bf229bca8bf92e11feb9aa64a52a90974fc2f375 braney Wed Sep 27 12:09:42 2017 -0700 clean up C code, add support for supertracks in Available Tracks diff --git src/hg/hgCollection/hgCollection.c src/hg/hgCollection/hgCollection.c index 2b230cb..d0f48b3 100644 --- src/hg/hgCollection/hgCollection.c +++ src/hg/hgCollection/hgCollection.c @@ -9,88 +9,55 @@ #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) +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); @@ -163,31 +130,31 @@ jsInlineF("</li>"); } 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) +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, hubName); fclose(f); @@ -203,176 +170,178 @@ 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) +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; } -bool isParentVisible( struct trackDb *tdb) +static bool isParentVisible(struct cart *cart, struct trackDb *tdb) // Are this track's parents visible? { if (tdb->parent == NULL) return TRUE; -if (!isParentVisible(tdb->parent)) +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; } -void checkForVisible(struct trackDbRef **list, struct trackDb *tdb) +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(list, subTdb); + checkForVisible(cart, list, subTdb); } else { - if (isParentVisible(tdb) && isSubtrackVisible(tdb)) + 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); } } } -int tdbRefCompare (const void *va, const void *vb) +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); } -void addVisibleTracks() +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 = fullTrackList; tdb; tdb = tdb->next) +for(tdb = trackList; tdb; tdb = tdb->next) { - checkForVisible(&tdbRefList, tdb); + checkForVisible(cart, &tdbRefList, tdb); } slSort(&tdbRefList, tdbRefCompare); jsInlineF("<ul>"); jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' name='%s'>%s", "visibile", "Visible Tracks"); jsInlineF("<ul>"); for(tdbRef = tdbRefList; tdbRef; tdbRef = tdbRef->next) printGroup("visible", tdbRef->tdb, FALSE, FALSE); jsInlineF("</ul>"); jsInlineF("</li>"); jsInlineF("</ul>"); } -void doTable() +static void doTable(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList) // output the tree table { -char *hubName = hubNameFromUrl(getHubName(database)); +char *hubName = hubNameFromUrl(getHubName(cart, db)); struct grp *curGroup; -for(curGroup = fullGroupList; curGroup; curGroup = curGroup->next) +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 struct trackDb *tdb; jsInlineF("$('#currentCollection').append(\""); - for(tdb = fullTrackList; tdb; tdb = tdb->next) + for(tdb = trackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { jsInlineF("<div id='%s' shortLabel='%s'>", trackHubSkipHubName(tdb->track), tdb->shortLabel); jsInlineF("<ul>"); printGroup("collections", tdb, TRUE, TRUE); jsInlineF("</ul>"); jsInlineF("</div>"); + printf("ignoring %s\n", tdb->track); + continue; } } jsInlineF("\");\n"); // print out all the tracks in this group jsInlineF("$('#collectionList').append(\""); - for(tdb = fullTrackList; tdb; tdb = tdb->next) + for(tdb = trackList; tdb; tdb = tdb->next) { if (sameString(tdb->grp, hubName)) { jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' id='%s' name='%s'>%s</li>", 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) +addVisibleTracks(cart, trackList); +for(curGroup = groupList; curGroup; curGroup = curGroup->next) { if ((hubName != NULL) && sameString(curGroup->name, hubName)) continue; jsInlineF("<ul>"); jsInlineF("<li data-jstree='{\\\"icon\\\":\\\"../images/folderC.png\\\"}' class='nodrop' name='%s'>%s", curGroup->name, curGroup->label ); struct trackDb *tdb; jsInlineF("<ul>"); - for(tdb = fullTrackList; tdb; tdb = tdb->next) + for(tdb = trackList; tdb; tdb = tdb->next) { if ( sameString(tdb->grp, curGroup->name)) { printGroup(curGroup->name, tdb, FALSE, FALSE); } } jsInlineF("</ul>"); jsInlineF("</li>"); jsInlineF("</ul>"); } jsInlineF("\");\n"); jsInlineF("hgCollection.init();\n"); } @@ -405,82 +374,65 @@ puts( " <div class='row gbTrackDescriptionPanel'>\n" " <div class='gbTrackDescription'>\n"); puts("<div class='dataInfo'>"); puts("</div>"); webIncludeHelpFileSubst("hgCollectionHelp", NULL, FALSE); puts("<div class='dataInfo'>"); puts("</div>"); puts( " </div>\n" " </div>\n"); } -void doMainPage() +static void doMainPage(struct cart *cart, char *db, struct grp *groupList, struct trackDb *trackList) /* Print out initial HTML of control page. */ { -webStartGbNoBanner(cart, database, "Collections"); +webStartGbNoBanner(cart, db, "Collections"); webIncludeResourceFile("gb.css"); webIncludeResourceFile("spectrum.min.css"); webIncludeResourceFile("hgGtexTrackSettings.css"); webIncludeFile("inc/hgCollection.html"); printHelp(); -doTable(); +doTable(cart, db, groupList, trackList); puts("<link rel='stylesheet' href='https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css' />"); puts("<script src='https://cdnjs.cloudflare.com/ajax/libs/jquery/1.12.1/jquery.min.js'></script>"); //puts("<script src=\"//code.jquery.com/jquery-1.12.1.min.js\"></script>"); puts("<script src=\"//code.jquery.com/ui/1.10.3/jquery-ui.min.js\"></script>"); puts("<script src=\"https://cdnjs.cloudflare.com/ajax/libs/jstree/3.3.4/jstree.min.js\"></script>\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) +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); } struct hashCookie cookie = hashFirst(tdb->settingsHash); struct hashEl *hel; @@ -511,35 +463,30 @@ char *shortLabel = collection->shortLabel; char *longLabel = collection->longLabel; fprintf(f,"track %s\n\ shortLabel %s\n\ compositeTrack on\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\ @@ -553,34 +500,34 @@ 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) +static void updateHub(struct cart *cart, char *db, struct track *collectionList, struct hash *nameHash) // save our state to the track hub { -char *hubName = getHubName(db); +char *hubName = getHubName(cart, 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; @@ -595,49 +542,49 @@ 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) +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; }; -void jsonObjStart(struct jsonElement *ele, char *name, +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); @@ -674,38 +621,38 @@ } } 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) +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(db, collectionList, nameHash); +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); } } @@ -748,63 +695,97 @@ *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) +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 doMiddle(struct cart *cart) /* Set up globals and make web page */ { -cart = theCart; -getDbAndGenome(cart, &database, &genome, oldVars); +char *db; +char *genome; +getDbAndGenome(cart, &db, &genome, oldVars); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); -cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); -pruneTrackList(&fullTrackList, &fullGroupList); + +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, fullTrackList); +buildNameHash(nameHash, superList); char *jsonIn = cgiUsualString("jsonp", NULL); fprintf(stderr, "BRANEY %s\n", jsonIn); if (jsonIn != NULL) { - doAjax(database, jsonIn, nameHash); + doAjax(cart, db, jsonIn, nameHash); apiOut("{\"serverSays\": \"Collections saved successfully.\"}", NULL); } else { - doMainPage(); + doMainPage(cart, db, groupList, superList); } } 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; }