d59d6cbe4dfc0ba40588132b1776cb2038f5216b chmalee Wed Jan 26 17:29:35 2022 -0800 Add missing hReplaceGbdb calls to various barChart functions, refs #28828 diff --git src/hg/lib/barChartUi.c src/hg/lib/barChartUi.c index c1b0fa3..dd744f5 100644 --- src/hg/lib/barChartUi.c +++ src/hg/lib/barChartUi.c @@ -1,522 +1,522 @@ /* Bar chart track controls */ /* Copyright (C) 2015 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "cheapcgi.h" #include "cart.h" #include "net.h" #include "errCatch.h" #include "web.h" #include "hui.h" #include "trackDb.h" #include "jsHelper.h" #include "hCommon.h" #include "rainbow.h" #include "htmlColor.h" #include "barChartCategory.h" #include "barChartUi.h" #include "facetedTable.h" #include "tablesTables.h" /* Restrict features on right-click (popup) version */ static boolean isPopup = FALSE; /* Convenience functions for category filter controls */ char *makeCategoryLabel(struct barChartCategory *categ) /* Display category color and label */ { char buf[256]; safef(buf, sizeof(buf), "<td class='bcColorPatch' bgcolor=#%06x></td>" "<td> %s</td>", categ->color, categ->label); return(cloneString(buf)); } struct categorySelect { struct categorySelect *next; char *name; char *label; boolean checked; }; static void makeGroupCheckboxes(char *name, char *title, struct categorySelect *selects) { #define TABLE_COLUMNS 1 if (title != NULL) printf("<tr><td colspan=10><i><b>%s</b></i></td></tr><tr>\n", title); int count = slCount(selects); struct categorySelect **categArray; AllocArray(categArray, count); int i=0; struct categorySelect *sel; for (i=0, sel = selects; sel != NULL; sel = sel->next, i++) categArray[i] = sel; int col=0; int row=0; int tableColumns=1; for (i=0; i<count; i++) { int j = row + col*(count/tableColumns+1); if (j>=count) { printf("</tr><tr>"); row++; col = 0; } j = row + col*(count/tableColumns+1); if (!isPopup) { printf("<td><input type=checkbox name=\"%s\" value=\"%s\" %s></td>" "<td>%s</td>\n", name, categArray[j]->name, categArray[j]->checked ? "checked" : "", categArray[j]->label); } col++; } if ((i % tableColumns) != 0) while ((i++ % tableColumns) != 0) printf("<td></td>"); printf("</tr><tr><td></td></tr>\n"); } static void makeCategoryCheckboxes(char *name, struct barChartCategory *categs, struct slName *checked) { puts("<style>\n"); puts(".bcColorPatch { padding: 0 10px; }\n"); puts("</style>\n"); struct hash *checkHash = hashNew(0); struct slName *sel; for (sel = checked; sel != NULL; sel = sel->next) hashAdd(checkHash, sel->name, sel->name); puts("<table borderwidth=0 cellpadding=1 cellspacing=4><tr>"); struct categorySelect *catSel; struct barChartCategory *categ; struct categorySelect *all = NULL; for (categ = categs; categ != NULL; categ = categ->next) { AllocVar(catSel); catSel->name = categ->name; catSel->label = makeCategoryLabel(categ); if (hashNumEntries(checkHash) == 0) catSel->checked = TRUE; else catSel->checked = (hashLookup(checkHash, categ->name) != NULL); slAddHead(&all, catSel); } slReverse(&all); makeGroupCheckboxes(name, NULL, all); puts("</tr></table>"); char buf[512]; safef(buf, sizeof(buf), "%s%s", cgiMultListShadowPrefix(), name); cgiMakeHiddenVar(buf, "0"); } /* Convenience functions for hgTrackUi */ boolean barChartIsLogTransformed(struct cart *cart, char *track, struct trackDb *tdb) /* Return TRUE if bar chart needs to be log transformed */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, BAR_CHART_LOG_TRANSFORM); boolean isLog = TRUE; char *trans = trackDbSetting(tdb, "transformFunc"); if (trans != NULL) isLog = sameWord(trans, "LOG"); return cartCgiUsualBoolean(cart, cartVar, isLog); } void barChartUiLogTransform(struct cart *cart, char *track, struct trackDb *tdb) /* Checkbox to select log-transformed RPKM values */ /* NOTE: this code from gtexUi.c. Consider sharing. