957f2123050742982ef6c7aefcab70d29144924c braney Mon Oct 9 17:49:04 2017 -0700 allow bedGraph. Change names in collections so they don't match names in trackDb, move the copying of custom tracks and collections to BEFORE the load of trackHubs, misc other bugs diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c index 2189d4a..84526e1 100644 --- src/hg/hgCollection/hgCollection.c +++ src/hg/hgCollection/hgCollection.c @@ -1,907 +1,910 @@ /* hgCollection - hub builder */ /* Copyright (C) 2017 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "cartTrackDb.h" #include "trackHub.h" #include "trashDir.h" #include "hubConnect.h" #include "hui.h" #include "grp.h" #include "cheapcgi.h" #include "jsHelper.h" #include "web.h" #include "knetUdc.h" #include "api.h" #include "genbank.h" #include "htmshell.h" #include "jsonParse.h" #include "customComposite.h" #include "stdlib.h" /* Global Variables */ struct hash *oldVars = NULL; /* The cart before new cgi stuff added. */ // Null terminated list of CGI Variables we don't want to save permanently: char *excludeVars[] = {"Submit", "submit", "cmd", "track", "collection", "jsonp", NULL,}; struct track { struct track *next; struct track *trackList; struct trackDb *tdb; char *name; char *shortLabel; char *longLabel; char *visibility; unsigned long color; char *viewFunc; }; struct trackDbRef { struct trackDbRef *next; struct trackDb *tdb; int order; }; static char *makeUnique(struct hash *nameHash, char *name) // Make the name of this track unique. { char *skipHub = trackHubSkipHubName(name); if (hashLookup(nameHash, skipHub) == NULL) { hashStore(nameHash, name); return skipHub; } unsigned count = 0; char buffer[4096]; for(;; count++) { safef(buffer, sizeof buffer, "%s%d", skipHub, count); if (hashLookup(nameHash, buffer) == NULL) { hashStore(nameHash, buffer); return cloneString(buffer); } } return NULL; } static boolean trackCanBeAdded(struct trackDb *tdb) // are we allowing this track into a custom composite { -return (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) && (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type)) ; +return (tdb->subtracks == NULL) && !startsWith("wigMaf",tdb->type) && (startsWith("wig",tdb->type) || startsWith("bigWig",tdb->type) || startsWith("bedGraph",tdb->type)) ; } static void printGroup(char *parent, struct trackDb *tdb, boolean folder, boolean user) // output list elements for a group { char *userString = ""; char *prefix = ""; -char *viewFunc = "show all"; +char *viewFunc = NULL; if (user) { - //prefix = "coll_"; if (tdb->parent && tdb->subtracks) { viewFunc = trackDbSetting(tdb, "viewFunc"); - if (viewFunc == NULL) - viewFunc = "show all"; - userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}'viewType='track'viewType='view' class='folder'"; + userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' viewType='view' class='folder'"; } else if (tdb->subtracks) userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' viewType='track' class='folder'"; else userString = "data-jstree='{\\\"icon\\\":\\\"../images/invisible16.png\\\"}' viewType='track'"; } else { - //prefix = "coll_"; if (tdb->parent && tdb->subtracks) userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}'viewType='track'class='nodrop' viewType='view'"; else if (tdb->subtracks) userString = "data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}'viewType='track'class='nodrop' viewType='track'"; else userString = "data-jstree='{\\\"icon\\\":\\\"../images/invisible16.png\\\"}'class='nodrop' viewType='track'"; } //userString = "viewType='track data-jstree='{'icon':'images/folderC.png'}''"; #define IMAKECOLOR_32(r,g,b) ( ((unsigned int)b<<0) | ((unsigned int)g << 8) | ((unsigned int)r << 16)) -jsInlineF("
