c0a00fe92704046502a278f29fc49cdacf331163
kate
  Thu Aug 14 11:07:00 2014 -0700
Add gtexDonor table.  Fix some table loading problems. refs #13504
diff --git src/hg/lib/gtexSampleData.c src/hg/lib/gtexSampleData.c
index 67a38ac..2a9d2be 100644
--- src/hg/lib/gtexSampleData.c
+++ src/hg/lib/gtexSampleData.c
@@ -1,155 +1,156 @@
 /* gtexSampleData.c was originally generated by the autoSql program, which also 
  * generated gtexSampleData.h and gtexSampleData.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 "gtexSampleData.h"
 
 
 
 char *gtexSampleDataCommaSepFieldNames = "geneId,sample,tissue,score";
 
 void gtexSampleDataStaticLoad(char **row, struct gtexSampleData *ret)
 /* Load a row from gtexSampleData table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->geneId = row[0];
 ret->sample = row[1];
 ret->tissue = row[2];
 ret->score = sqlFloat(row[3]);
 }
 
 struct gtexSampleData *gtexSampleDataLoad(char **row)
 /* Load a gtexSampleData from row fetched with select * from gtexSampleData
  * from database.  Dispose of this with gtexSampleDataFree(). */
 {
 struct gtexSampleData *ret;
 
 AllocVar(ret);
 ret->geneId = cloneString(row[0]);
 ret->sample = cloneString(row[1]);
 ret->tissue = cloneString(row[2]);
 ret->score = sqlFloat(row[3]);
 return ret;
 }
 
 struct gtexSampleData *gtexSampleDataLoadAll(char *fileName) 
 /* Load all gtexSampleData from a whitespace-separated file.
  * Dispose of this with gtexSampleDataFreeList(). */
 {
 struct gtexSampleData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = gtexSampleDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexSampleData *gtexSampleDataLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexSampleData from a chopper separated file.
  * Dispose of this with gtexSampleDataFreeList(). */
 {
 struct gtexSampleData *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexSampleDataLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexSampleData *gtexSampleDataCommaIn(char **pS, struct gtexSampleData *ret)
 /* Create a gtexSampleData out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexSampleData */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->geneId = sqlStringComma(&s);
 ret->sample = sqlStringComma(&s);
 ret->tissue = sqlStringComma(&s);
 ret->score = sqlFloatComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexSampleDataFree(struct gtexSampleData **pEl)
 /* Free a single dynamically allocated gtexSampleData such as created
  * with gtexSampleDataLoad(). */
 {
 struct gtexSampleData *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->geneId);
 freeMem(el->sample);
 freeMem(el->tissue);
 freez(pEl);
 }
 
 void gtexSampleDataFreeList(struct gtexSampleData **pList)
 /* Free a list of dynamically allocated gtexSampleData's */
 {
 struct gtexSampleData *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexSampleDataFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexSampleDataOutput(struct gtexSampleData *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexSampleData.  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);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->sample);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tissue);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->score);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void gtexSampleDataCreateTable(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"
 "    sample varchar(255) not null,     # GTEx sample identifier\n"
 "    tissue varchar(255) not null,     # Tissue name\n"
 "    score float not null,	# Expression level (RPKM)\n"
 "              #Indices\n"
-"    PRIMARY KEY(geneId)\n"
+"    KEY(geneId),\n"
+"    KEY(tissue)\n"
 ")\n",   table);
 sqlRemakeTable(conn, table, query);
 }