6ecf4a7fdccf43addd6ca15bc2dedaa239852784 braney Tue May 9 16:09:07 2017 -0700 ongoing work on hgComposite. Support add all visible button diff --git src/hg/hgComposite/hgComposite.c src/hg/hgComposite/hgComposite.c index 4c89acc..5e34817 100644 --- src/hg/hgComposite/hgComposite.c +++ src/hg/hgComposite/hgComposite.c @@ -1,850 +1,896 @@ -/* hgVai - Variant Annotation Integrator. */ +/* hgComposite --- build a composite */ -/* Copyright (C) 2014 The Regents of the University of California +/* Copyright (C) 2017 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "jksql.h" #include "htmshell.h" #include "web.h" #include "cheapcgi.h" #include "cart.h" #include "cartTrackDb.h" #include "genbank.h" #include "hgConfig.h" #include "hgHgvs.h" #include "hui.h" #include "grp.h" #include "hCommon.h" #include "hgFind.h" #include "hPrint.h" #include "jsHelper.h" #include "memalloc.h" #include "textOut.h" #include "trackHub.h" #include "hubConnect.h" #include "twoBit.h" #include "gpFx.h" #include "bigGenePred.h" #include "udc.h" #include "knetUdc.h" #include "cartTrackDb.h" #include "trashDir.h" #include "customComposite.h" #define hgCompEditPrefix "hgCompositeEdit_" #define hgsAddTrack hgCompEditPrefix "addTrack" +#define hgsAddVisTrack hgCompEditPrefix "addVisTrack" #define hgsChangeGroup hgCompEditPrefix "changeGroup" #define hgsCurrentGroup hgCompEditPrefix "currentGroup" #define hgsCurrentComposite hgCompEditPrefix "currentComposite" #define hgsNewCompositeName hgCompEditPrefix "newCompositeName" #define hgsNewCompositeShortLabel hgCompEditPrefix "newCompositeShortLabel" #define hgsNewCompositeLongLabel hgCompEditPrefix "newCompositeLongLabel" //#define hgCompositePrefix "hgComposite_" #define hgDoNewComposite hgCompEditPrefix "doNewComposite" struct track { struct track *next; char *name; char *shortLabel; char *longLabel; }; struct composite { struct composite *next; char *name; char *shortLabel; char *longLabel; struct track *trackList; }; /* Global Variables */ struct cart *cart; /* CGI and other variables */ struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */ char *genome = NULL; /* Name of genome - mouse, human, etc. */ char *database = NULL; /* Current genome database - hg17, mm5, etc. */ struct grp *fullGroupList = NULL; /* List of all groups. */ // Null terminated list of CGI Variables we don't want to save permanently: -char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", hgsAddTrack, hgsNewCompositeName, hgsNewCompositeShortLabel, hgsNewCompositeLongLabel, hgsChangeGroup, NULL}; +char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", hgsAddTrack, hgsNewCompositeName, hgsNewCompositeShortLabel, hgsNewCompositeLongLabel, hgsChangeGroup, hgsAddVisTrack, NULL}; void nbSpaces(int count) /* Print some non-breaking spaces. */ { int i; for (i=0; i<count; ++i) printf(" "); } void addSomeCss() /*#*** This should go in a .css file of course. */ { printf("<style>\n" "div.sectionLite { border-width: 1px; border-color: #"HG_COL_BORDER"; border-style: solid;" " background-color: #FFFFFF; padding-left: 10px; padding-right: 10px; " " padding-top: 8px; padding-bottom: 5px; margin-top: 5px; margin-bottom: 5px }\n" ".sectionLiteHeader { font-weight: bold; font-size:larger; color:#000000;" " text-align:left; vertical-align:bottom; white-space:nowrap; }\n" "div.sectionLiteHeader.noReorderRemove { padding-bottom:5px; }\n" "div.sourceFilter { padding-top: 5px; padding-bottom: 5px }\n" "</style>\n"); } INLINE void startCollapsibleSection(char *sectionSuffix, char *title, boolean onByDefault) // Wrap shared args to