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, BAR_CHART_LOG_TRANSFORM); puts("<b>Log10(x+1) transform:</b>\n"); boolean isLogTransform = barChartIsLogTransformed(cart, track, tdb); cgiMakeCheckBoxWithId(cartVar, isLogTransform, cartVar); jsOnEventByIdF("change", cartVar, "barChartUiTransformChanged('%s');", track); } double barChartUiMaxMedianScore(struct trackDb *tdb) /* Max median score, for scaling */ { char *setting = trackDbSettingClosestToHome(tdb, BAR_CHART_MAX_LIMIT); if (setting != NULL) { double max = sqlDouble(setting); if (max > 0.0) return max; } return BAR_CHART_MAX_LIMIT_DEFAULT; } double barChartCurViewMax(struct cart *cart, char *trackName, struct trackDb *tdb) /* Look up max value to scale for this bar chart - consults both cart and trackDb defaults. */ { char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", trackName, BAR_CHART_MAX_VIEW_LIMIT); char *limitString = trackDbSettingOrDefault(tdb, BAR_CHART_LIMIT, "50"); double limit = atof(limitString); if (limit <= 0) limit = 0.001; return cartCgiUsualDouble(cart, cartVar, limit); } void barChartUiViewLimits(struct cart *cart, char *track, struct trackDb *tdb) /* Set viewing limits if log transform not checked */ /* NOTE: this code from gtexUi.c. Consider sharing. */ { char buf[512]; boolean isLogTransform = barChartIsLogTransformed(cart, track, tdb); safef(buf, sizeof buf, "%sViewLimitsMaxLabel %s", track, isLogTransform ? "disabled" : ""); printf("<span class='%s'><b>View limits maximum:</b></span>\n", buf); double viewMax = barChartCurViewMax(cart, track, tdb); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, BAR_CHART_MAX_VIEW_LIMIT); cgiMakeDoubleVarWithExtra(cartVar, viewMax, 4, isLogTransform ? "disabled" : ""); char *unit = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_UNIT, ""); printf("<span class='%s'> %s (range 0-%d)</span>\n", buf, unit, round(barChartUiMaxMedianScore(tdb))); } // TODO: libify static boolean isUrl(char *url) { return startsWith("http://", url) || startsWith("https://", url) || startsWith("ftp://", url); } static void getCategsFromSettings(char *track, char *labelSetting, char *colorSetting, struct slName **retLabels, struct slName **colors) /* Get category labels and optionally colors, from track settings */ { if (isEmpty(labelSetting)) { errAbort("barChart track %s missing required setting: %s or %s\n", track, BAR_CHART_CATEGORY_LABELS, BAR_CHART_CATEGORY_URL); } char *words[BAR_CHART_MAX_CATEGORIES]; int labelCount = chopLine(cloneString(labelSetting), words); struct slName *labelList = *retLabels = slNameListFromStringArray(words, labelCount); /* Strip out underbars from trackDb early */ struct slName *label; for (label = labelList; label != NULL; label = label->next) subChar(label->name, '_', ' '); if (isNotEmpty(colorSetting)) { int colorCount = chopLine(cloneString(colorSetting), words); if (colorCount != labelCount) errAbort("barChart track %s settings mismatch: %s (%d) and %s (%d)\n", track, BAR_CHART_CATEGORY_LABELS, labelCount, BAR_CHART_CATEGORY_COLORS, colorCount); *colors = slNameListFromStringArray(words, labelCount); } } static void getCategsFromFile(char *track, char *categUrl, struct slName **labels, struct slName **colors) /* Get category labels and optionally colors, from category file. * This is tab-sep file, column 1 is category label, optional column 2 is a color spec */ { if (!labels || !colors) return; struct lineFile *lf = NULL; // protect against network error struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { if (isUrl(categUrl)) lf = netLineFileOpen(categUrl); else lf = lineFileMayOpen(categUrl, TRUE); } errCatchEnd(errCatch); if (errCatch->gotError) { if (isNotEmpty(errCatch->message->string)) errAbort("unable to open %s track file %s: %s", track, categUrl, errCatch->message->string); } errCatchFree(&errCatch); char *line = NULL; int cols = 0; while (lineFileNextReal(lf, &line)) { char *words[2]; int wordCount = chopTabs(line, words); if (cols) { if (wordCount != cols) errAbort("barChart track %s category file %s expecting %d words, got %d", track, categUrl, cols, wordCount); } else { cols = wordCount; } slAddHead(&labels, slNameNew(words[0])); if (wordCount == 2) slAddHead(&colors, slNameNew(words[1])); } slReverse(&labels); slReverse(&colors); } static void getCategsFromMergeList(struct