3846f517009c43abc65d227a4695645c9b5f3e8a braney Fri Feb 15 18:31:21 2013 -0800 changes necessary to support assembly hubs (#8072) diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c index 2e083ba..1bb8925 100644 --- src/hg/hgTracks/hgTracks.c +++ src/hg/hgTracks/hgTracks.c @@ -1752,64 +1752,64 @@ { hvGfxTextCentered(hvg, insideX, y, insideWidth, titleHeight,MG_BLACK, font, baseTitle); *rulerClickHeight += titleHeight; y += titleHeight; } if (baseShowPos||baseShowAsm) { char txt[256]; char numBuf[SMALLBUF]; char *freezeName = NULL; freezeName = hFreezeFromDb(database); sprintLongWithCommas(numBuf, winEnd-winStart); if (freezeName == NULL) freezeName = "Unknown"; if (baseShowPos&&baseShowAsm) - safef(txt,sizeof(txt),"%s %s %s (%s bp)",organism, + safef(txt,sizeof(txt),"%s %s %s (%s bp)",trackHubRemoveHubName(organism), freezeName, addCommasToPos(database, position), numBuf); else if (baseShowPos) safef(txt,sizeof(txt),"%s (%s bp)",addCommasToPos(database, position),numBuf); else - safef(txt,sizeof(txt),"%s %s",organism,freezeName); + safef(txt,sizeof(txt),"%s %s",trackHubRemoveHubName(organism),freezeName); hvGfxTextCentered(hvg, insideX, y, insideWidth, showPosHeight,MG_BLACK, font, txt); *rulerClickHeight += showPosHeight; freez(&freezeName); y += showPosHeight; } if (baseShowScaleBar) { char scaleText[32]; int numBases = winEnd-winStart; int scaleBases = computeScaleBar(numBases, scaleText, sizeof(scaleText)); int scalePixels = (int)((double)insideWidth*scaleBases/numBases); int scaleBarX = insideX + (int)(((double)insideWidth-scalePixels)/2); int scaleBarEndX = scaleBarX + scalePixels; int scaleBarY = y + 0.5 * scaleBarTotalHeight; *rulerClickHeight += scaleBarTotalHeight; hvGfxTextRight(hvg, insideX, y + scaleBarPad, (scaleBarX-2)-insideX, scaleBarHeight, MG_BLACK, font, scaleText); hvGfxLine(hvg, scaleBarX, scaleBarY, scaleBarEndX, scaleBarY, MG_BLACK); hvGfxLine(hvg, scaleBarX, y+scaleBarPad, scaleBarX, y+scaleBarTotalHeight-scaleBarPad, MG_BLACK); hvGfxLine(hvg, scaleBarEndX, y+scaleBarPad, scaleBarEndX, y+scaleBarTotalHeight-scaleBarPad, MG_BLACK); if(cartUsualBoolean(cart, BASE_SHOWASM_SCALEBAR, TRUE)) { int fHeight = vgGetFontPixelHeight(hvg->vg, font); hvGfxText(hvg, scaleBarEndX + 10, y + (scaleBarTotalHeight - fHeight)/2 + ((font == mgSmallFont()) ? 1 : 0), - MG_BLACK, font, database); + MG_BLACK, font, trackHubRemoveHubName(database)); } y += scaleBarTotalHeight; } if (baseShowRuler) { hvGfxDrawRulerBumpText(hvg, insideX, y, rulerHeight, insideWidth, MG_BLACK, font, relNumOff, winBaseCount, 0, 1); } *newWinWidth = makeRulerZoomBoxes(hvg, cart,winStart,winEnd,insideWidth,seqBaseCount, rulerClickY,*rulerClickHeight); if (zoomedToBaseLevel || rulerCds) { Color baseColor = MG_BLACK; int start, end, chromSize; @@ -3405,31 +3405,31 @@ trackLayoutSetPicWidth(&tl, words[2]); } } } for (ct = ctList; ct != NULL; ct = ct->next) { hasCustomTracks = TRUE; tg = newCustomTrack(ct); slAddHead(pTrackList, tg); } } void loadTrackHubs(struct track **pTrackList, struct trackHub **pHubList) /* Load up stuff from data hubs and append to lists. */ { -struct hubConnectStatus *hub, *hubList = hubConnectStatusListFromCart(cart); +struct hubConnectStatus *hub, *hubList = hubConnectGetHubs(); for (hub = hubList; hub != NULL; hub = hub->next) { if (isEmpty(hub->errorMessage)) { /* error catching in so it won't just abort */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { struct trackDb *tdbList = hubAddTracks(hub, database, pHubList); addTdbListToTrackList(tdbList, NULL, pTrackList); // we're going to free the hubConnectStatus list hub->trackHub = NULL; } errCatchEnd(errCatch); @@ -4519,31 +4519,31 @@ } else { if (sameString(organism, "Archaea")) { hPrintf("%s %s on Archaeon %s Assembly", organization, browserName, freezeName); } else { if (stringIn(database, freezeName)) hPrintf("%s %s on %s %s Assembly", organization, browserName, organism, freezeName); else hPrintf("%s %s on %s %s Assembly (%s)", - organization, browserName, organism, freezeName, database); + organization, browserName, trackHubRemoveHubName(organism), freezeName, trackHubRemoveHubName(database)); } } hPrintf("</B></span><BR>\n"); /* This is a clear submit button that browsers will use by default when enter is pressed in position box. */ hPrintf("<INPUT TYPE=IMAGE BORDER=0 NAME=\"hgt.dummyEnterButton\" src=\"../images/DOT.gif\">"); /* Put up scroll and zoom controls. */ #ifndef USE_NAVIGATION_LINKS hWrites("move "); hButtonWithOnClick("hgt.left3", "<<<", "move 95% to the left", "return imageV2.navigateButtonClick(this);"); hButtonWithOnClick("hgt.left2", " <<", "move 47.5% to the left", "return imageV2.navigateButtonClick(this);"); hButtonWithOnClick("hgt.left1", " < ", "move 10% to the left", "return imageV2.navigateButtonClick(this);"); @@ -4611,33 +4611,36 @@ if (containsStringNoCase(database, "zoo")) { hPuts("Organism "); printAssemblyListHtmlExtra(database, javascript); } sprintf(buf, "%s:%d-%d", chromName, winStart+1, winEnd); position = cloneString(buf); hPrintf("<span class='positionDisplay' id='positionDisplay' title='click to copy position to input box'>%s</span>", addCommasToPos(database, position)); hPrintf("<input type='hidden' name='position' id='position' value='%s'>\n", buf); sprintLongWithCommas(buf, winEnd - winStart); hPrintf(" <span id='size'>%s</span> bp. ", buf); hPrintf("<input class='positionInput' type='text' name='hgt.positionInput' id='positionInput' size='60'>\n"); hWrites(" "); hButton("hgt.jump", "go"); + if (!trackHubDatabase(database)) + { jsonObjectAdd(jsonForClient, "assemblySupportsGeneSuggest", newJsonBoolean(assemblySupportsGeneSuggest(database))); if(assemblySupportsGeneSuggest(database)) hPrintf("<input type='hidden' name='hgt.suggestTrack' id='suggestTrack' value='%s'>\n", assemblyGeneSuggestTrack(database)); + } if (survey && differentWord(survey, "off")) hPrintf(" <span style='background-color:yellow;'>" "<A HREF='%s' TARGET=_BLANK><EM><B>%s</EM></B></A></span>\n", survey, surveyLabel ? surveyLabel : "Take survey"); hPutc('\n'); } } /* Make chromsome ideogram gif and map. */ makeChromIdeoImage(&trackList, psOutput, ideoTn); #ifdef USE_NAVIGATION_LINKS hPrintf("<TABLE BORDER=0 CELLPADDING=0 width='%d'><tr style='font-size:small;'>\n", tl.picWidth);//min(tl.picWidth, 800)); hPrintf("<td width='40' align='left'><a href='?hgt.left3=1' " @@ -5468,31 +5471,31 @@ hFreeConn(&conn); } void chromInfoPage() /* Show list of chromosomes (or scaffolds, etc) on which this db is based. */ { char *position = cartUsualString(cart, "position", hDefaultPos(database)); char *defaultChrom = hDefaultChrom(database); char *freeze = hFreezeFromDb(database); struct dyString *title = dyStringNew(512); if (stringIn(database, freeze)) dyStringPrintf(title, "%s %s Browser