23ecc080ba35d0563c208e8ff96f9852475e34f6
chmalee
  Mon Jun 18 14:23:06 2018 -0700
Adding url, urls, urlLabel and extraFields support to bigBarChart tracks

diff --git src/hg/hgc/barChartClick.c src/hg/hgc/barChartClick.c
index b06c711..241a7ba 100644
--- src/hg/hgc/barChartClick.c
+++ src/hg/hgc/barChartClick.c
@@ -37,54 +37,68 @@
 char *categs = trackDbSetting(tdb, BAR_CHART_CATEGORY_LABELS);
 char *words[BAR_CHART_MAX_CATEGORIES];
 int wordCt;
 wordCt = chopLine(cloneString(categs), words);
 int i;
 struct hash *categoryHash = hashNew(0);
 for (i=0; i<wordCt; i++)
     {
     hashStore(categoryHash, words[i]);
     }
 return categoryHash;
 }
 
 static struct barChartBed *getBarChartFromFile(struct trackDb *tdb, char *file, 
                                                 char *item, char *chrom, int start, int end, 
-                                                struct asObject **retAs)
+                                                struct asObject **retAs, char **extraFieldsRet,
+                                                int *extraFieldsCountRet)
 /* Retrieve barChart BED item from big file */
 {
 boolean hasOffsets = TRUE;
 struct bbiFile *bbi = bigBedFileOpen(file);
 struct asObject *as = bigBedAsOrDefault(bbi);
 if (retAs != NULL)
     *retAs = as;
 hasOffsets = (
     asColumnFind(as, BARCHART_OFFSET_COLUMN) != NULL && 
     asColumnFind(as, BARCHART_LEN_COLUMN) != NULL);
 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 *rest = cloneString(bb->rest);
     char startBuf[16], endBuf[16];
     char *row[32];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, ArraySize(row));
     struct barChartBed *barChart = barChartBedLoadOptionalOffsets(row, hasOffsets);
     if (barChart == NULL)
         continue;
     if (sameString(barChart->name, item))
+        {
+        char *restFields[256];
+        int restCount = chopTabs(rest, restFields);
+        int restBedFields = (6 + (hasOffsets ? 2 : 0));
+        if (restCount > restBedFields)
+            {
+            int i;
+            for (i = 0; i < restCount - restBedFields; i++)
+                extraFieldsRet[i] = restFields[restBedFields + i];
+            *extraFieldsCountRet = (restCount - restBedFields);
+            }
         return barChart;
         }
+    }
 return NULL;
 }
 
 static struct barChartBed *getBarChartFromTable(struct trackDb *tdb, char *table, 
                                                 char *item, char *chrom, int start, int end)
 /* Retrieve barChart BED item from track table */
 {
 struct sqlConnection *conn = NULL;
 struct customTrack *ct = lookupCt(tdb->track);
 if (ct == NULL)
     conn = hAllocConnTrack(database, tdb);
 else
     {
     conn = hAllocConn(CUSTOM_TRASH);
     table = ct->dbTableName;
@@ -104,37 +118,37 @@
                     "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 = barChartBedLoadOptionalOffsets(row, hasOffsets);
         }
     sqlFreeResult(&sr);
     }
 hFreeConn(&conn);
 return barChart;
 }
 
 static struct barChartBed *getBarChart(struct trackDb *tdb, char *item, char *chrom, int start, int end,
-                                        struct asObject **retAs)
+                                        struct asObject **retAs, char **extraFieldsReg, int *extraFieldsCountRet)
 /* Retrieve barChart BED item from track */
 {
 struct barChartBed *barChart = NULL;
 char *file = trackDbSetting(tdb, "bigDataUrl");
 if (file != NULL)
-    barChart = getBarChartFromFile(tdb, file, item, chrom, start, end, retAs);
+    barChart = getBarChartFromFile(tdb, file, item, chrom, start, end, retAs, extraFieldsReg, extraFieldsCountRet);
 else
     barChart = getBarChartFromTable(tdb, tdb->table, item, chrom, start, end);
 return barChart;
 }
 