facetedTableMergedOffset *mergeList, struct slName **labels, struct slName **colors) /* Given merged list, return separate list of labels and colors */ { struct facetedTableMergedOffset *tmo; for (tmo = mergeList; tmo != NULL; tmo = tmo->next) { slNameAddHead(labels, tmo->name); slNameAddHead(colors, tmo->color); } slReverse(labels); slReverse(colors); } static struct barChartCategory *createCategs(char *track, struct slName *labels, struct slName *colors) /* Populate category structs from label and color lists. Assign rainbow if no color list */ { struct barChartCategory *categs = NULL, *categ = NULL; int count = slCount(labels); struct rgbColor *rainbow = NULL; if (!colors) { rainbow = getRainbow(&saturatedRainbowAtPos, count); } int i; char buf[6]; for (i=0 ; i<count && labels; i++) { AllocVar(categ); categ->id = i; safef(buf, sizeof buf, "%d", i); categ->name = cloneString(buf); categ->label = labels->name; if (!colors) { // rainbow categ->color = ((rainbow[i].r & 0xff)<<16) + ((rainbow[i].g & 0xff)<<8) + ((rainbow[i].b & 0xff)); } else { // colors from user unsigned rgb = 0; char *color = colors->name; if (!htmlColorForCode(color, &rgb)) { if (!htmlColorForName(color, &rgb)) { /* try r,g,b */ if (index(color, ',')) { unsigned char r, g, b; parseColor(color, &r, &g, &b); htmlColorFromRGB(&rgb, r, g, b); } else { warn("barChart track %s unknown color %s. Must r,g,b or #ffffff or one of %s\n", track, color, slNameListToString(htmlColorNames(),',')); } } } categ->color = rgb; } slAddHead(&categs, categ); labels = labels->next; if (colors) colors = colors->next; } slReverse(&categs); return categs; } struct barChartCategory *barChartUiGetCategories(char *database, struct trackDb *tdb, struct facetedTableMergedOffset *mergeList) /* Get category colors and descriptive labels. If mergeList is non-NULL gets it from there,else use labels in tab-sep file specified by barChartCategoryUrl setting, o/w in barChartBars setting. If colors are not specified via barChartColors setting or second column in category file, assign rainbow colors. Colors are specified as #fffff or r,g,b or html color name) */ { struct slName *labels = NULL, *colors = NULL; -char *categUrl = trackDbSetting(tdb, BAR_CHART_CATEGORY_URL); +char *categUrl = hReplaceGbdb(trackDbSetting(tdb, BAR_CHART_CATEGORY_URL)); if (mergeList != NULL) { getCategsFromMergeList(mergeList, &labels, &colors); } else if (isNotEmpty(categUrl)) getCategsFromFile(tdb->track, categUrl, &labels, &colors); else { char *labelSetting = trackDbSetting(tdb, BAR_CHART_CATEGORY_LABELS); char *colorSetting = trackDbSetting(tdb, BAR_CHART_CATEGORY_COLORS); getCategsFromSettings(tdb->track, labelSetting, colorSetting, &labels, &colors); } return createCategs(tdb->track, labels, colors); } struct barChartCategory *barChartUiGetCategoryById(int id, char *database, struct trackDb *tdb, struct facetedTableMergedOffset *mergeList) /* Get category info by id */ { struct barChartCategory *categ; struct barChartCategory *categs = barChartUiGetCategories(database, tdb, mergeList); for (categ = categs; categ != NULL; categ = categ->next) if (categ->id == id) return categ; return NULL; } char *barChartUiGetCategoryLabelById(int id, char *database, struct trackDb *tdb, struct facetedTableMergedOffset *mergeList) /* Get label for a category id */ { struct barChartCategory *categ = barChartUiGetCategoryById(id, database, tdb, mergeList); if (categ == NULL) return "Unknown"; return categ->label; } void barChartCfgUiSelectEachBar(char *database, struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed) /* Bar chart track type */ { printf("\n<table id=barChartControls style='font-size:%d%%' %s>\n<tr><td>", isPopup ? 75 : 100, boxed ?" width='100%'":""); /* Data transform. When selected, the next control (view limits max) is disabled */ puts("<div>"); barChartUiLogTransform(cart, track, tdb); /* Viewing limits max. This control is disabled if log transform is selected */ // construct class so JS can toggle puts(" "); barChartUiViewLimits(cart, track, tdb); puts("</div>"); /* Category filter */ printf("<br>"); char *categoryLabel = trackDbSettingClosestToHomeOrDefault(tdb, BAR_CHART_CATEGORY_LABEL, BAR_CHART_CATEGORY_LABEL_DEFAULT); char *db = cartString(cart, "db"); struct barChartCategory *categs = barChartUiGetCategories(db, tdb, NULL); printf("<div><b>%s:</b>\n", categoryLabel); char cartVar[1024]; safef(cartVar, sizeof(cartVar), "%s.