jsBeginCollapsibleSectionFontSize { jsBeginCollapsibleSectionFontSize(cart, "hgva", sectionSuffix, title, onByDefault, "1.1em"); } INLINE void startSmallCollapsibleSection(char *sectionSuffix, char *title, boolean onByDefault) // Wrap shared args to jsBeginCollapsibleSectionFontSize { jsBeginCollapsibleSectionFontSize(cart, "hgva", sectionSuffix, title, onByDefault, "0.9em"); } #define endCollapsibleSection jsEndCollapsibleSection static struct dyString *onChangeStart() /* Start up a javascript onChange command */ { struct dyString *dy = jsOnChangeStart(); return dy; } static char *onChangeClade() /* Return javascript executed when they change clade. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); dyStringAppend(dy, " document.hiddenForm.org.value=0;"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); return jsOnChangeEnd(&dy); } static char *onChangeOrg() /* Return javascript executed when they change organism. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "org"); dyStringAppend(dy, " document.hiddenForm.db.value=0;"); return jsOnChangeEnd(&dy); } static char *onChangeDb() /* Return javascript executed when they change database. */ { struct dyString *dy = onChangeStart(); jsDropDownCarryOver(dy, "clade"); jsDropDownCarryOver(dy, "db"); return jsOnChangeEnd(&dy); } INLINE void printOption(char *val, char *selectedVal, char *label) /* For rolling our own select without having to build conditional arrays/lists. */ { printf("<OPTION VALUE='%s'%s>%s\n", val, (sameString(selectedVal, val) ? " SELECTED" : ""), label); } static struct composite *getCompositeList(char *db, char *hubName, struct hash *nameHash) { struct composite *compositeList = NULL; FILE *f; if ((hubName != NULL) && ((f = fopen(hubName, "r")) != NULL)) { fclose(f); // read hub to find names of composites and add them to compositeList struct trackDb *tdbList = trackDbFromRa(hubName, NULL); struct trackDb *tdb, *tdbNext; struct composite *composite = NULL; struct track *track = NULL; for(tdb = tdbList; tdb; tdb = tdbNext) { hashAdd(nameHash, tdb->track, tdb); tdbNext = tdb->next; trackDbFieldsFromSettings(tdb); if (trackDbSetting(tdb, "compositeTrack")) { AllocVar(composite); slAddHead(&compositeList, composite); composite->name = tdb->track; composite->shortLabel = tdb->shortLabel; composite->longLabel = tdb->shortLabel; } else { if (composite == NULL) errAbort("track not in composite"); AllocVar(track); track->name = tdb->track; track->shortLabel = tdb->shortLabel; track->longLabel = tdb->shortLabel; slAddHead(&composite->trackList, track); } } } return compositeList; } static char *getSqlBigWig(char *db, struct trackDb *tdb) { struct sqlConnection *conn = hAllocConn(db); char buffer[4096]; safef(buffer, sizeof buffer, "NOSQLINJ select fileName from %s", tdb->table); return sqlQuickString(conn, buffer); } static int snakePalette2[] = { 0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 }; void outTdb(char *db, FILE *f, char *name, struct trackDb *tdb, char *parent, unsigned int color) { char *dataUrl = NULL; char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl == NULL) { if (startsWith("bigWig", tdb->type)) dataUrl = getSqlBigWig(db, tdb); } struct hashCookie cookie = hashFirst(tdb->settingsHash); struct hashEl *hel; fprintf(f, "\ttrack %s\n", name); while ((hel = hashNext(&cookie)) != NULL) { if (differentString(hel->name, "parent") && differentString(hel->name, "polished")&& differentString(hel->name, "color")&& differentString(hel->name, "track")) fprintf(f, "\t%s %s\n", hel->name, (char *)hel->val); } if (bigDataUrl == NULL) { if (dataUrl != NULL) fprintf(f, "\tbigDataUrl %s\n", dataUrl); } fprintf(f, "\tparent %s\n",parent); fprintf(f, "\tcolor %d,%d,%d\n", (color >> 16) & 0xff,(color >> 8) & 0xff,color & 0xff); fprintf(f, "\n"); } static void outComposite(FILE *f, struct composite *composite) { char *parent = composite->name; char *shortLabel = composite->shortLabel; char *longLabel = composite->longLabel; fprintf(f,"track %s\n\ shortLabel %s\n\ compositeTrack on\n\ aggregate none\n\ longLabel %s\n\ %s on\n\ type wig \n\ visibility full\n\n", parent, shortLabel, longLabel, CUSTOM_COMPOSITE_SETTING); } static struct trackDb *findTrack(char *name, struct trackDb *fullTrackList) { struct trackDb *tdb; for (tdb = fullTrackList; tdb != NULL; tdb = tdb->next) { if (sameString(name, tdb->track)) return tdb; } errAbort("cannot find track"); return NULL; } static void outHubHeader(FILE *f, char *db, char *hubName) { char *hubFile = strrchr(hubName, '/') + 1; fprintf(f,"hub hub1\n\ shortLabel User Composite\n\ longLabel User Composite\n\ genomesFile %s\n\ email braney@soe.ucsc.edu\n\ descriptionUrl hub.html\n\n", hubFile); fprintf(f,"genome %s\n\ trackDb %s\n\n", db, hubFile); } static char *getHubName(char *db) { struct tempName hubTn; char buffer[4096]; safef(buffer, sizeof buffer, "%s-%s", customCompositeCartName, db); char *hubName = cartOptionalString(cart, buffer); if (hubName == NULL) { trashDirDateFile(&hubTn, "hgComposite", "hub", ".txt"); hubName = cloneString(hubTn.forCgi); cartSetString(cart, buffer, hubName); FILE *f = mustOpen(hubName, "a"); outHubHeader(f, db, hubName); fclose(f); cartSetString(cart, "hubUrl", hubName); cartSetString(cart, hgHubConnectRemakeTrackHub, hubName); } return hubName; } //static void outputCompositeHub(char *db, char *hubName, struct trackDb *fullTrackList, struct composite *compositeList, struct hash *nameHash) static void outputCompositeHub(char *db, char *hubName, struct composite *compositeList, struct hash *nameHash) { // Do we already have a hub? chmod(hubName, 0666); FILE *f = mustOpen(hubName, "w"); outHubHeader(f, db, hubName); int useColor = 0; struct composite *composite; for(composite = compositeList; composite; composite = composite->next) { outComposite(f, composite); struct trackDb *tdb; struct track *track; for (track = composite->trackList; track; track = track->next) { tdb = hashMustFindVal(nameHash, track->name); //tdb = findTrack(track->name, fullTrackList); outTdb(db, f, track->name,tdb, composite->name, snakePalette2[useColor]); useColor++; if (useColor == (sizeof snakePalette2 / sizeof(int))) useColor = 0; } } fclose(f); } void topLabelSpansStart(char *label) { printf("<span style='display: inline-block; padding-right: 5px;'>" "<span style='display: block;'>%s</span>\n" "<span style='display: block; padding-bottom: 5px;'>\n", label); } void topLabelSpansEnd() { printf("</span></span>"); } void printCtAndHubButtons() /* Print a div with buttons for hgCustom and hgHubConnect */ { boolean hasCustomTracks = customTracksExist(cart, NULL); puts("<div style='padding-top: 5px; padding-bottom: 5px'>"); hOnClickButton("prtCtHub_CtBut", "document.customTrackForm.submit(); return false;", hasCustomTracks ? CT_MANAGE_BUTTON_LABEL : CT_ADD_BUTTON_LABEL); printf(" "); if (hubConnectTableExists()) hOnClickButton("prtCtHub_TrkHub", "document.trackHubForm.submit(); return false;", "track hubs"); nbSpaces(3); printf("To reset <B>all</B> user cart settings (including custom tracks), \n" "<A HREF=\"cartReset?destination=%s\">click here</A>.