549dcd456f5d557e15426176e487f91246363548
kate
  Mon Apr 10 17:21:22 2017 -0700
Better integration with bigBed cod. Fixes loading problem and allows labelFields code to operate (not yet tested). refs #18736

diff --git src/hg/hgc/barChartClick.c src/hg/hgc/barChartClick.c
index c298bfe..62c46fa 100644
--- src/hg/hgc/barChartClick.c
+++ src/hg/hgc/barChartClick.c
@@ -1,221 +1,220 @@
 /* Details pages for barChart tracks */
 
 /* Copyright (C) 2015 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "hdb.h"
 #include "hvGfx.h"
 #include "trashDir.h"
 #include "hgc.h"
 #include "hCommon.h"
 
 #include "barChartBed.h"
 #include "barChartCategory.h"
 #include "barChartData.h"
 #include "barChartSample.h"
 #include "barChartUi.h"
 
 // TODO: Consider moving these to lib/{barChartBed,bigBarChart}.c
 
-static struct barChartBed *getBarChartFromFile(char *item, char *chrom, int start, int end, 
+static struct bed *getBarChartFromFile(char *item, char *chrom, int start, int end, 
                                                         char *file)
 /* Retrieve barChart BED item from big file */
 {
 struct bbiFile *bbi = bigBedFileOpen(file);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList =  bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     char startBuf[16], endBuf[16];
     char *bedRow[32];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, bedRow, ArraySize(bedRow));
-    struct barChartBed *barChart = barChartBedLoad(bedRow);
+    struct bed *barChart = barChartSimpleBedLoad(bedRow);
     if (sameString(barChart->name, item))
         return barChart;
     }
 return NULL;
 }
 
-static struct barChartBed *getBarChartFromTable(char *item, char *chrom, int start, int end, 
+static struct bed *getBarChartFromTable(char *item, char *chrom, int start, int end, 
                                                         char *table)
 /* Retrieve barChart BED item from track table */
 {
-struct barChartBed *barChart = NULL;
+struct bed *barChart = NULL;
 struct sqlConnection *conn = hAllocConn(database);
 char **row;
 char query[512];
 struct sqlResult *sr;
 if (sqlTableExists(conn, table))
     {
     sqlSafef(query, sizeof query, 
                 "SELECT * FROM %s WHERE name='%s'"
                     "AND chrom='%s' AND chromStart=%d AND chromEnd=%d", 
                                 table, item, chrom, start, end);
     sr = sqlGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
         {
-        barChart = barChartBedLoad(row);
+        barChart = barChartSimpleBedLoad(row);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return barChart;
 }
 
-static struct barChartBed *getBarChart(char *item, char *chrom, int start, int end, 
+static struct bed *getBarChart(char *item, char *chrom, int start, int end, 
                                                         struct trackDb *tdb)
 /* Retrieve barChart BED item from track */
 {
-struct barChartBed *barChart = NULL;
+struct bed *barChart = NULL;
 char *file = trackDbSetting(tdb, "bigDataUrl");
 if (file != NULL)
     barChart = getBarChartFromFile(item, chrom, start, end, file);
 else
     barChart = getBarChartFromTable(item, chrom, start, end, tdb->table);
 return barChart;
 }
 
 static struct barChartData *getSampleVals(char *track, char *item)
 /* Get data values for this item (locus) from all samples */
 {
 char table[256];
 safef(table, sizeof(table), "%s%s", track, "Data");
 struct sqlConnection *conn = hAllocConn(database);
 if (!sqlTableExists(conn, table))
     {
     hFreeConn(&conn);
     conn = hAllocConn("hgFixed");
     if (!sqlTableExists(conn, table))
         {
         hFreeConn(&conn);
         return NULL;
         }
     }
 struct barChartData *vals = barChartDataLoadForLocus(conn, table, item);
 hFreeConn(&conn);
 return vals;
 }
 
 static char *makeDataFrame(char *track, struct barChartData *vals)
 /* Create R data frame from sample data.  This is a tab-sep file, one row per sample.
    Return filename. */
 {
 // Get category for samples 
 char table[256];
 safef(table, sizeof(table), "%s%s", track, "Sample");
 struct sqlConnection *conn = hAllocConn(database);
 if (!sqlTableExists(conn, table))
     {
     hFreeConn(&conn);
     conn = hAllocConn("hgFixed");
     if (!sqlTableExists(conn, table))
         {
         hFreeConn(&conn);
         return NULL;
         }
 }
 char query[512];
 sqlSafef(query, sizeof(query), "SELECT * FROM %s", table);
 struct barChartSample *sample, *samples = barChartSampleLoadByQuery(conn, query);
 hFreeConn(&conn);
 struct hash *sampleHash = hashNew(0);
 for (sample = samples; sample != NULL; sample = sample->next)
     {
     hashAdd(sampleHash, sample->sample, sample);
     }
 