  • %s", tdb->shortLabel, tdb->longLabel,IMAKECOLOR_32(tdb->colorR,tdb->colorG,tdb->colorB), viewFunc, hStringFromTv(tdb->visibility), prefix, trackHubSkipHubName(tdb->track), userString, tdb->shortLabel ); +char buffer[1024]; +char *viewFuncString = ""; +if (viewFunc != NULL) + { + safef(buffer, sizeof buffer, "viewFunc='%s' ", viewFunc); + viewFuncString = buffer; + } + +jsInlineF("
  • %s", tdb->shortLabel, tdb->longLabel,IMAKECOLOR_32(tdb->colorR,tdb->colorG,tdb->colorB), viewFuncString, hStringFromTv(tdb->visibility), prefix, trackHubSkipHubName(tdb->track), userString, tdb->shortLabel ); jsInlineF(" (%s)", tdb->longLabel); if (tdb->subtracks) { struct trackDb *subTdb; jsInlineF(""); } jsInlineF("
    • "); } static void outHubHeader(FILE *f, char *db) // output a track hub header { fprintf(f,"hub hub1\n\ shortLabel User Composite\n\ longLabel User Composite\n\ useOneFile on\n\ email genome-www@soe.ucsc.edu\n\n"); fprintf(f,"genome %s\n\n", db); } static char *getHubName(struct cart *cart, char *db) // get the name of the hub to use for user collections { 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); fclose(f); cartSetString(cart, "hubUrl", hubName); cartSetString(cart, hgHubConnectRemakeTrackHub, hubName); } return hubName; } static bool subtrackEnabledInTdb(struct trackDb *subTdb) /* Return TRUE unless the subtrack was declared with "subTrack ... off". */ { bool enabled = TRUE; char *words[2]; char *setting; if ((setting = trackDbLocalSetting(subTdb, "parent")) != NULL) { if (chopLine(cloneString(setting), words) >= 2) if (sameString(words[1], "off")) enabled = FALSE; } else return subTdb->visibility != tvHide; return enabled; } static bool isSubtrackVisible(struct cart *cart, struct trackDb *tdb) /* Has this subtrack not been deselected in hgTrackUi or declared with * * "subTrack ... off"? -- assumes composite track is visible. */ { boolean overrideComposite = (NULL != cartOptionalString(cart, tdb->track)); bool enabledInTdb = subtrackEnabledInTdb(tdb); char option[1024]; safef(option, sizeof(option), "%s_sel", tdb->track); boolean enabled = cartUsualBoolean(cart, option, enabledInTdb); if (overrideComposite) enabled = TRUE; return enabled; } static bool isParentVisible(struct cart *cart, struct trackDb *tdb) // Are this track's parents visible? { if (tdb->parent == NULL) return TRUE; if (!isParentVisible(cart, tdb->parent)) return FALSE; char *cartVis = cartOptionalString(cart, tdb->parent->track); boolean vis; if (cartVis != NULL) vis = differentString(cartVis, "hide"); else if (tdbIsSuperTrack(tdb->parent)) vis = tdb->parent->isShow; else vis = tdb->parent->visibility != tvHide; return vis; } static void checkForVisible(struct cart *cart, struct trackDbRef **list, struct trackDb *tdb) /* Walk the trackDb hierarchy looking for visible leaf tracks. */ { struct trackDb *subTdb; char buffer[4096]; if (tdb->subtracks) { for(subTdb = tdb->subtracks; subTdb; subTdb = subTdb->next) checkForVisible(cart, list, subTdb); } else { if (isParentVisible(cart, tdb) && isSubtrackVisible(cart, tdb)) { struct trackDbRef *tdbRef; AllocVar(tdbRef); tdbRef->tdb = tdb; slAddHead(list, tdbRef); safef(buffer, sizeof buffer, "%s_imgOrd", tdb->track); tdbRef->order = cartUsualInt(cart, buffer, 0); } } } static int tdbRefCompare (const void *va, const void *vb) // Compare to sort on imgTrack->order. { const struct trackDbRef *a = *((struct trackDbRef **)va); const struct trackDbRef *b = *((struct trackDbRef **)vb); return (a->order - b->order); } static void addVisibleTracks(struct cart *cart, struct trackDb *trackList) // add the visible tracks table rows. { struct