\n", cgiScriptName()); puts("</div>"); } void hgGatewayCladeGenomeDb() /* Make a row of labels and row of buttons like hgGateway, but not using tables. */ { boolean gotClade = hGotClade(); if (gotClade) { topLabelSpansStart("clade"); printCladeListHtml(genome, "change", onChangeClade()); topLabelSpansEnd(); } topLabelSpansStart("genome"); if (gotClade) printGenomeListForCladeHtml(database, "change", onChangeOrg()); else printGenomeListHtml(database, "change", onChangeOrg()); topLabelSpansEnd(); topLabelSpansStart("assembly"); printAssemblyListHtml(database, "change", onChangeDb()); topLabelSpansEnd(); puts("<BR>"); topLabelSpansEnd(); topLabelSpansStart(""); printf("</span>\n"); topLabelSpansEnd(); puts("<BR>"); } void printAssemblySection() /* Print assembly-selection stuff. * Redrawing the whole page when the assembly changes seems fine to me. */ { //#*** ---------- More copied verbatim, from hgTables/mainPage.c: ----------- /* Hidden form - for benefit of javascript. */ { static char *saveVars[] = { "clade", "org", "db", }; jsCreateHiddenForm(cart, cgiScriptName(), saveVars, ArraySize(saveVars)); } hPrintf("<FORM ACTION='%s' NAME='changeGroupForm'>", cgiScriptName()); cartSaveSession(cart); cgiMakeHiddenVar(hgsCurrentGroup, ""); hPrintf("</FORM>\n"); hPrintf("<FORM ACTION='%s' NAME='changeCompositeForm'>", cgiScriptName()); cartSaveSession(cart); cgiMakeHiddenVar(hgsCurrentComposite, ""); hPrintf("</FORM>\n"); hPrintf("<FORM ACTION='%s' NAME='makeNewCompositeForm'>", cgiScriptName()); cartSaveSession(cart); cgiMakeHiddenVar(hgsNewCompositeName, ""); cgiMakeHiddenVar(hgsNewCompositeShortLabel, ""); cgiMakeHiddenVar(hgsNewCompositeLongLabel, ""); hPrintf("</FORM>\n"); +hPrintf("<FORM ACTION='%s' NAME='addVisTrackForm'>", cgiScriptName()); +cartSaveSession(cart); +cgiMakeHiddenVar(hgsAddVisTrack, ""); +hPrintf("</FORM>\n"); + hPrintf("<FORM ACTION='%s' NAME='addTrackForm'>", cgiScriptName()); cartSaveSession(cart); cgiMakeHiddenVar(hgsAddTrack, ""); hPrintf("</FORM>\n"); /* Hidden form for jumping to custom tracks CGI. */ hPrintf("<FORM ACTION='%s' NAME='customTrackForm'>", hgCustomName()); cartSaveSession(cart); hPrintf("</FORM>\n"); /* Hidden form for jumping to track hub manager CGI. */ hPrintf("<FORM ACTION='%s' NAME='trackHubForm'>", hgHubConnectName()); cartSaveSession(cart); hPrintf("</FORM>\n"); printf("<FORM ACTION=\"%s\" NAME=\"mainForm\" ID=\"mainForm\" METHOD=%s>\n", cgiScriptName(), cartUsualString(cart, "formMethod", "GET")); cartSaveSession(cart); //#*** ------------------ end verbatim --------------- printf("<div class='sectionLiteHeader noReorderRemove'>" "Select Genome Assembly</div>\n"); /* Print clade, genome and assembly line. */ hgGatewayCladeGenomeDb(); } static void printCompositeList(struct composite *compositeList, struct composite *currentComposite) { if (compositeList == NULL) return; printf("<div class='sectionLiteHeader noReorderRemove'>" "My Composites</div>\n"); int count = slCount(compositeList); char *labels[count]; char *names[count]; count = 0; for(; compositeList; compositeList = compositeList->next) { labels[count] = compositeList->shortLabel; names[count] = compositeList->name; count++; } cgiMakeDropListFull("compositeList", labels, names, count, currentComposite->name, "change", "var e = document.getElementById('compositeList'); \ var strUser = e.options[e.selectedIndex].value; \ document.changeCompositeForm.elements['"hgsCurrentComposite"'].value = strUser; \ document.changeCompositeForm.submit();"); //document.addTrackForm.elements['hgComp_track'] = strUser;"); } static void makeAddComposite() { printf("<BR>"); printf("<BR>"); printf("<H3>Make