%s", track, BAR_CHART_CATEGORY_SELECT); if (isPopup) { printf("<a href='%s?g=%s'><button type='button'>Change</button><a>", hTrackUiForTrack(track), track); } else { jsMakeCheckboxGroupSetClearButton(cartVar, TRUE); puts(" "); jsMakeCheckboxGroupSetClearButton(cartVar, FALSE); } printf("</div>"); struct slName *selectedValues = NULL; if (cartListVarExistsAnyLevel(cart, tdb, FALSE, BAR_CHART_CATEGORY_SELECT)) selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, BAR_CHART_CATEGORY_SELECT); makeCategoryCheckboxes(cartVar, categs, selectedValues); puts("\n</table>\n"); } void wrapColor(struct fieldedTable *table, struct fieldedRow *row, char *field, char *val, char *shortVal, void *context) /* Write out wrapper draws a SVG bar*/ { printf("<div style=\"background-color:%s\">  </span>", val); // printf("<TD><TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0><TR>"); } void barChartFacetedUi(char *database, struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed) /* Bar chart track type that has an associated facets tables */ { puts("<br>"); barChartUiLogTransform(cart, track, tdb); puts(" "); barChartUiViewLimits(cart, track, tdb); char *facets = trackDbSetting(tdb, "barChartFacets"); char *statsFile = trackDbRequiredSetting(tdb, "barChartStatsUrl"); /* Write html to make white background */ hInsideStyleToWhite(); /* Set up url that has enough context to get back to us. */ struct dyString *returnUrl = dyStringNew(0); dyStringPrintf(returnUrl, "../cgi-bin/hgTrackUi?g=%s", track); dyStringPrintf(returnUrl, "&%s", cartSidUrlString(cart)); /* Load up table from tsv file */ char *requiredStatsFields[] = {"count",}; struct fieldedTable *table = fieldedTableFromTabFile(statsFile, statsFile, requiredStatsFields, ArraySize(requiredStatsFields)); /* Update facet selections from users input if any and get selected part of table */ struct facetedTable *facTab = facetedTableFromTable(table, tdb->track, facets); facTab->mergeFacetsOk = trackDbSettingOn(tdb, "barChartMerge"); facetedTableUpdateOnClick(facTab, cart); struct facetField **selectedFf = NULL; struct fieldedTable *selected = facetedTableSelect(facTab, cart, &selectedFf); /* Add wrapper function(s) */ struct hash *wrapperHash = hashNew(0); hashAdd(wrapperHash, "color", wrapColor); /* Pick which fields to display. We'll take the first field whatever it is * named, color if possible, and also count, and any faceted fields. */ struct dyString *displayList = dyStringNew(0); int colorIx = fieldedTableFindFieldIx(selected, "color"); if (colorIx >= 0) dyStringPrintf(displayList, "color,"); dyStringAppend(displayList, selected->fields[0]); dyStringPrintf(displayList, ",count"); struct slName *facetNameList = slNameListFromComma(facets); struct slName *facetName; for (facetName = facetNameList; facetName != NULL; facetName = facetName->next) { if (fieldedTableFindFieldIx(selected, facetName->name)) dyStringPrintf(displayList, ",%s", facetName->name); } /* Put up facets and table */ facetedTableWriteHtml(facTab, cart, selected, selectedFf, displayList->string, returnUrl->string, 40, wrapperHash, NULL, 7); /* Clean up and go home. */ facetedTableFree(&facTab); } void barChartCfgUi(char *database, struct cart *cart, struct trackDb *tdb, char *track, char *title, boolean boxed) /* Put up facets in certain situations. */ { if (cartVarExists(cart, "ajax")) isPopup = TRUE; boxed = cfgBeginBoxAndTitle(tdb, boxed, title); if (startsWith("big", tdb->type)) labelCfgUi(database, cart, tdb, track); char *facets = trackDbSetting(tdb, "barChartFacets"); if (facets != NULL) barChartFacetedUi(database, cart, tdb, track, title, boxed); else barChartCfgUiSelectEachBar(database, cart, tdb, track, title, boxed); cfgEndBox(boxed); }