a7ab24571507f19cc40e4ef65800401b43000a0f braney Mon Dec 6 13:16:27 2021 -0800 support itemRgb for bigPsl, remove overload of lf->extra field for USE_ITEM_RGB and replace it with a reasonably named field in lf (useItemRbg) diff --git src/hg/hgTracks/wikiTrack.c src/hg/hgTracks/wikiTrack.c index 0a8aaf9..7cf6437 100644 --- src/hg/hgTracks/wikiTrack.c +++ src/hg/hgTracks/wikiTrack.c @@ -1,260 +1,260 @@ /* wikiTrack - wikiTrack functions */ /* Copyright (C) 2012 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "jksql.h" #include "hgTracks.h" #include "hdb.h" #include "ra.h" #include "itemAttr.h" #include "bedCart.h" #include "wikiLink.h" #include "wikiTrack.h" #include "hgConfig.h" static void wikiTrackMapItem(struct track *tg, struct hvGfx *hvg, void *item, char *itemName, char *mapItemName, int start, int end, int x, int y, int width, int height) /* create a special map box item with different i=hgcClickName and * pop-up statusLine with the item name */ { char *userName; /* already been determined to be enabled by getting here, need to verify * userName vs editors and vs owner */ (void) wikiTrackEnabled(database, &userName); char *hgcClickName = tg->mapItemName(tg, item); char *statusLine = tg->itemName(tg, item); boolean editor = isWikiEditor(userName); struct wikiTrack *wikiItem = NULL; boolean enableHgcClick = FALSE; /* allow hgc click (i.e. delete privs) if the following are true 1. this is the item 0 "add new item" 2. logged into the wiki 3. user is an editor or user is the owner */ if (differentWord("0", hgcClickName)) wikiItem = findWikiItemId(hgcClickName); else enableHgcClick = TRUE; /* item 0 "add new item" must go to hgc */ if (wikiItem) { if (isNotEmpty(userName) && sameWord(userName, wikiItem->owner)) enableHgcClick = TRUE; /* owner has delete privls */ if (editor) enableHgcClick = TRUE; /* editors have delete privls */ } if (enableHgcClick) { mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, hgcClickName, statusLine, NULL, FALSE, NULL ); } else { /* go directly to the wiki description */ char *directUrl = wikiUrl(wikiItem); mapBoxHgcOrHgGene(hvg, start, end, x, y, width, height, tg->track, hgcClickName, statusLine, directUrl, FALSE, NULL); freeMem(directUrl); } } static char *wikiTrackMapItemName(struct track *tg, void *item) /* Return the unique id track item. */ { struct itemAttr *ia; char id[64]; int iid = 0; struct linkedFeatures *lf = item; if (lf->itemAttr != NULL) { ia = lf->itemAttr; iid = (int)(ia->chromStart); } safef(id,ArraySize(id),"%d", iid); return cloneString(id); } static int hexToDecimal(char *hexString) /* return decimal value for hex string (from utils/subChar/subChar.c) */ { int acc = 0; char c; tolowers(hexString); stripChar(hexString, '#'); /* can start with # (as in html) */ while ((c = *hexString++) != 0) { acc <<= 4; if (c >= '0' && c <= '9') acc += c - '0'; else if (c >= 'a' && c <= 'f') acc += c + 10 - 'a'; /* ignoring bad characters else errAbort("Expecting hexadecimal character got %s", hexString); */ } return acc; } static void wikiTrackLoadItems(struct track *tg) /* Load the items from the wikiTrack table */ { struct bed *bed; struct sqlConnection *wikiConn = wikiConnect(); struct sqlResult *sr; char **row; int rowOffset; char where[256]; struct linkedFeatures *lfList = NULL, *lf; int scoreMin = 0; int scoreMax = 99999; safef(where, ArraySize(where), "db='%s'", database); sr = hRangeQuery(wikiConn, tg->table, chromName, winStart, winEnd, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct wikiTrack *item = wikiTrackLoad(row); AllocVar(bed); bed->chrom = cloneString(item->chrom); bed->chromStart = item->chromStart; bed->chromEnd = item->chromEnd; bed->name = cloneString(item->name); bed->score = item->score; safecpy(bed->strand, sizeof(bed->strand), item->strand); bed->thickStart = item->chromStart; bed->thickEnd = item->chromEnd; bed->itemRgb = hexToDecimal(item->color); bed8To12(bed); lf = lfFromBedExtra(bed, scoreMin, scoreMax); - lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->useItemRgb = TRUE; lf->filterColor=bed->itemRgb; /* overload itemAttr fields to be able to pass id to hgc click box */ struct itemAttr *id; AllocVar(id); id->chromStart = item->id; lf->itemAttr = id; slAddHead(&lfList, lf); wikiTrackFree(&item); } sqlFreeResult(&sr); wikiDisconnect(&wikiConn); slSort(&lfList, linkedFeaturesCmp); /* read-only option 2012-06-25 */ if ((! wikiTrackReadOnly()) && wikiTrackEnabled(database, NULL)) { // add special item to allow creation of new entries AllocVar(bed); bed->chrom = chromName; bed->chromStart = winStart; bed->chromEnd = winEnd; bed->name = cloneString("Make new entry"); bed->score = 100; bed->strand[0] = ' '; /* no barbs when strand is unknown */ bed->thickStart = winStart; bed->thickEnd = winEnd; bed->itemRgb = 0xcc0000; bed8To12(bed); lf = lfFromBedExtra(bed, scoreMin, scoreMax); - lf->extra = (void *)USE_ITEM_RGB; /* signal for coloring */ + lf->useItemRgb = TRUE; lf->filterColor=bed->itemRgb; slAddHead(&lfList, lf); } tg->items = lfList; } /* static void wikiTrackLoadItems(struct track *tg) */ struct bed *wikiTrackGetBedRange(char *table, char *chromName, int start, int end) /* fetch wiki track items as simple bed 3 list in given range */ { struct bed *bed, *bedList = NULL; struct sqlConnection *wikiConn = wikiConnect(); struct sqlResult *sr; char **row; char where[256]; int rowOffset; safef(where, ArraySize(where), "db='%s'", database); sr = hRangeQuery(wikiConn, table, chromName, start, end, where, &rowOffset); while ((row = sqlNextRow(sr)) != NULL) { struct wikiTrack *item = wikiTrackLoad(row); AllocVar(bed); bed->chrom = cloneString(item->chrom); bed->chromStart = item->chromStart; bed->chromEnd = item->chromEnd; slAddHead(&bedList, bed); wikiTrackFree(&item); } sqlFreeResult(&sr); wikiDisconnect(&wikiConn); return bedList; } void addWikiTrack(struct track **pGroupList) /* Add wiki track and append to group list. */ { if (wikiTrackEnabled(database, NULL)) { struct track *tg = trackNew(); static char longLabel[80]; struct trackDb *tdb; struct sqlConnection *wikiConn = wikiConnect(); if (! sqlTableExists(wikiConn,WIKI_TRACK_TABLE)) errAbort("loadWikiTrack configuration error, set wikiTrack.URL in hg.conf"); linkedFeaturesMethods(tg); AllocVar(tdb); tg->track = WIKI_TRACK_TABLE; tg->table = WIKI_TRACK_TABLE; tg->canPack = TRUE; tg->visibility = tvHide; tg->hasUi = TRUE; tg->shortLabel = cloneString(WIKI_TRACK_LABEL); safef(longLabel, sizeof(longLabel), WIKI_TRACK_LONGLABEL); tg->longLabel = longLabel; tg->loadItems = wikiTrackLoadItems; tg->itemName = linkedFeaturesName; tg->mapItemName = wikiTrackMapItemName; tg->mapItem = wikiTrackMapItem; tg->priority = WIKI_TRACK_PRIORITY; tg->defaultPriority = WIKI_TRACK_PRIORITY; tg->groupName = cloneString("map"); tg->defaultGroupName = cloneString("map"); tg->exonArrows = TRUE; tg->nextItemButtonable = TRUE; tdb->track = cloneString(tg->track); tdb->canPack = tg->canPack; tdb->table = cloneString(tg->table); tdb->shortLabel = cloneString(tg->shortLabel); tdb->longLabel = cloneString(tg->longLabel); tdb->useScore = 1; tdb->grp = cloneString(tg->groupName); tdb->priority = tg->priority; trackDbPolish(tdb); tg->tdb = tdb; slAddHead(pGroupList, tg); wikiDisconnect(&wikiConn); } } void wikiTrackMethods(struct track *tg) /* establish loadItems function for wiki track */ { tg->loadItems = wikiTrackLoadItems; }