trackDb *tdb; struct trackDbRef *tdbRefList = NULL, *tdbRef; //checkForVisible(fullTrackList); for(tdb = trackList; tdb; tdb = tdb->next) { checkForVisible(cart, &tdbRefList, tdb); } slSort(&tdbRefList, tdbRefCompare); jsInlineF(""); } static void doTable(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList) // output the tree table { char *hubName = hubNameFromUrl(getHubName(cart, db)); struct grp *curGroup; for(curGroup = groupList; curGroup; curGroup = curGroup->next) { if ((hubName != NULL) && sameString(curGroup->name, hubName)) break; } if (curGroup != NULL) { - // print out all the tracks in this group + // print out all the tracks in all the collections struct trackDb *tdb; jsInlineF("$('#currentCollection').append(\""); for(tdb = trackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { jsInlineF("
    ", trackHubSkipHubName(tdb->track), tdb->shortLabel); jsInlineF(""); jsInlineF("
    "); continue; } } jsInlineF("\");\n"); - // print out all the tracks in this group + // print out all the collections jsInlineF("$('#collectionList').append(\""); for(tdb = trackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { jsInlineF("
  • %s
    • ", trackHubSkipHubName(tdb->track),trackHubSkipHubName(tdb->track), tdb->shortLabel); //printGroup("collections", tdb, TRUE, TRUE); } } jsInlineF("\");\n"); } jsInlineF("$('#tracks').append(\""); addVisibleTracks(cart, trackList); for(curGroup = groupList; curGroup; curGroup = curGroup->next) { if ((hubName != NULL) && sameString(curGroup->name, hubName)) continue; jsInlineF(""); } jsInlineF("\");\n"); jsInlineF("hgCollection.init();\n"); } static void onclickJumpToTop(char *id) /* CSP-safe click handler arrows that cause scroll to top */ { jsOnEventById("click", id, "$('html,body').scrollTop(0);"); } static void printHelp() // print out the help page { puts( "\n" "
    \n" "
    Help
    \n" "
    \n" ); #define DATA_INFO_JUMP_ARROW_ID "hgGtexDataInfo_jumpArrow" printf( " \n", DATA_INFO_JUMP_ARROW_ID ); onclickJumpToTop(DATA_INFO_JUMP_ARROW_ID); puts( "
    \n" "
    \n" ); puts( "
    \n" "
    \n"); puts("
    "); puts("
    "); webIncludeHelpFileSubst("hgCollectionHelp", NULL, FALSE); puts("
    "); puts("
    "); puts( "
    \n" "
    \n"); } static void doMainPage(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList) /* Print out initial HTML of control page. */ { webStartGbNoBanner(cart, db, "Collections"); webIncludeResourceFile("gb.css"); webIncludeResourceFile("spectrum.min.css"); webIncludeResourceFile("hgGtexTrackSettings.css"); webIncludeFile("inc/hgCollection.html"); printHelp(); doTable(cart, db, groupList, trackList); puts(""); puts(""); //puts(""); puts(""); puts("\n"); jsIncludeFile("utils.js", NULL); jsIncludeFile("ajax.js", NULL); jsIncludeFile("spectrum.min.js", NULL); jsIncludeFile("hgCollection.js", NULL); webEndGb(); } static char *getSqlBigWig(struct sqlConnection *conn, char *db, struct trackDb *tdb) // figure out the bigWig for native tables { char buffer[4096]; safef(buffer, sizeof buffer, "NOSQLINJ select fileName from %s", tdb->table); return sqlQuickString(conn, buffer); } static void outTdb(struct sqlConnection *conn, char *db, FILE *f, char *name, struct trackDb *tdb, char *parent, char *visibility, unsigned int color, struct track *track, struct hash *nameHash, struct hash *collectionNameHash, int numTabs, int priority) // out the trackDb for one track { char *dataUrl = NULL; char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); char *tabs = "\t"; if (numTabs == 2) tabs = "\t\t"; if (bigDataUrl == NULL) { if (startsWith("bigWig", tdb->type)) dataUrl = getSqlBigWig(conn, db, tdb); } + +char *tdbType = trackDbSetting(tdb, "tdbType"); +if (tdbType != NULL) + hashReplace(tdb->settingsHash, "type", tdbType); + struct hashCookie cookie = hashFirst(tdb->settingsHash); struct hashEl *hel; fprintf(f, "%strack %s\n",tabs, makeUnique(collectionNameHash, name)); fprintf(f, "%sshortLabel %s\n",tabs, track->shortLabel); fprintf(f, "%slongLabel %s\n",tabs, track->longLabel); while ((hel = hashNext(&cookie)) != NULL) { if (differentString(hel->name, "parent") && differentString(hel->name, "polished")&& differentString(hel->name, "shortLabel")&& differentString(hel->name, "longLabel")&& differentString(hel->name, "color")&& differentString(hel->name, "visibility")&& differentString(hel->name, "track")&& differentString(hel->name, "trackNames")&& differentString(hel->name, "superTrack")&& differentString(hel->name, "priority")&& differentString(hel->name, "group")) fprintf(f, "%s%s %s\n", tabs,hel->name, (char *)hel->val); } if (bigDataUrl == NULL) { if (dataUrl != NULL) fprintf(f, "%sbigDataUrl %s\n", tabs,dataUrl); } fprintf(f, "%sparent %s\n",tabs,parent); fprintf(f, "%scolor %d,%d,%d\n", tabs,(color >> 16) & 0xff,(color >> 8) & 0xff,color & 0xff); fprintf(f, "%svisibility %s\n",tabs,visibility); fprintf(f, "%spriority %d\n",tabs,priority); fprintf(f, "\n"); } static void outComposite(FILE *f, struct track *collection) // output a composite header for user composite { char *parent = collection->name; char *shortLabel = collection->shortLabel; char *longLabel = collection->longLabel; fprintf(f,"track %s\n\ shortLabel %s\n\ compositeTrack on\n\ autoScale on\n\ aggregate none\n\ longLabel %s\n\ %s on\n\ color %ld,%ld,%ld \n\ type wig \n\ visibility full\n\n", parent, shortLabel, longLabel, CUSTOM_COMPOSITE_SETTING, 0xff& (collection->color >> 16),0xff& (collection->color >> 8),0xff& (collection->color)); } -static char *skipColl(char *str) -{ -if (startsWith("coll_", str)) - return &str[5]; -return str; -} - -static int outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash, int priority) +static int outView(FILE *f, struct sqlConnection *conn, char *db, struct track *view, char *parent, struct hash *nameHash, struct hash *collectionNameHash, int priority, char *hubName) // output a view to a trackhub { fprintf(f,"\ttrack %s\n\ \tshortLabel %s\n\ \tlongLabel %s\n\ \tview %s \n\ \tcontainer mathWig\n\ \tautoScale on \n\ \tparent %s \n\ \tcolor %ld,%ld,%ld \n\ \tpriority %d\n\ \tviewFunc %s \n\ \tvisibility %s\n", view->name, view->shortLabel, view->longLabel, view->name, parent, 0xff& (view->color >> 16),0xff& (view->color >> 8),0xff& (view->color), priority++, view->viewFunc, view->visibility); //fprintf(f,"\tequation +\n"); fprintf(f, "\n"); //int useColor = 0; struct track *track = view->trackList; for(; track; track = track->next) { - struct trackDb *tdb = hashMustFindVal(nameHash, skipColl(track->name)); + struct trackDb *tdb = hashMustFindVal(nameHash, track->name); + if ((tdb->grp == NULL) || differentString(tdb->grp, hubName)) + { + // this is a new track in the collection. We want to make sure + // it gets a different name than the track in trackDb + hashStore(collectionNameHash, tdb->track); + } - outTdb(conn, db, f, skipColl(track->name),tdb, view->name, track->visibility, track->color, track, nameHash, collectionNameHash, 2, priority++); + outTdb(conn, db, f, track->name,tdb, view->name, track->visibility, track->color, track, nameHash, collectionNameHash, 2, priority++); //useColor++; } return priority; } static void updateHub(struct cart *cart, char *db, struct track *collectionList, struct hash *nameHash) // save our state to the track hub { -char *hubName = getHubName(cart, db); +char *filename = getHubName(cart, db); +char *hubName = hubNameFromUrl(filename); + +FILE *f = mustOpen(filename, "w"); +chmod(filename, 0666); -chmod(hubName, 0666); -FILE *f = mustOpen(hubName, "w"); struct hash *collectionNameHash = newHash(6); outHubHeader(f, db); -//int useColor = 0; struct track *collection; struct sqlConnection *conn = hAllocConn(db); for(collection = collectionList; collection; collection = collection->next) { outComposite(f, collection); struct trackDb *tdb; struct track *track; int priority = 1; for (track = collection->trackList; track; track = track->next) { - if (track->trackList != NULL) + if (track->viewFunc != NULL) { - priority = outView(f, conn, db, track, collection->name, nameHash, collectionNameHash, priority); + priority = outView(f, conn, db, track, collection->name, nameHash, collectionNameHash, priority, hubName); } else { tdb = hashMustFindVal(nameHash, track->name); + if ((tdb->grp == NULL) || differentString(tdb->grp, hubName)) + { + // this is a new track in the collection. We want to make sure + // it gets a different name than the track in trackDb + hashStore(collectionNameHash, tdb->track); + } outTdb(conn, db, f, track->name,tdb, collection->name, track->visibility, track->color, track, nameHash, collectionNameHash, 1, priority++); - /* - useColor++; - if (useColor == (sizeof snakePalette2 / sizeof(int))) - useColor = 0; - */ } } } fclose(f); hFreeConn(&conn); } static unsigned long hexStringToLong(char *str) { -/* -char buffer[1024]; - -strcpy(buffer, "0x"); -strcat(buffer, &str[1]); -*/ - return strtol(&str[1], NULL, 16); } struct jsonParseData { struct track **collectionList; struct hash *trackHash; }; static void jsonObjStart(struct jsonElement *ele, char *name, boolean isLast, void *context) { struct jsonParseData *jpd = (struct jsonParseData *)context; struct track **collectionList = jpd->collectionList; struct hash *trackHash = jpd->trackHash; struct track *track; if ((name == NULL) && (ele->type == jsonObject)) { struct hash *objHash = jsonObjectVal(ele, "name"); struct jsonElement *parentEle = hashFindVal(objHash, "id"); char *parentId = jsonStringEscape(parentEle->val.jeString); parentEle = hashFindVal(objHash, "parent"); char *parentName = jsonStringEscape(parentEle->val.jeString); AllocVar(track); if (sameString(parentName, "#")) slAddHead(collectionList, track); else { struct track *parent = hashMustFindVal(trackHash, parentName); slAddTail(&parent->trackList, track); } struct jsonElement *attEle = hashFindVal(objHash, "li_attr"); if (attEle) { struct hash *attrHash = jsonObjectVal(attEle, "name"); struct jsonElement *strEle = (struct jsonElement *)hashMustFindVal(attrHash, "name"); track->name = jsonStringEscape(strEle->val.jeString); hashAdd(trackHash, parentId, track); strEle = (struct jsonElement *)hashMustFindVal(attrHash, "shortlabel"); track->shortLabel = jsonStringEscape(strEle->val.jeString); strEle = (struct jsonElement *)hashMustFindVal(attrHash, "longlabel"); track->longLabel = jsonStringEscape(strEle->val.jeString); strEle = (struct jsonElement *)hashMustFindVal(attrHash, "visibility"); track->visibility = jsonStringEscape(strEle->val.jeString); strEle = (struct jsonElement *)hashMustFindVal(attrHash, "color"); track->color = hexStringToLong(jsonStringEscape(strEle->val.jeString)); strEle = (struct jsonElement *)hashFindVal(attrHash, "viewfunc"); if (strEle) track->viewFunc = jsonStringEscape(strEle->val.jeString); } } } static struct track *parseJsonElements( struct jsonElement *collectionElements) // parse the JSON returned from the ap { struct track *collectionList = NULL; struct hash *trackHash = hashNew(5); struct jsonParseData jpd = {&collectionList, trackHash}; jsonElementRecurse(collectionElements, NULL, FALSE, jsonObjStart, NULL, &jpd); slReverse(&collectionList); return collectionList; } static void doAjax(struct cart *cart, char *db, char *jsonText, struct hash *nameHash) // Save our state { cgiDecodeFull(jsonText, jsonText, strlen(jsonText)); struct jsonElement *collectionElements = jsonParse(jsonText); struct track *collectionList = parseJsonElements(collectionElements); updateHub(cart, db, collectionList, nameHash); } static void buildNameHash(struct hash *nameHash, struct trackDb *list) { if (list == NULL) return; struct trackDb *tdb = list; for(tdb = list; tdb; tdb = tdb->next) { hashAdd(nameHash, trackHubSkipHubName(tdb->track), tdb); buildNameHash(nameHash, tdb->subtracks); } } static struct trackDb *traverseTree(struct trackDb *oldList, struct hash *groupHash) // add acceptable tracks to our tree { struct trackDb *newList = NULL, *tdb, *tdbNext; for(tdb = oldList; tdb ; tdb = tdbNext) { tdbNext = tdb->next; if (tdb->subtracks) { tdb->subtracks = traverseTree(tdb->subtracks, groupHash); if (tdb->subtracks) { hashStore(groupHash, tdb->grp); slAddHead(&newList, tdb); } } else { if (trackCanBeAdded(tdb)) { hashStore(groupHash, tdb->grp); slAddHead(&newList, tdb); } } } slReverse(&newList); return newList; } static void pruneTrackList(struct trackDb **fullTrackList, struct grp **fullGroupList) // drop track types we don't grok yet { struct hash *groupHash = newHash(5); *fullTrackList = traverseTree(*fullTrackList, groupHash); struct grp *newGroupList = NULL, *grp, *nextGrp; for (grp = *fullGroupList; grp; grp = nextGrp) { nextGrp = grp->next; if (hashLookup(groupHash, grp->name)) slAddHead(&newGroupList, grp); } slReverse(&newGroupList); *fullGroupList = newGroupList; } static struct trackDb *addSupers(struct trackDb *trackList) /* Insert supertracks into the hierarchy. */ { struct trackDb *newList = NULL; struct trackDb *tdb, *nextTdb; struct hash *superHash = newHash(5); for(tdb = trackList; tdb; tdb = nextTdb) { nextTdb = tdb->next; if (tdb->parent) { // part of a super track if (hashLookup(superHash, tdb->parent->track) == NULL) { hashStore(superHash, tdb->parent->track); slAddHead(&newList, tdb->parent); } slAddHead(&tdb->parent->subtracks, tdb); } else slAddHead(&newList, tdb); } slReverse(&newList); return newList; } static void outOneTdb(char *db, struct sqlConnection *conn, FILE *f, struct trackDb *tdb, int numTabs) /* Put out a single trackDb entry to our collections hub. */ { char *tabs = ""; if (numTabs == 1) tabs = "\t"; else if (numTabs == 2) tabs = "\t\t"; else if (numTabs == 3) tabs = "\t\t\t"; struct hashEl *hel = hashLookup(tdb->settingsHash, "track"); fprintf(f, "%s%s %s\n", tabs,hel->name, trackHubSkipHubName((char *)hel->val)); char *dataUrl = NULL; char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl == NULL) { if (startsWith("bigWig", tdb->type)) dataUrl = getSqlBigWig(conn, db, tdb); } struct hashCookie cookie = hashFirst(tdb->settingsHash); while ((hel = hashNext(&cookie)) != NULL) { if (sameString("parent", hel->name)) fprintf(f, "%s%s %s\n", tabs,hel->name, trackHubSkipHubName((char *)hel->val)); else if (!