 static struct barChartItemData *getSampleValsFromFile(struct trackDb *tdb, 
                         struct hash *categoryHash, struct barChartBed *bed, 
                         char *dataFile, char *sampleFile)
 /* Get all data values in a file for this item (locus) */
 {
 // Get sample categories from sample file
 // Format: id, category, extras
 struct lineFile *lf = udcWrapShortLineFile(sampleFile, NULL, 0);
 struct hash *sampleHash = hashNew(0);
 char *words[2];
@@ -350,64 +364,83 @@
 struct asColumn *asFindColByIx(struct asObject *as, int ix)
 /* Find AS column by index */
 {
 struct asColumn *asCol;
 int i;
 for (i=0, asCol = as->columnList; asCol != NULL && i<ix; asCol = asCol->next, i++);
 return asCol;
 }
 
 void doBarChartDetails(struct trackDb *tdb, char *item)
 /* Details of barChart item */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 struct asObject *as = NULL;
-struct barChartBed *chartItem = getBarChart(tdb, item, seqName, start, end, &as);
+char *extraFields[256];
+int extraFieldCount;
+int numColumns;
+struct barChartBed *chartItem = getBarChart(tdb, item, seqName, start, end, &as, extraFields, &extraFieldCount);
 if (chartItem == NULL)
     errAbort("Can't find item %s in barChart table/file %s\n", item, tdb->table);
 
 genericHeader(tdb, item);
 
 // get name and name2 from trackDb, .as file, or use defaults
 struct asColumn *nameCol = NULL, *name2Col = NULL;
+//struct asColumn *name2Col;
 char *nameLabel = NULL, *name2Label = NULL;
 if (as != NULL)
     {
+    numColumns = slCount(as->columnList);
     nameCol = asFindColByIx(as, BARCHART_NAME_COLUMN_IX);
     name2Col = asFindColByIx(as, BARCHART_NAME2_COLUMN_IX);
     }
-nameLabel = trackDbSettingClosestToHomeOrDefault(tdb, "bedNameLabel", nameCol ? nameCol->comment : "Item"),
+nameLabel = trackDbSettingClosestToHomeOrDefault(tdb, "bedNameLabel", nameCol ? nameCol->comment : "Item");
+if (trackDbSettingClosestToHomeOrDefault(tdb, "url", NULL) != NULL)
+    printCustomUrl(tdb, item, TRUE);
+else
     printf("<b>%s: </b>%s<br>\n", nameLabel, chartItem->name);
 name2Label = name2Col ? name2Col->comment : "Alternative name";
-if (differentString(chartItem->name2, ""))
+if (differentString(chartItem->name2, "")) {
+    if (trackDbSettingClosestToHomeOrDefault(tdb, "url2", NULL) != NULL)
+        printOtherCustomUrl(tdb, chartItem->name2, "url2", TRUE);
+    else
         printf("<b>%s: </b> %s<br>\n", name2Label, chartItem->name2);
+}
 
 int categId;
 float highLevel = barChartMaxValue(chartItem, &categId);
 char *units = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_UNIT, "units");
 char *metric = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_METRIC, "");
 printf("<b>Total all %s values: </b> %0.2f %s<br>\n", metric, barChartTotalValue(chartItem), units);
 printf("<b>Maximum %s value: </b> %0.2f %s in %s<br>\n", 
                 metric, highLevel, units, barChartUiGetCategoryLabelById(categId, database, tdb));
 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);
 printf("<b>Strand: </b> %s\n", chartItem->strand); 
+
+// print any remaining extra fields
+if (numColumns > 11)
+    {
+    extraFieldsPrint(tdb, NULL, extraFields, extraFieldCount);
+    }
+
 char *matrixUrl = NULL, *sampleUrl = NULL;
 struct barChartItemData *vals = getSampleVals(tdb, chartItem, &matrixUrl, &sampleUrl);
 if (vals != NULL)
     {
     // Print boxplot
     puts("<p>");
     char *df = makeDataFrame(tdb->table, vals);
     char *colorFile = makeColorFile(tdb);
     printBoxplot(df, item, chartItem->name2, units, colorFile);
     printf("<br><a href='%s'>View all data points for %s%s%s%s</a>\n", df, 
                         chartItem->name, 
                         chartItem->name2 ? " (" : "",
                         chartItem->name2 ? chartItem->name2 : "",
                         chartItem->name2 ? ")" : "");
     }