5440b4ccf5796778b6a65186bf83c17970f00d7a markd Sun Aug 16 18:43:46 2026 -0700 Support PDF output in hgRenderTracks via hgt.psOutput. refs #38118 hgRenderTracks had PDF output wired up behind a compile-time PDF_OUTPUT define that was set to 0, so it could only be reached by editing and rebuilding. Select it at runtime with hgt.psOutput=on instead, which is the same variable the hgTracks View->PDF menu item already uses. PNG remains the default. Also return from handlePostscript after doTrackForm when trackImgOnly is set. In that case makeActiveImage has already converted the eps, written the PDF to stdout and unlinked the eps, so the convertEpsToPdf that follows aborted on the missing file. The client never saw it because the PDF was already flushed and hPrintDisable swallowed the error page, but every request logged "Couldn't open ... .eps" to the apache error log. Document the new parameter in the hgRenderTracks section of customTrackText.html and in the hgRenderTracks tip in allTipsRaw.html. diff --git src/hg/hgTracks/renderMain.c src/hg/hgTracks/renderMain.c index acc3c2766fd..71ef4e7b212 100644 --- src/hg/hgTracks/renderMain.c +++ src/hg/hgTracks/renderMain.c @@ -1,191 +1,190 @@ /* renderMain - execute enough of browser to render list of tracks without touching cart or * writing form. . */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "htmshell.h" #include "options.h" #include "errAbort.h" #include "portable.h" #include "cheapcgi.h" #include "ra.h" #include "hdb.h" #include "net.h" #include "hgTracks.h" #include "imageV2.h" #include "botDelay.h" static void usage() /* Print out usage and exit - just temporary. */ { errAbort( "hgRenderTracks - execute enough of browser to render a list of tracks\n" "usage:\n" " hgTrackRender track.ra cart.ra output.ps\n" "where track.ra is a trackDb.ra entry flattened out to include stuff inherited from parent\n" "and cart.ra is a file with the cart settings. Both .ra files should just have a single stanza\n" ); } static struct optionSpec options[] = { {NULL, 0}, }; long enteredMainTime = 0; struct trackDb *hTrackDbForTrackAndAncestors(char *db, char *track); /* Load trackDb object for a track. If need be grab its ancestors too. * This does not load children. hTrackDbForTrack will handle children, and * is actually faster if being called on lots of tracks. This function * though is faster on one or two tracks. */ static void hashIntoHash(struct hash *newStuff, struct hash *hash) /* Add newStuff into hash. */ { struct hashCookie cookie = hashFirst(newStuff); struct hashEl *hel; while ((hel = hashNext(&cookie)) != NULL) hashAdd(hash, hel->name, hel->val); } struct track *trackFromSettingsHash(struct hash *settings) /* Wrap a trackDb, and then a track around settings, and return track. */ { char *trackName = hashMustFindVal(settings, "track"); struct trackDb *tdb = hTrackDbForTrackAndAncestors(database, trackName); hashIntoHash(settings, tdb->settingsHash); trackDbFieldsFromSettings(tdb); trackDbAddTableField(tdb); return trackFromTrackDb(tdb); } static void hgTrackRenderFromCommandLine(char *trackFile, char *cartFile, char *outFile) /* Generate tracks from trackFile and cart from cartFile, both in .ra format. Then * call makeActiveImage, the heart of the genome browser.