(sameString("track", hel->name) || sameString("polished", hel->name) || sameString("group", hel->name))) fprintf(f, "%s%s %s\n", tabs,hel->name, (char *)hel->val); } if (bigDataUrl == NULL) { if (dataUrl != NULL) fprintf(f, "%sbigDataUrl %s\n", tabs,dataUrl); } fprintf(f, "\n"); } static void outTrackDbList(char *db, struct sqlConnection *conn, FILE *f, char *hubName, struct trackDb *list, char *collectionName, struct trackDb *newTdb, int numTabs) /* Put a list of trackDb entries into a collection, adding a new track to the collection. */ { if (list == NULL) return; struct trackDb *tdb; for(tdb = list; tdb; tdb = tdb->next) { if (tdb->grp != NULL) if ((hubName == NULL) || differentString(hubName, tdb->grp)) continue; outOneTdb(db, conn, f, tdb, numTabs); struct hashEl *hel = hashLookup(tdb->settingsHash, "track"); if ((hel != NULL) && (hel->val != NULL) && sameString((char *)hel->val, collectionName)) outOneTdb(db, conn, f, newTdb, numTabs + 1); outTrackDbList(db, conn, f, hubName, tdb->subtracks, collectionName, newTdb, numTabs + 1); } } static void doAddTrack(struct cart *cart, char *db, struct trackDb *trackList, char *trackName, char *collectionName, struct hash *nameHash) /* Add a track to a collection in a hub. */ { char *fileName = getHubName(cart, db); char *hubName = hubNameFromUrl(fileName); FILE *f = fopen(fileName, "w"); struct trackDb *newTdb = hashMustFindVal(nameHash, trackName); hashReplace(newTdb->settingsHash, "track", makeUnique(nameHash, trackName)); hashReplace(newTdb->settingsHash, "parent", trackHubSkipHubName(collectionName)); outHubHeader(f, db); struct sqlConnection *conn = hAllocConn(db); outTrackDbList(db, conn, f, hubName, trackList, collectionName, newTdb, 0); hFreeConn(&conn); fclose(f); } static void doMiddle(struct cart *cart) /* Set up globals and make web page */ { char *db; char *genome; getDbAndGenome(cart, &db, &genome, oldVars); initGenbankTableNames(db); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); struct trackDb *trackList; struct grp *groupList; cartTrackDbInit(cart, &trackList, &groupList, TRUE); pruneTrackList(&trackList, &groupList); struct trackDb *superList = addSupers(trackList); struct hash *nameHash = newHash(5); buildNameHash(nameHash, superList); char *cmd = cartOptionalString(cart, "cmd"); if (cmd == NULL) { doMainPage(cart, db, groupList, superList); } else if (sameString("addTrack", cmd)) { char *trackName = cgiString("track"); char *collectionName = cgiString("collection"); doAddTrack(cart, db, superList, trackName, collectionName, nameHash); apiOut("{\"serverSays\": \"added %s to collection\"}", NULL); } else if (sameString("newCollection", cmd)) { char *trackName = cgiString("track"); char *collectionName = makeUnique(nameHash, "coll"); char *shortLabel = "New Collection"; char *longLabel = "Description of New Collection"; struct trackDb *tdb; AllocVar(tdb); slAddHead(&superList, tdb); tdb->settingsHash = newHash(5); tdb->type = cloneString("wig"); hashAdd(tdb->settingsHash, "track", collectionName); hashAdd(tdb->settingsHash, "shortLabel", shortLabel); hashAdd(tdb->settingsHash, "longLabel", longLabel); hashAdd(tdb->settingsHash, "autoScale", "on"); hashAdd(tdb->settingsHash, "compositeTrack", "on"); hashAdd(tdb->settingsHash, "aggregate", "none"); hashAdd(tdb->settingsHash, "type", "wig"); hashAdd(tdb->settingsHash, "visibility", "full"); hashAdd(tdb->settingsHash, "color", "0,0,0"); hashAdd(tdb->settingsHash, CUSTOM_COMPOSITE_SETTING, "on"); doAddTrack(cart, db, superList, trackName, collectionName, nameHash); apiOut("{\"serverSays\": \"new %s to collection\"}", NULL); } else if (sameString("saveCollection", cmd)) { char *jsonIn = cgiUsualString("jsonp", NULL); doAjax(cart, db, jsonIn, nameHash); apiOut("{\"serverSays\": \"Collections gaved successfully.\"}", NULL); } } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); cgiSpoof(&argc, argv); boolean isCommandLine = (cgiOptionalString("cgiSpoof") != NULL); if (!isCommandLine) htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ oldVars = hashNew(10); cartEmptyShellNoContent(doMiddle, hUserCookie(), excludeVars, oldVars); if (! isCommandLine) cgiExitTime("hgCollection", enteredMainTime); return 0; }