New Composite</H3>"); printf("name "); cgiMakeTextVar(hgsNewCompositeName, "", 29); printf("<BR>short label "); cgiMakeTextVar(hgsNewCompositeShortLabel, "", 29); printf("<BR>long label "); cgiMakeTextVar(hgsNewCompositeLongLabel, "", 29); printf("<BR>"); hOnClickButton("selVar_MakeNewComposite", "var e = document.getElementById('"hgsNewCompositeName"'); \ document.makeNewCompositeForm.elements['"hgsNewCompositeName"'].value = e.value; \ var e = document.getElementById('"hgsNewCompositeShortLabel"'); \ document.makeNewCompositeForm.elements['"hgsNewCompositeShortLabel"'].value = e.value; \ var e = document.getElementById('"hgsNewCompositeLongLabel"'); \ document.makeNewCompositeForm.elements['"hgsNewCompositeLongLabel"'].value = e.value; \ document.makeNewCompositeForm.submit(); return false;", "submit"); printf("<BR>"); } static void printTrackList(struct composite *composite) { printf("<div class='sectionLiteHeader noReorderRemove'>" "Tracks in Composite</div>\n"); printf("<BR>"); printf("<div style=\"max-width:1024px\">"); printf("<table id=\"sessionTable\" class=\"sessionTable stripe hover row-border compact\" borderwidth=0>\n"); printf("<thead><tr>"); printf("<TH><TD><B>Name</B></TD></TH>"); printf("</tr></thead><tbody>"); struct track *track; if (composite) for(track = composite->trackList; track; track = track->next) { printf("<TR><TD>%s</TD></TR>\n",track->shortLabel); } //printf("<TR><TD>track1</TD></TR>"); //printf("<TR><TD>track2</TD></TR>"); printf("</table>"); } static boolean trackCanBeAdded(struct trackDb *tdb) { return (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) && (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type)) ; } static void availableTracks(char *db, struct grp *groupList, struct trackDb *fullTrackList) { printf("<H4>Add tracks from %s</H4>", db); char *curGroupName = cartOptionalString(cart, hgsCurrentGroup); printf("<BR>groups: "); char **labels, **names; int count = slCount(groupList); AllocArray(labels, count); AllocArray(names, count); count = 0; struct grp *grp; for(grp = groupList; grp; grp = grp->next) { labels[count] = grp->label; names[count] = grp->name; count++; } cgiMakeDropListFull("availGroups", labels, names, count, curGroupName, "change", "var e = document.getElementById('availGroups'); \ var strUser = e.options[e.selectedIndex].value; \ document.changeGroupForm.elements['"hgsCurrentGroup"'].value = strUser; \ document.changeGroupForm.submit();"); struct grp *curGroup; if (curGroupName == NULL) curGroup = groupList; else { for(curGroup = groupList; curGroup; curGroup = curGroup->next) { if (sameString(curGroupName, curGroup->name)) break; } if (curGroup == NULL) errAbort("cannot find current group"); } struct trackDb *tdb; count = 0; for(tdb = fullTrackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, curGroup->name)) count++; } //char **labels, **names; AllocArray(labels, count); AllocArray(names, count); count = 0; for(tdb = fullTrackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, curGroup->name)) { labels[count] = tdb->shortLabel; names[count] = tdb->track; count++; } } printf("track:"); cgiMakeDropListFull("availTracks", labels, names, count, *names, "change", "var e = document.getElementById('availTracks'); \ var strUser = e.options[e.selectedIndex].value; \ document.addTrackForm.elements['"hgsAddTrack"'].value = strUser;"); //document.addTrackForm.elements['hgComp_track'] = strUser;"); hOnClickButton("addTrack", "var e = document.getElementById('availTracks'); \ var strUser = e.options[e.selectedIndex].value; \ document.addTrackForm.elements['"hgsAddTrack"'].value = strUser; \ document.addTrackForm.submit();" , "add track"); printf("<BR>"); printf("<BR>"); printf("<BR>"); -hOnClickButton("selVar_AddAllVis", "document.trackHubForm.submit(); return false;", "Add All Visibile Wiggles"); +hOnClickButton("selVar_AddAllVis", "document.addVisTrackForm.submit(); return false;", "Add All Visibile Wiggles"); } void doMainPage(char *db, struct grp *groupList, struct trackDb *fullTrackList, struct composite *currentComposite, struct composite *compositeList) /* Print out initial HTML of control page. */ { //struct composite *currentComposite = compositeList; jsInit(); webIncludeResourceFile("jquery-ui.css"); webIncludeResourceFile("ui.dropdownchecklist.css"); boolean alreadyAgreed = cartUsualBoolean(cart, "hgva_agreedToDisclaimer", FALSE); jsInlineF( "$(document).ready(function() { hgva.disclaimer.init(%s, hgva.userClickedAgree); });\n" , alreadyAgreed ? "true" : "false"); addSomeCss(); printAssemblySection(); puts("<BR>"); printf("<div class='sectionLiteHeader noReorderRemove'>" "Add Hubs and Custom Tracks </div>\n"); printCtAndHubButtons(); //struct hashEl *hel = cartFindPrefix(cart, hgCompEditPrefix); //if (hel != NULL) { // printf("printing EditCom\n"); /// printEditComposite(); } printf("</FORM>"); puts("<BR>"); puts("<BR>"); printCompositeList(compositeList, currentComposite); makeAddComposite(); puts("<BR>"); printTrackList(currentComposite); puts("<BR>"); availableTracks(db, groupList, fullTrackList); puts("<BR>"); // Make wrapper table for collapsible sections: //selectVariants(); //char *geneTrack = selectGenes(); //if (geneTrack != NULL) { //selectRegulatory(); //selectAnnotations(geneTrack); //selectFilters(); //selectOutput(); //submitAndDisclaimer(); } printf("</FORM>"); jsReloadOnBackButton(cart); webNewSection("Using the Composite Builder"); -webIncludeHelpFileSubst("hgCompositeHelpText", cart, FALSE); +webIncludeHelpFileSubst("hgCompositeHelp", cart, FALSE); jsIncludeFile("jquery-ui.js", NULL); jsIncludeFile("hgVarAnnogrator.js", NULL); jsIncludeFile("ui.dropdownchecklist.js", NULL); jsIncludeFile("ddcl.js", NULL); } void doUi(char *db, struct grp *groupList, struct trackDb *fullTrackList,struct composite *currentComposite, struct composite *compositeList) /* Set up globals and make web page */ { cartWebStart(cart, db, "Composite Editor"); doMainPage(database, groupList, fullTrackList, currentComposite, compositeList); cartWebEnd(); /* Save variables. */ //cartCheckout(&cart); } static struct hash *addWigs(struct trackDb **wigList, struct trackDb *list) { struct hash *hash = newHash(4); if (list == NULL) return hash; struct trackDb *tdb, *tdbNext; for(tdb = list; tdb; tdb = tdbNext) { tdbNext = tdb->next; addWigs(wigList, tdb->subtracks); if (trackCanBeAdded(tdb)) { slAddHead(wigList, tdb); hashStore(hash, tdb->grp); } } return hash; } char *makeUnique(struct hash *nameHash, struct trackDb *tdb) { if (hashLookup(nameHash, tdb->track) == NULL) { hashAdd(nameHash, tdb->track, tdb); return tdb->track; } unsigned count = 0; char buffer[4096]; for(;; count++) { safef(buffer, sizeof buffer, "%s%d", tdb->track, count); if (hashLookup(nameHash, buffer) == NULL) { hashAdd(nameHash, buffer, tdb); return cloneString(buffer); } } return NULL; } +bool trackVisible(struct trackDb *tdb) +{ +if ((tdb->parent != NULL) && !trackVisible(tdb->parent)) + return FALSE; + +boolean vis = tdb->visibility != tvHide; +char *cartVis = cartOptionalString(cart, tdb->track); + +if (cartVis != NULL) + { + if (differentString(cartVis, "hide")) + vis = TRUE; + else + vis = FALSE; + } + +return vis; +} + + int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); if (hIsPrivateHost()) pushCarefulMemHandler(LIMIT_2or6GB); cgiSpoof(&argc, argv); htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ oldVars = hashNew(10); cart = cartAndCookie(hUserCookie(), excludeVars, oldVars); /* Set up global variables. */ getDbAndGenome(cart, &database, &genome, oldVars); initGenbankTableNames(database); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */ struct trackDb *wigTracks = NULL; /* List of all wig tracks */ cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); struct hash *groupHash = addWigs(&wigTracks, fullTrackList); struct grp *grp, *grpNext, *groupList = NULL; for(grp = fullGroupList; grp; grp = grpNext) { grpNext = grp->next; if (hashLookup(groupHash, grp->name) != NULL) slAddHead(&groupList, grp); } slReverse(&groupList); /* struct grp *grpList; struct trackDb *tdbList = hubCollectTracks(database, &grpList); addWigs(&wigTracks, tdbList); */ char *hubName = getHubName(database); struct hash *nameHash = newHash(5); struct composite *compositeList = getCompositeList(database, hubName, nameHash); struct composite *currentComposite = NULL; char *currentCompositeName = cartOptionalString(cart, hgsCurrentComposite); if (currentCompositeName != NULL) { for (currentComposite = compositeList; currentComposite; currentComposite = currentComposite->next) if (sameString(currentComposite->name, currentCompositeName)) break; } if (currentComposite == NULL) currentComposite = compositeList; char *newCompositeName = cartOptionalString(cart, hgsNewCompositeName); if (newCompositeName != NULL) { if (isEmpty(newCompositeName)) warn("Composite name must not be empty string"); else { struct composite *composite; AllocVar(composite); slAddHead(&compositeList, composite); currentComposite = composite; composite->name = cloneString(newCompositeName); char *newCompositeShortLabel = cartOptionalString(cart, hgsNewCompositeShortLabel); if (isEmpty(newCompositeShortLabel)) composite->shortLabel = composite->name; else composite->shortLabel = cloneString(newCompositeShortLabel); char *newCompositeLongLabel = cartOptionalString(cart, hgsNewCompositeLongLabel); if (isEmpty(newCompositeLongLabel)) composite->longLabel = composite->name; else composite->longLabel = cloneString(newCompositeLongLabel); } } if (currentCompositeName == NULL) currentComposite = compositeList; +char *addAllVisible = cartOptionalString(cart, hgsAddVisTrack); +if (addAllVisible != NULL) + { + struct trackDb *tdb; + + for(tdb = fullTrackList; tdb; tdb = tdb->next) + { + if (trackCanBeAdded(tdb) && trackVisible(tdb)) + { + struct track *track; + AllocVar(track); + track->name = makeUnique(nameHash, tdb); + track->shortLabel = tdb->shortLabel; + track->longLabel = tdb->longLabel; + slAddHead(¤tComposite->trackList, track); + } + } + } + char *newTrackName = cartOptionalString(cart, hgsAddTrack); if (newTrackName != NULL) { if (currentComposite == NULL) warn("cannot add track without specifying a composite"); else { struct trackDb *tdb = findTrack(newTrackName, wigTracks); struct track *track; AllocVar(track); track->name = makeUnique(nameHash, tdb); track->shortLabel = tdb->shortLabel; + track->longLabel = tdb->longLabel; slAddHead(¤tComposite->trackList, track); } } //struct trackDb *fullTrackList = getFullTrackList(cart); doUi(database, groupList, wigTracks, currentComposite, compositeList); outputCompositeHub(database, hubName, compositeList, nameHash); cartCheckout(&cart); cgiExitTime("hgComposite", enteredMainTime); return 0; }