1b074613b1c6b7f84953c3f490631b91d844c9a9 galt Thu Sep 8 22:40:20 2022 -0700 Adapting Angie's existing variant effects to the new dbSnp that uses SPDI and provided via json formatted data. So users can see variant effects with version 153 or later. refs #29989 diff --git src/hg/lib/hui.c src/hg/lib/hui.c index a160a29..2aaa664 100644 --- src/hg/lib/hui.c +++ src/hg/lib/hui.c @@ -4607,30 +4607,45 @@ void labelMakeCheckBox(struct cart *cart, struct trackDb *tdb, char *sym, char *desc, boolean defaultOn) /* add a checkbox for the user to select a component of a label (e.g. ID, name, other info). * NOTE: This does not have a track name argument, so the correct tdb must be passed in: * if setting is at composite level, then pass in composite tdb, likewise for view. */ { char suffix[512]; safef(suffix, sizeof(suffix), "label.%s", sym); boolean option = cartUsualBooleanClosestToHome(cart, tdb, FALSE, suffix, defaultOn); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.%s", tdb->track, suffix); cgiMakeCheckBox(cartVar, option); printf(" %s ", desc); } +void geneTrackMakeCheckBox(struct cart *cart, struct trackDb *tdb, char *sym, char *desc, + boolean defaultOn) +/* add a checkbox for the user to select a component of a label (e.g. ID, name, other info). + * NOTE: This does not have a track name argument, so the correct tdb must be passed in: + * if setting is at composite level, then pass in composite tdb, likewise for view. */ +{ +char suffix[512]; +safef(suffix, sizeof(suffix), "geneTrack.%s", sym); +boolean option = cartUsualBooleanClosestToHome(cart, tdb, FALSE, suffix, defaultOn); +char cartVar[1024]; +safef(cartVar, sizeof cartVar, "%s.%s", tdb->track, suffix); +cgiMakeCheckBox(cartVar, option); +printf(" %s ", desc); +} + static void freqSourceSelect(struct cart *cart, struct trackDb *tdb, char *name) /* Make a select input for preferred source of allele frequencies from * trackDb setting freqSourceOrder. */ { char *freqSourceOrder = cloneString(trackDbSetting(tdb, "freqSourceOrder")); if (isEmpty(freqSourceOrder)) return; int fsCount = countSeparatedItems(freqSourceOrder, ','); char *values[fsCount]; chopCommas(freqSourceOrder, values); char *menu[fsCount]; int i; for (i = 0; i < fsCount; i++) { // Change label of GnomAD to "GnomAD genomes" for clarity when "GnomAD_exomes" is present. @@ -4639,77 +4654,198 @@ else { menu[i] = cloneString(values[i]); strSwapChar(menu[i], '_', ' '); } } boolean parentLevel = isNameAtParentLevel(tdb, name); char *freqProj = cartOptionalStringClosestToHome(cart, tdb, parentLevel, "freqProj"); puts("<b>Frequency source/project to use for Minor Allele Frequency (MAF):</b>"); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.freqProj", name); cgiMakeDropListWithVals(cartVar, menu, values, ArraySize(menu), freqProj); puts("<br>"); } -static struct trackDb *tdbOrAncestorByName(struct trackDb *tdb, char *name) +struct trackDb *tdbOrAncestorByName(struct trackDb *tdb, char *name) /* For reasons Angie cannot fathom, if a composite or view is passed to cfgByCfgType then * cfgByCfgType passes a leaf subtrack to its callees like bigDbSnpCfgUi. That is why we * see so many calls to isNameAtParentLevel, which returns true if the tdb was originally * at the composite or view level, which we can only tell by comparing with the original track name. * labelMakeCheckBox, called by many handlers in hgTrackUi that must be always top-level * (or have a special