b3b21d1f65841f24a262706daf65f784f3077f1f
kate
  Wed Jul 8 14:42:42 2015 -0700
Get new GTEX data and the color scheme, from GTEX portal.  Follow-up from 2015 GTEX meeting. refs #13504

diff --git src/hg/lib/gtexTissue.c src/hg/lib/gtexTissue.c
index f7acd94..91b671e 100644
--- src/hg/lib/gtexTissue.c
+++ src/hg/lib/gtexTissue.c
@@ -1,103 +1,106 @@
 /* gtexTissue.c was originally generated by the autoSql program, which also 
  * generated gtexTissue.h and gtexTissue.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 "gtexTissue.h"
 
 
 
-char *gtexTissueCommaSepFieldNames = "id,name,description,organ";
+char *gtexTissueCommaSepFieldNames = "id,name,description,organ,color";
 
 void gtexTissueStaticLoad(char **row, struct gtexTissue *ret)
 /* Load a row from gtexTissue table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->id = sqlUnsigned(row[0]);
 ret->name = row[1];
 ret->description = row[2];
 ret->organ = row[3];
+ret->color = sqlUnsigned(row[4]);
 }
 
 struct gtexTissue *gtexTissueLoad(char **row)
 /* Load a gtexTissue from row fetched with select * from gtexTissue
  * from database.  Dispose of this with gtexTissueFree(). */
 {
 struct gtexTissue *ret;
 
 AllocVar(ret);
 ret->id = sqlUnsigned(row[0]);
 ret->name = cloneString(row[1]);
 ret->description = cloneString(row[2]);
 ret->organ = cloneString(row[3]);
+ret->color = sqlUnsigned(row[4]);
 return ret;
 }
 
 struct gtexTissue *gtexTissueLoadAll(char *fileName) 
 /* Load all gtexTissue from a whitespace-separated file.
  * Dispose of this with gtexTissueFreeList(). */
 {
 struct gtexTissue *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[4];
+char *row[5];
 
 while (lineFileRow(lf, row))
     {
     el = gtexTissueLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissue *gtexTissueLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexTissue from a chopper separated file.
  * Dispose of this with gtexTissueFreeList(). */
 {
 struct gtexTissue *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[4];
+char *row[5];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexTissueLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexTissue *gtexTissueCommaIn(char **pS, struct gtexTissue *ret)
 /* Create a gtexTissue out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexTissue */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->description = sqlStringComma(&s);
 ret->organ = sqlStringComma(&s);
+ret->color = sqlUnsignedComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexTissueFree(struct gtexTissue **pEl)
 /* Free a single dynamically allocated gtexTissue such as created
  * with gtexTissueLoad(). */
 {
 struct gtexTissue *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->name);
 freeMem(el->description);
 freeMem(el->organ);
 freez(pEl);
@@ -120,36 +123,22 @@
 /* Print out gtexTissue.  Separate fields with sep. Follow last field with lastSep. */
 {
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->description);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->organ);
 if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->color);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
-void gtexTissueCreateTable(struct sqlConnection *conn, char *table)
-/* Create expression record format table of given name. */
-{
-char query[1024];
-
-sqlSafef(query, sizeof(query),
-"CREATE TABLE %s (\n"
-"    id int unsigned not null,	# internal id\n"
-"    name varchar(255) not null,       # short UCSC identifier\n"
-"    description varchar(255) not null, # GTEx tissue type detail\n"
-"    organ varchar(255) not null,      # GTEx tissue collection area\n"
-"              #Indices\n"
-"    PRIMARY KEY(id)\n"
-")\n",   table);
-sqlRemakeTable(conn, table, query);
-}