 // Create data frame with columns for sample, category, value */
 struct tempName dfTn;
 trashDirFile(&dfTn, "hgc", "barChart", ".df.txt");
 FILE *f = fopen(dfTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", dfTn.forCgi);
 fprintf(f, "sample\tcategory\tvalue\n");
 int i = 0;
 struct barChartData *val;
 for (val = vals; val != NULL; val = val->next)
     {
     struct barChartSample *sample = hashFindVal(sampleHash, val->sample);
     if (sample == NULL)
         warn("barChart track %s: unknown category for sample %s", track, val->sample);
     else
         fprintf(f, "%d\t%s\t%0.3f\n", i++, sample->category, val->value);
     }
 fclose(f);
 return cloneString(dfTn.forCgi);
 }
 
 char *makeColorFile(struct trackDb *tdb)
 /* Make a file with category + color */
 {
 struct tempName colorTn;
 trashDirFile(&colorTn, "hgc", "barChartColors", ".txt");
 FILE *f = fopen(colorTn.forCgi, "w");
 if (f == NULL)
     errAbort("can't create temp file %s", colorTn.forCgi);
 struct barChartCategory *categs = barChartUiGetCategories(database, tdb);
 struct barChartCategory *categ;
 fprintf(f, "%s\t%s\n", "category", "color");
 for (categ = categs; categ != NULL; categ = categ->next)
     {
     //fprintf(f, "%s\t#%06X\n", categ->label, categ->color);
     fprintf(f, "%s\t%d\n", categ->label, categ->color);
     }
 fclose(f);
 return cloneString(colorTn.forCgi);
 }
 
 static void printBoxplot(char *df, char *item, char *units, char *colorFile)
 /* Plot data frame to image file and include in HTML */
 {
 struct tempName pngTn;
 trashDirFile(&pngTn, "hgc", "barChart", ".png");
 
 /* Exec R in quiet mode, without reading/saving environment or workspace */
 char cmd[256];
 safef(cmd, sizeof(cmd), "Rscript --vanilla --slave hgcData/barChartBoxplot.R %s %s %s %s %s",
                                 item, units, colorFile, df, pngTn.forHtml);
 int ret = system(cmd);
 if (ret == 0)
     printf("<img src = \"%s\" border=1><br>\n", pngTn.forHtml);
 }
 
 void doBarChartDetails(struct trackDb *tdb, char *item)
-
 /* Details of barChart item */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
-struct barChartBed *chartItem = getBarChart(item, seqName, start, end, tdb);
+struct bed *chartItem = getBarChart(item, seqName, start, end, tdb);
 if (chartItem == NULL)
     errAbort("Can't find item %s in barChart table %s\n", item, tdb->table);
 
 genericHeader(tdb, item);
 int categId;
-float highLevel = barChartHighestValue(chartItem, &categId);
+float highLevel = barChartMaxValue(chartItem, &categId);
 char *units = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_UNIT, "");
 printf("<b>Maximum value: </b> %0.2f %s in %s<br>\n", 
                 highLevel, units, barChartUiGetCategoryLabelById(categId, database, tdb));
 printf("<b>Total all values: </b> %0.2f<br>\n", barChartTotalValue(chartItem));
 printf("<b>Score: </b> %d<br>\n", chartItem->score); 
 printf("<b>Genomic position: "
                 "</b>%s <a href='%s&db=%s&position=%s%%3A%d-%d'>%s:%d-%d</a><br>\n", 
                     database, hgTracksPathAndSettings(), database, 
                     chartItem->chrom, chartItem->chromStart+1, chartItem->chromEnd,
                     chartItem->chrom, chartItem->chromStart+1, chartItem->chromEnd);
 struct barChartData *vals = getSampleVals(tdb->table, item);
 if (vals != NULL)
     {
     // Print boxplot
     puts("<p>");
     char *df = makeDataFrame(tdb->table, vals);
     char *colorFile = makeColorFile(tdb);
     printBoxplot(df, item, units, colorFile);
     }
 puts("<br>");
 printTrackHtml(tdb);
 }