handler that bypasses cfgByCfgType like refSeqComposite), * is blissfully unaware of this. It uses the same tdb for looking in cart ClosestToHome * and for making the HTML element's cart var name, trusting that the correct tdb has been * handed to it. * So in order for a callee of cfgByCfgType to call labelMakeCheckBox with the correct tdb, * we need to walk back up comparing name like isNameAtParentLevel does. * If name doesn't match tdb or any of its ancestors then this returns NULL. */ { struct trackDb *correctTdb; for (correctTdb = tdb; correctTdb != NULL; correctTdb = correctTdb->parent) if (startsWithWordByDelimiter(correctTdb->track, '.', name)) return correctTdb; return NULL; } +void snp153MakeCheckboxGroupSetClearButton(char *buttonVar, boolean isSet) +/* Make a button for setting or clearing a set of checkboxes with the same name. + * Uses only javascript to change the checkboxes, no resubmit. */ +{ +char id[256]; +char javascript[256]; +safef(javascript, sizeof(javascript), + "$(\"input:checkbox[name^='%s']\").each(function(){this.checked = %s;$(this).trigger('change');})", + buttonVar, isSet ? "true" : "false"); +safef(id, sizeof id, "%s_grp%sBut", buttonVar, isSet ? "Set" : "Clr"); +cgiMakeOnClickButton(id, javascript, isSet ? JS_SET_ALL_BUTTON_LABEL : JS_CLEAR_ALL_BUTTON_LABEL); +} + + +struct trackDb *snp125FetchGeneTracks(char *database, struct cart *cart) +/* Get a list of genePred tracks. */ +{ +struct trackDb *tdbList = NULL; +struct hash *trackHash = trackHashMakeWithComposites(database,NULL,&tdbList,FALSE); + +struct sqlConnection *conn = hAllocConn(database); +struct slName *justGenePredTables = hTrackTablesOfType(conn, "genePred%%"), *gt; +struct slName *bigGenePredTables = hTrackTablesOfType(conn, "bigGenePred"); +struct slName *genePredTables = slCat(justGenePredTables,bigGenePredTables); +struct trackDb *geneTdbList = NULL, *gTdb; +if (genePredTables != NULL) + { + for (gt = genePredTables; gt != NULL; gt = gt->next) + { + gTdb = hashFindVal(trackHash, gt->name); + if (gTdb && sameString(gTdb->grp, "genes")) + { + // We are going to overwrite gTdb's next pointer and possibly its priority, + // so make a shallow copy: + gTdb = CloneVar(gTdb); + if (gTdb->parent) + gTdb->priority = (gTdb->parent->priority + gTdb->priority/1000); + slAddHead(&geneTdbList, gTdb); + } + } + slSort(&geneTdbList, trackDbCmp); + } +hFreeConn(&conn); +return geneTdbList; +} + +void snp153OfferGeneTracksForFunction(char *database, struct cart *cart, char *name, struct trackDb *tdb, struct trackDb *correctTdb) +/* Get a list of genePred tracks and make checkboxes to enable hgc's functional + * annotations. */ +{ +struct trackDb *geneTdbList = NULL, *gTdb; +geneTdbList = snp125FetchGeneTracks(database, cart); +if (geneTdbList) + { + + char sectionVar[256]; + safef(sectionVar, sizeof(sectionVar), "%s.geneTracks", name); + jsBeginCollapsibleSection(cart, name, sectionVar, + "Use Gene Tracks for Functional Annotation", FALSE); + printf("<BR><B>On details page, show function and coding differences relative to: </B>\n"); + + char buttonVarPrefix[256]; + safef(buttonVarPrefix, sizeof(buttonVarPrefix), "%s.geneTrack", name); + snp153MakeCheckboxGroupSetClearButton(buttonVarPrefix, TRUE); + snp153MakeCheckboxGroupSetClearButton(buttonVarPrefix, FALSE); + + struct slName *defaultGeneTracks = slNameListFromComma(trackDbSetting(tdb, "defaultGeneTracks")); + + int i; + int numCols = 4; + int