f72f493cde054def4770a6726c6231f0a7f7b406 braney Mon Sep 25 13:52:49 2017 -0700 don't put multiWig options (overlay,stacked) on collections diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c index 6201768..2b230cb 100644 --- src/hg/hgCollection/hgCollection.c +++ src/hg/hgCollection/hgCollection.c @@ -1,811 +1,810 @@ /* 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 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. */ char *regionType = NULL; /* genome, ENCODE pilot regions, or specific position range. */ struct grp *fullGroupList = NULL; /* List of all groups. */ struct trackDb *fullTrackList = NULL; /* List of all tracks in database. */ struct pipeline *compressPipeline = (struct pipeline *)NULL; // Null terminated list of CGI Variables we don't want to save permanently: char *excludeVars[] = {"Submit", "submit", "hgva_startQuery", "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; }; char *getString(char **input) // grab a quoted string out of text blob { char *ptr = *input; if (*ptr != '"') errAbort("string must start with \""); ptr++; char *ret = ptr; for(; *ptr != '"'; ptr++) ; *ptr = 0; ptr++; if (*ptr == ',') ptr++; if (startsWith("coll_", ret)) ret = ret + 5; *input = ptr; return ret; } 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)) ; } 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"; 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'"; } 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 ); jsInlineF(" (%s)", tdb->longLabel); if (tdb->subtracks) { struct trackDb *subTdb; jsInlineF(""); } jsInlineF("
    • "); } static void outHubHeader(FILE *f, char *db, char *hubName) // 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(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, hubName); 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; } bool isSubtrackVisible(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; } bool isParentVisible( struct trackDb *tdb) // Are this track's parents visible? { if (tdb->parent == NULL) return TRUE; if (!isParentVisible(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; } void checkForVisible(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(list, subTdb); } else { if (isParentVisible(tdb) && isSubtrackVisible(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); } } } 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); } void addVisibleTracks() // add the visible tracks table rows. { struct trackDb *tdb; struct trackDbRef *tdbRefList = NULL, *tdbRef; //checkForVisible(fullTrackList); for(tdb = fullTrackList; tdb; tdb = tdb->next) { checkForVisible(&tdbRefList, tdb); } slSort(&tdbRefList, tdbRefCompare); jsInlineF(""); } void doTable() // output the tree table { char *hubName = hubNameFromUrl(getHubName(database)); struct grp *curGroup; for(curGroup = fullGroupList; curGroup; curGroup = curGroup->next) { if ((hubName != NULL) && sameString(curGroup->name, hubName)) break; } if (curGroup != NULL) { // print out all the tracks in this group struct trackDb *tdb; jsInlineF("$('#currentCollection').append(\""); for(tdb = fullTrackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { jsInlineF("
    ", trackHubSkipHubName(tdb->track), tdb->shortLabel); jsInlineF(""); jsInlineF("
    "); } } jsInlineF("\");\n"); // print out all the tracks in this group jsInlineF("$('#collectionList').append(\""); for(tdb = fullTrackList; 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("$('#tracks').append(\""); addVisibleTracks(); for(curGroup = fullGroupList; curGroup; curGroup = curGroup->next) { if ((hubName != NULL) && sameString(curGroup->name, hubName)) continue; jsInlineF(""); } jsInlineF("\");\n"); jsInlineF("hgCollection.init();\n"); } static void onclickJumpToTop(char *id) /* CSP-safe click handler arrows that cause scroll to top */ { jsOnEventById("click", id, "$('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"); } void doMainPage() /* Print out initial HTML of control page. */ { webStartGbNoBanner(cart, database, "Collections"); webIncludeResourceFile("gb.css"); webIncludeResourceFile("spectrum.min.css"); webIncludeResourceFile("hgGtexTrackSettings.css"); webIncludeFile("inc/hgCollection.html"); printHelp(); doTable(); 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); } char *getUrl(struct sqlConnection *conn, char *db, struct track *track, struct hash *nameHash) // get the bigDataUrl for a track { struct trackDb *tdb = hashMustFindVal(nameHash, track->name); if (tdb == NULL) errAbort("cannot find trackDb for %s\n", track->name); char *bigDataUrl = trackDbSetting(tdb, "bigDataUrl"); if (bigDataUrl == NULL) { if (startsWith("bigWig", tdb->type)) bigDataUrl = getSqlBigWig(conn, db, tdb); } return bigDataUrl; } 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); } 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\ -aggregate none\n\ autoScale on\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)); } int snakePalette2[] = { 0x1f77b4, 0xaec7e8, 0xff7f0e, 0xffbb78, 0x2ca02c, 0x98df8a, 0xd62728, 0xff9896, 0x9467bd, 0xc5b0d5, 0x8c564b, 0xc49c94, 0xe377c2, 0xf7b6d2, 0x7f7f7f, 0xc7c7c7, 0xbcbd22, 0xdbdb8d, 0x17becf, 0x9edae5 }; 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) // 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)); outTdb(conn, db, f, skipColl(track->name),tdb, view->name, track->visibility, track->color, track, nameHash, collectionNameHash, 2, priority++); //useColor++; } return priority; } void updateHub(char *db, struct track *collectionList, struct hash *nameHash) // save our state to the track hub { char *hubName = getHubName(db); chmod(hubName, 0666); FILE *f = mustOpen(hubName, "w"); struct hash *collectionNameHash = newHash(6); outHubHeader(f, db, hubName); //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) { priority = outView(f, conn, db, track, collection->name, nameHash, collectionNameHash, priority); } else { tdb = hashMustFindVal(nameHash, track->name); 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); } 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; }; 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; } void doAjax(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(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; } void doMiddle(struct cart *theCart) /* Set up globals and make web page */ { cart = theCart; getDbAndGenome(cart, &database, &genome, oldVars); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); pruneTrackList(&fullTrackList, &fullGroupList); struct hash *nameHash = newHash(5); buildNameHash(nameHash, fullTrackList); char *jsonIn = cgiUsualString("jsonp", NULL); fprintf(stderr, "BRANEY %s\n", jsonIn); if (jsonIn != NULL) { doAjax(database, jsonIn, nameHash); apiOut("{\"serverSays\": \"Collections saved successfully.\"}", NULL); } else { doMainPage(); } } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); initGenbankTableNames(database); 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; }