*/ { struct track *track, *trackList = NULL; /* Load in cart file into a single hash and then wrap a cart around it. * We need to set cart before we can make tracks. */ struct hash *cartHash = raReadSingle(cartFile); cart = cartFromHash(cartHash); database = hashMustFindVal(cartHash, "db"); position = cloneString(hashMustFindVal(cartHash, "position")); if (!hgParseChromRange(NULL, position, &chromName, &winStart, &winEnd)) errAbort("position not in chrom:start-end format"); /* Initialize layout. */ initTl(); setLayoutGlobals(); /* Make list of tracks out of track file. */ struct lineFile *lf = lineFileOpen(trackFile, TRUE); struct hash *trackRa; while ((trackRa = raNextRecord(lf)) != NULL) { track = trackFromSettingsHash(trackRa); slAddHead(&trackList, track); } slReverse(&trackList); lineFileClose(&lf); verboseTime(2, "Before load %d tracks", slCount(trackList)); /* Prepare track list for drawing. */ for (track = trackList; track != NULL; track = track->next) { track->loadItems(track); } verboseTime(2, "After load"); /* Initialize global image box. */ int sideSliceWidth = 0; // Just being explicit if (withLeftLabels) sideSliceWidth = (insideX - gfxBorder*3) + 2; theImgBox = imgBoxStart(database,chromName,winStart,winEnd,(!revCmplDisp),sideSliceWidth,tl.picWidth); makeActiveImage(trackList, NULL); verboseTime(2,"After makeActiveImage"); } boolean issueBotWarning; int main(int argc, char *argv[]) { cgiSpoof(&argc, argv); if(argc == 1) { enteredMainTime = clock1000(); issueBotWarning = earlyBotCheck(enteredMainTime, "hgRenderTracks", delayFraction, 0, 0, "html"); // CGI call // htmlPushEarlyHandlers(); XXXX do I need to do this? hPrintDisable(); oldVars = hashNew(10); struct cart *cart = cartForSession(hUserCookie(), excludeVars, oldVars); // setup approriate CGI variables which tell hgTracks code what to do. cartSetBoolean(cart, "hgt.trackImgOnly", TRUE); if(cartVarExists(cart, "jsonp")) { // experimental code to support remote rendering via a jsonp callback // e.g.: /cgi-bin/hgRenderTracks?track=bamMMS9MbutiPygmy&track=...&jsonp=remoteTrackCallback&postion=...&pix=800 cartSetString(cart, "hgt.contentType", "jsonp"); cartSetString(cart, "hgt.trackNameFilter", cartString(cart, "track")); cartSetString(cart, cartString(cart, "track"), cartUsualString(cart, "vis", "pack")); } else { // remote rendering of hgTracks PNG image based on contents of a session; caller may pass in a subset of // hgTracks parameters: e.g. db, hgsid, pix, position and tracks with explicit visibilities (e.g. knownGene=pack). -#define PDF_OUTPUT 0 -#if PDF_OUTPUT + // hgt.psOutput=on asks for PDF instead of PNG. Same variable the hgTracks + // View->PDF menu item uses, so callers do not have to learn a second name. + if (cartUsualBoolean(cart, "hgt.psOutput", FALSE)) cartSetString(cart, "hgt.contentType", "pdf"); - cartSetString(cart, "hgt.psOutput", "on"); -#else + else cartSetString(cart, "hgt.contentType", "png"); -#endif cartSetBoolean(cart, "hgt.imageV1", TRUE); if(!cartVarExists(cart, "hgt.internal")) { if(!cartVarExists(cart, "hgt.baseShowAsm")) cartSetBoolean(cart, "hgt.baseShowAsm", TRUE); if(!cartVarExists(cart, "hgt.baseShowPos")) cartSetBoolean(cart, "hgt.baseShowPos", TRUE); } // XXXX support track filtering? - if(cartVarExists(cart, "hgt.trackNameFilter")) } doMiddle(cart); cgiExitTime("hgRenderTracks", enteredMainTime); } else { // XXXX remove this code ... well, maybe not - this still might be useful for a stand-alone remote renderer. // command line call /* Set up some timing since we're trying to optimize things very often. */ long enteredMainTime = clock1000(); verboseTimeInit(); /* Push very early error handling - this is just * for the benefit of the cgiVarExists, which * somehow can't be moved effectively into doMiddle. */ // htmlPushEarlyHandlers(); /* Set up cgi vars from command line. */ // cgiSpoof(&argc, argv); optionInit(&argc, argv, options); if (argc != 4) usage(); hgTrackRenderFromCommandLine(argv[1], argv[2], argv[3]); verbose(2, "Overall total time: %ld millis<BR>\n", clock1000() - enteredMainTime); } return 0; }