menuSize = slCount(geneTdbList); + char **values = needMem(menuSize*sizeof(char *)); + char **labels = needMem(menuSize*sizeof(char *)); + for (i = 0, gTdb = geneTdbList; i < menuSize && gTdb != NULL; i++, gTdb = gTdb->next) + { + values[i] = gTdb->track; + if (gTdb->parent != NULL) + { + struct dyString *dy = dyStringNew(0); + if (gTdb->parent->parent != NULL && + !startsWith(gTdb->parent->parent->shortLabel, gTdb->parent->shortLabel)) + dyStringPrintf(dy, "%s: ", gTdb->parent->parent->shortLabel); + if (!startsWith(gTdb->parent->shortLabel, gTdb->shortLabel)) + dyStringPrintf(dy, "%s: ", gTdb->parent->shortLabel); + dyStringPrintf(dy, "%s", gTdb->shortLabel); + labels[i] = dyStringCannibalize(&dy); + } + else + labels[i] = gTdb->shortLabel; + } + + printf("<BR>\n"); + + puts("<TABLE BORDERWIDTH=0><TR>"); + for (i = 0; i < menuSize; ++i) + { + if (i > 0 && (i % numCols) == 0) + printf("</TR><TR>"); + printf("<TD>"); + geneTrackMakeCheckBox(cart, correctTdb, values[i], labels[i], slNameInList(defaultGeneTracks, values[i]) ); + printf("</TD>"); + } + if ((i % numCols) != 0) + while ((i++ % numCols) != 0) + printf("<TD></TD>"); + puts("</TR></TABLE>"); + + jsEndCollapsibleSection(); + + } +} + void bigDbSnpCfgUi(char *db, struct cart *cart, struct trackDb *leafTdb, char *name, char *title, boolean boxed) /* UI for bigDbSnp a.k.a. "dbSNP 2.0". */ { boxed = cfgBeginBoxAndTitle(leafTdb, boxed, title); freqSourceSelect(cart, leafTdb, name); puts("<br>"); puts("<b>Label:</b>"); struct trackDb *correctTdb = tdbOrAncestorByName(leafTdb, name); labelMakeCheckBox(cart, correctTdb, "rsId", "rs# identifier", TRUE); labelMakeCheckBox(cart, correctTdb, "refAlt", "reference/alternate allele", TRUE); labelMakeCheckBox(cart, correctTdb, "majMin", "major/minor allele", FALSE); labelMakeCheckBox(cart, correctTdb, "maf", "MAF if available", FALSE); labelMakeCheckBox(cart, correctTdb, "func", "Most severe functional impact on gene if any", FALSE); puts("<br>"); scoreCfgUi(db, cart, leafTdb, name, "", 0, FALSE); puts("For more information about the "Interesting or anomalous properties", " "see <a href='#ucscNotes'>below</a>."); puts("<br><br>"); puts("<b>Minimum MAF:</b>"); boolean parentLevel = isNameAtParentLevel(leafTdb, name); double minMaf = cartUsualDoubleClosestToHome(cart, leafTdb, parentLevel, "minMaf", 0.0); char cartVar[1024]; safef(cartVar, sizeof cartVar, "%s.minMaf", name); cgiMakeDoubleVarWithLimits(cartVar, minMaf, "MAF", 0, 0.0, 0.5); -puts("range: 0.0 - 0.5"); +puts("range: 0.0 - 0.5<br>"); + +// Make wrapper table for collapsible sections: +puts("<TABLE border=0 cellspacing=0 cellpadding=0>"); + +snp153OfferGeneTracksForFunction(db, cart, name, leafTdb, correctTdb); + +// End wrapper table for collapsible sections: +puts("</TABLE>"); + cfgEndBox(boxed); } void cfgByCfgType(eCfgType cType,char *db, struct cart *cart, struct trackDb *tdb,char *prefix, char *title, boolean boxed) // Methods for putting up type specific cfgs used by composites/subtracks in hui.c { // When only one subtrack, then show it's cfg settings instead of composite/view level settings // This simplifies the UI where hgTrackUi won't have 2 levels of cfg, // while hgTracks still supports rightClick cfg of the subtrack. if (configurableByAjax(tdb,cType) > 0) // Only if subtrack's configurable by ajax do we { // consider this option if (tdbIsComposite(tdb) // called for the composite && !isCustomComposite(tdb)