s);
-    }
-s = sqlEatChar(s, '}');
-s = sqlEatChar(s, ',');
-}
+ret->tissue = sqlStringComma(&s);
+ret->min = sqlDoubleComma(&s);
+ret->q1 = sqlDoubleComma(&s);
+ret->median = sqlDoubleComma(&s);
+ret->q3 = sqlDoubleComma(&s);
+ret->max = sqlDoubleComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexTissueDataFree(struct gtexTissueData **pEl)
 /* Free a single dynamically allocated gtexTissueData such as created
  * with gtexTissueDataLoad(). */
 {
 struct gtexTissueData *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneId);
-freeMem(el->scores);
+freeMem(el->tissue);
 freez(pEl);
 }
 
 void gtexTissueDataFreeList(struct gtexTissueData **pList)
 /* Free a list of dynamically allocated gtexTissueData's */
 {
 struct gtexTissueData *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexTissueDataFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexTissueDataOutput(struct gtexTissueData *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexTissueData.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->geneId);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
-fprintf(f, "%u", el->tissueCount);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->tissue);
+if (sep == ',') fputc('"',f);
 fputc(sep,f);
-{
-int i;
-if (sep == ',') fputc('{',f);
-for (i=0; i<el->tissueCount; ++i)
-    {
-    fprintf(f, "%g", el->scores[i]);
-    fputc(',', f);
-    }
-if (sep == ',') fputc('}',f);
-}
+fprintf(f, "%g", el->min);
+fputc(sep,f);
+fprintf(f, "%g", el->q1);
+fputc(sep,f);
+fprintf(f, "%g", el->median);
+fputc(sep,f);
+fprintf(f, "%g", el->q3);
+fputc(sep,f);
+fprintf(f, "%g", el->max);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
-void gtexTissueDataCreateTable(struct sqlConnection *conn, char *table)
-/* Create expression record format table of given name. */
-{
-char query[1024];
-
-sqlSafef(query, sizeof(query),
-"CREATE TABLE %s (\n"
-"    geneId varchar(255) not null,     # Gene identifier (ensembl)\n"
-"    tissueCount int unsigned not null,# Number of tissues\n"
-"    scores longblob not null,	       # Median expression levels for tissues (RPKM)\n"
-"              #Indices\n"
-"    PRIMARY KEY(geneId)\n"
-")\n",   table);
-sqlRemakeTable(conn, table, query);
-}
-