832926811b278d5c656957e1565acdde48522def
kate
  Mon Apr 27 17:59:12 2020 -0700
Update GTEx gene track click handler and track settings to handle V8 (add Kidney Medulla tissue, support TPM and RPKM). refs #25130

diff --git src/hg/lib/gtexInfo.c src/hg/lib/gtexInfo.c
index 96b4c3a..3067250 100644
--- src/hg/lib/gtexInfo.c
+++ src/hg/lib/gtexInfo.c
@@ -1,242 +1,247 @@
 /* gtexInfo.c was originally generated by the autoSql program, which also 
  * generated gtexInfo.h and gtexInfo.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 "gtexInfo.h"
 #include "gtexGeneBed.h"
 
 
 
 char *gtexInfoCommaSepFieldNames = "version,releaseDate,maxScore,maxMedianScore";
 
 void gtexInfoStaticLoad(char **row, struct gtexInfo *ret)
 /* Load a row from gtexInfo table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->version = row[0];
 ret->releaseDate = row[1];
 ret->maxScore = sqlDouble(row[2]);
 ret->maxMedianScore = sqlDouble(row[3]);
 }
 
 struct gtexInfo *gtexInfoLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all gtexInfo 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 gtexInfoFreeList(). */
 {
 struct gtexInfo *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = gtexInfoLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void gtexInfoSaveToDb(struct sqlConnection *conn, struct gtexInfo *el, char *tableName, int updateSize)
 /* Save gtexInfo 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)", 
 	tableName,  el->version,  el->releaseDate,  el->maxScore,  el->maxMedianScore);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 struct gtexInfo *gtexInfoLoad(char **row)
 /* Load a gtexInfo from row fetched with select * from gtexInfo
  * from database.  Dispose of this with gtexInfoFree(). */
 {
 struct gtexInfo *ret;
 
 AllocVar(ret);
 ret->version = cloneString(row[0]);
 ret->releaseDate = cloneString(row[1]);
 ret->maxScore = sqlDouble(row[2]);
 ret->maxMedianScore = sqlDouble(row[3]);
 return ret;
 }
 
 struct gtexInfo *gtexInfoLoadAll(char *fileName) 
 /* Load all gtexInfo from a whitespace-separated file.
  * Dispose of this with gtexInfoFreeList(). */
 {
 struct gtexInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileRow(lf, row))
     {
     el = gtexInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexInfo *gtexInfoLoadAllByChar(char *fileName, char chopper) 
 /* Load all gtexInfo from a chopper separated file.
  * Dispose of this with gtexInfoFreeList(). */
 {
 struct gtexInfo *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[4];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = gtexInfoLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct gtexInfo *gtexInfoCommaIn(char **pS, struct gtexInfo *ret)
 /* Create a gtexInfo out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new gtexInfo */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->version = sqlStringComma(&s);
 ret->releaseDate = sqlStringComma(&s);
 ret->maxScore = sqlDoubleComma(&s);
 ret->maxMedianScore = sqlDoubleComma(&s);
 *pS = s;
 return ret;
 }
 
 void gtexInfoFree(struct gtexInfo **pEl)
 /* Free a single dynamically allocated gtexInfo such as created
  * with gtexInfoLoad(). */
 {
 struct gtexInfo *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->version);
 freeMem(el->releaseDate);
 freez(pEl);
 }
 
 void gtexInfoFreeList(struct gtexInfo **pList)
 /* Free a list of dynamically allocated gtexInfo's */
 {
 struct gtexInfo *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     gtexInfoFree(&el);
     }
 *pList = NULL;
 }
 
 void gtexInfoOutput(struct gtexInfo *el, FILE *f, char sep, char lastSep) 
 /* Print out gtexInfo.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->version);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->releaseDate);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->maxScore);
 fputc(sep,f);
 fprintf(f, "%g", el->maxMedianScore);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 void gtexInfoCreateTable(struct sqlConnection *conn, char *table)
 /* Create GTEx info table */
 {
 char query[1024];
 
 sqlSafef(query, sizeof(query),
 "CREATE TABLE %s (\n"
 "    version varchar(255) not null,	# GTEX data release (e.g. V4, V6)\n"
 "    releaseDate varchar(255) not null,	# Release date\n"
 "    maxScore double not null,	# Maximum score observed (use to scale display)\n"
 "    maxMedianScore double not null,	# Maximum score observed for a tissue median (use to scale display)\n"
 "        #Indices\n"
 "    PRIMARY KEY(version)\n"
 ")\n",   table);
 sqlRemakeTable(conn, table, query);
 }
 
 char *gtexVersionSuffix(char *table)
 /* Return version string for a GTEx track table.  Supporting V4, V6, V8 (default, no suffix )*/                                        
 {
 if (table)
     {
     if (endsWith(table, "V4"))
         return("V4");
 /* 
     TODO: Handle default case more generically
     
     if (endsWith(table, "V6"))
         return("V6");
 */
     if (endsWith(table, "V8"))
         return("V8");
     }
 return("");
 }
 
 char *gtexVersion(char *table)
 /* Return version string based on table suffix. Default version tables have no suffix */
 {
 char *suffix = gtexVersionSuffix(table);
 return (sameString(suffix, "")) ? GTEX_DEFAULT_VERSION : suffix;
 }
 
 char *gtexVersionSuffixFromVersion(char *version)
 /* Return version table suffix for a version */
 {
 if (!version)
     version = GTEX_DEFAULT_VERSION;
 return (sameString(version, GTEX_DEFAULT_VERSION)) ? "" : version;
 }
 
 double gtexMaxMedianScore(char *version)
 /* Retrieve max median score for latest (or named) version */
 {
 char query[1024];
 struct sqlConnection *conn = hAllocConn("hgFixed");
 if (!conn)
     return 0;
-// TODO: trackDB setting for this
 if (!version || sameString(version, ""))
     version = GTEX_DEFAULT_VERSION;
 sqlSafef(query, sizeof query, "select maxMedianScore from gtexInfo where version='%s'", version);
 double score = sqlQuickDouble(conn, query);
 if (score == 0.0)
     errAbort("Internal error: GTEx version \"%s\" not found in gtexInfo table", version);
 hFreeConn(&conn);
 return score;
 }
+
+char *gtexExprUnit(char *version)
+/* Units of gene expression */
+{
+return (sameString(version, "V8") ? "TPM" : "RPKM");
+}