Sequences", hOrganism(database), freeze); else dyStringPrintf(title, "%s %s (%s) Browser Sequences", - hOrganism(database), freeze, database); + trackHubRemoveHubName(hOrganism(database)), freeze, trackHubRemoveHubName(database)); webStartWrapperDetailedNoArgs(cart, database, "", title->string, FALSE, FALSE, FALSE, FALSE); printf("<FORM ACTION=\"%s\" NAME=\"posForm\" METHOD=GET>\n", hgTracksName()); cartSaveSession(cart); puts("Enter a position, or click on a sequence name to view the entire " "sequence in the genome browser.<P>"); puts("position "); hTextVar("position", addCommasToPos(database, position), 30); cgiMakeButton("Submit", "submit"); puts("<P>"); hTableStart(); cgiSimpleTableRowStart(); cgiSimpleTableFieldStart(); puts("Sequence name "); @@ -5522,55 +5525,62 @@ /* Reset vars except for position and database. */ { static char *except[] = {"db", "position", NULL}; char *cookieName = hUserCookie(); int sessionId = cgiUsualInt(cartSessionVarName(), 0); char *hguidString = findCookieData(cookieName); int userId = (hguidString == NULL ? 0 : atoi(hguidString)); struct cart *oldCart = cartNew(userId, sessionId, NULL, NULL); cartRemoveExcept(oldCart, except); cartCheckout(&oldCart); cgiVarExcludeExcept(except); } static void addDataHubs(struct cart *cart) { -hubCheckForNew(database, cart); +hubCheckForNew(cart); cartSetString(cart, hgHubConnectRemakeTrackHub, "on"); } void doMiddle(struct cart *theCart) /* Print the body of an html file. */ { hgBotDelay(); char *debugTmp = NULL; /* Uncomment this to see parameters for debugging. */ /* struct dyString *state = NULL; */ /* Initialize layout and database. */ cart = theCart; measureTiming = hPrintStatus() && isNotEmpty(cartOptionalString(cart, "measureTiming")); if (measureTiming) measureTime("Get cart of %d for user:%u session:%u", theCart->hash->elCount, theCart->userId, theCart->sessionId); /* #if 1 this to see parameters for debugging. */ /* Be careful though, it breaks if custom track * is more than 4k */ #if 0 state = cgiUrlString(); printf("State: %s\n", state->string); #endif + +/* check for new data/assembly hub */ +if (cartVarExists(cart, hgHubDataText)) + { + addDataHubs(cart); + } + getDbAndGenome(cart, &database, &organism, oldVars); protDbName = hPdbFromGdb(database); debugTmp = cartUsualString(cart, "hgDebug", "off"); if(sameString(debugTmp, "on")) hgDebug = TRUE; else hgDebug = FALSE; if (hIsGisaidServer()) { validateGisaidUser(cart); } int timeout = cartUsualInt(cart, "udcTimeout", 300); @@ -5618,36 +5628,30 @@ #endif///def LOWELAB webIncludeResourceFile("jquery-ui.css"); if (!searching) // NOT doing search { webIncludeResourceFile("jquery.contextmenu.css"); jsIncludeFile("jquery.contextmenu.js", NULL); webIncludeResourceFile("ui.dropdownchecklist.css"); jsIncludeFile("ui.dropdownchecklist.js", NULL); jsIncludeFile("ddcl.js", NULL); } hPrintf("<div id='hgTrackUiDialog' style='display: none'></div>\n"); } -/* check for new data hub */ -if (cartVarExists(cart, hgHubDataText)) - { - addDataHubs(cart); - } - if (cartVarExists(cart, "chromInfoPage")) { cartRemove(cart, "chromInfoPage"); chromInfoPage(); } else if (differentString(cartUsualString(cart, TRACK_SEARCH,"0"),"0")) { doSearchTracks(groupList); } else if (sameWord(configPageCall, "configure") || sameWord(configPageCall, "configure tracks and display")) { cartRemove(cart, "hgTracksConfigPage"); configPage(); }