e60bbad4978e2942453c6177f35cbe9291bfb930 braney Wed Nov 30 15:36:51 2016 -0800 make blat custom track names conform (mostly) with the requests in #2811 diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c index f0621ef..4e8dea3 100644 --- src/hg/hgBlat/hgBlat.c +++ src/hg/hgBlat/hgBlat.c @@ -275,31 +275,31 @@ char buf[4096]; char *twoBitDir; if (trackHubDatabase(db)) { struct trackHubGenome *genome = trackHubGetGenome(db); twoBitDir = genome->twoBitPath; } else { safef(buf, sizeof(buf), "/gbdb/%s", db); twoBitDir = hReplaceGbdbSeqDir(buf, db); safef(buf, sizeof(buf), "%s%s.2bit", twoBitDir, db); twoBitDir = buf; } -safef(cmdBuffer, sizeof(cmdBuffer), "loader/bedToBigBed -udcDir=%s -extraIndex=name -sizesIs2Bit -tab -as=loader/bigPsl.as -type=bed9+16 %s %s %s", +safef(cmdBuffer, sizeof(cmdBuffer), "loader/bedToBigBed -verbose=0 -udcDir=%s -extraIndex=name -sizesIs2Bit -tab -as=loader/bigPsl.as -type=bed9+16 %s %s %s", udcDefaultDir(), bigPslTn.forCgi, twoBitDir, outputBigBed); system(cmdBuffer); unlink(bigPslTn.forCgi); } void showAliPlaces(char *pslName, char *faName, char *customText, char *database, enum gfType qType, enum gfType tType, char *organism, boolean feelingLucky) /* Show all the places that align. */ { struct lineFile *lf = pslFileOpen(pslName); struct psl *pslList = NULL, *psl; char *browserUrl = hgTracksName(); char *hgcUrl = hgcName(); char uiState[64]; @@ -515,63 +515,146 @@ int i, size = seq->size, count = 0; char *s = seq->dna; for (i=0; i<size; ++i) if (s[i] != unknown) ++count; return count; } void uToT(struct dnaSeq *seqList) /* Convert any u's in sequence to t's. */ { struct dnaSeq *seq; for (seq = seqList; seq != NULL; seq = seq->next) subChar(seq->dna, 'u', 't'); } -static char *getUnusedName(char *database, struct cart *cart) -// Find a track name that isn't currently a custom track. +static struct slName *namesInPsl(struct psl *psl) +/* Find all the unique names in a list of psls. */ +{ +struct hash *hash = newHash(3); +struct slName *nameList = NULL; +struct slName *name; +for(; psl; psl = psl->next) + { + if (hashLookup(hash, psl->qName) == NULL) + { + name = slNameNew(psl->qName); + slAddHead(&nameList, name); + hashStore(hash, psl->qName); + } + } +slReverse(&nameList); +return nameList; +} + +static char *makeNameUnique(char *name, char *database, struct cart *cart) +/* Make sure track name will create a unique custom track. */ { struct slName *browserLines = NULL; struct customTrack *ctList = customTracksParseCart(database, cart, &browserLines, NULL); struct customTrack *ct; int count = 0; char buffer[4096]; +safef(buffer, sizeof buffer, "%s", name); for(;;count++) { + char *customName = customTrackTableFromLabel(buffer); for (ct=ctList; ct != NULL; ct=ct->next) { - safef(buffer, sizeof buffer, "ct_BlatResults%d", count); - if (startsWith(buffer, ct->tdb->track)) + if (startsWith(customName, ct->tdb->track)) // Found a track with this name. break; } if (ct == NULL) break; + + safef(buffer, sizeof buffer, "%s (%d)", name, count + 1); } -safef(buffer, sizeof buffer, "Blat Results (%d)", count); + +return cloneString(buffer); +} + +static void getCustomName(char *database, struct cart *cart, struct psl *psl, char **pName, char **pDescription) +// Find a track name that isn't currently a custom track. Also fill in description. +{ +struct slName *names = namesInPsl(psl); +char shortName[4096]; +char description[4096]; + +unsigned count = slCount(names); +if (count == 1) + { + safef(shortName, sizeof shortName, "blat %s", names->name); + safef(description, sizeof description, "blat on %s", names->name); + } +else if (count == 2) + { + safef(shortName, sizeof shortName, "blat %s+%d", names->name, count - 1); + safef(description, sizeof description, "blat on %d queries (%s, %s)", count, names->name, names->next->name); + } +else + { + safef(shortName, sizeof shortName, "blat %s+%d", names->name, count - 1); + safef(description, sizeof description, "blat on %d queries (%s, %s, ...)", count, names->name, names->next->name); + } + +*pName = makeNameUnique(shortName, database, cart); +*pDescription = cloneString(description); +} + +static char *outBigPsl(char *db, struct psl *pslList, char *pslFilename, char *faFilename, boolean isProt) +// Make a bigPsl from a list of psls and return its name. +{ +struct tempName bigBedTn; +trashDirFile(&bigBedTn, "hgBlat", "bp", ".bb"); +makeBigPsl(pslFilename, faFilename, db, bigBedTn.forCgi); +struct tempName customTextTn; +trashDirFile(&customTextTn, "hgBlat", "ct", ".txt"); +FILE *fp = fopen(customTextTn.forCgi, "w"); +char* host = getenv("HTTP_HOST"); +char* reqUrl = getenv("REQUEST_URI"); +// remove everything after / in URL +char *e = strrchr(reqUrl, '/'); +if (e) *e = 0; + +char *trackName = NULL; +char *trackDescription = NULL; + +getCustomName(db, cart, pslList, &trackName, &trackDescription); +char *customTextTemplate = "track type=bigPsl visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s/%s/%s name=\"%s\" description=\"%s\"\n"; +char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases"; + +if (isProt) + extraForMismatch = ""; +fprintf(fp, customTextTemplate, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName, trackDescription); +fclose(fp); + +char buffer[4096]; +safef(buffer, sizeof buffer, "http://%s/%s/%s", host, reqUrl, customTextTn.forCgi); return cloneString(buffer); } void blatSeq(char *userSeq, char *organism, char *database) /* Blat sequence user pasted in. */ { -boolean useBigPsl = cfgOptionBooleanDefault("useBlatBigPsl", FALSE); +boolean doHyper = sameString(cartUsualString(cart, "output", outputList[0]), "hyperlink");; +boolean useBigPsl = cfgOptionBooleanDefault("useBlatBigPsl", FALSE) && doHyper; FILE *f; struct dnaSeq *seqList = NULL, *seq; struct tempName pslTn, faTn; int maxSingleSize, maxTotalSize, maxSeqCount; int minSingleSize = minMatchShown; char *genome, *db; char *type = cgiString("type"); char *seqLetters = cloneString(userSeq); struct serverTable *serve; int conn; int oneSize, totalSize = 0, seqCount = 0; boolean isTx = FALSE; boolean isTxTx = FALSE; boolean txTxBoth = FALSE; struct gfOutput *gvo; @@ -749,58 +832,42 @@ } } else { gfAlignStrand(&conn, serve->nibDir, seq, FALSE, minMatchShown, tFileCache, gvo); reverseComplement(seq->dna, seq->size); conn = gfConnect(serve->host, serve->port); gfAlignStrand(&conn, serve->nibDir, seq, TRUE, minMatchShown, tFileCache, gvo); } gfOutputQuery(gvo, f); } carefulClose(&f); if (useBigPsl) { - // make bigPsl - struct tempName bigBedTn; - trashDirFile(&bigBedTn, "hgBlat", "bp", ".bb"); - makeBigPsl(pslTn.forCgi, faTn.forCgi, serve->db, bigBedTn.forCgi); - struct tempName customTextTn; - trashDirFile(&customTextTn, "hgBlat", "ct", ".txt"); - FILE *fp = fopen(customTextTn.forCgi, "w"); - char* host = getenv("HTTP_HOST"); - char* reqUrl = getenv("REQUEST_URI"); - // remove everything after / in URL - char *e = strrchr(reqUrl, '/'); - if (e) *e = 0; - - char *trackName = getUnusedName(database, cart); - char *customTextTemplate = "track type=bigPsl visibility=pack showAll=on htmlUrl=http://%s/goldenPath/help/hgUserPsl.html %s bigDataUrl=http://%s/%s/%s name=\"%s\"\n"; - char *extraForMismatch = "showDiffBasesAllScales=. baseColorUseSequence=lfExtra baseColorDefault=diffBases"; - - if (qIsProt) - extraForMismatch = ""; - fprintf(fp, customTextTemplate, host, extraForMismatch, host, reqUrl, bigBedTn.forCgi, trackName); - fclose(fp); + struct psl *pslList = pslLoadAll(pslTn.forCgi); - char buffer[4096]; - safef(buffer, sizeof buffer, "http://%s/%s/%s", host, reqUrl, customTextTn.forCgi); - showAliPlaces(pslTn.forCgi, faTn.forCgi, buffer, serve->db, qType, tType, + if (pslList != NULL) + { + char *customTrack = outBigPsl(database, pslList, pslTn.forCgi, faTn.forCgi, qIsProt); + showAliPlaces(pslTn.forCgi, faTn.forCgi, customTrack, serve->db, qType, tType, organism, feelingLucky); } else + puts("<table><tr><td><hr>Sorry, no matches found<hr><td></tr></table>"); + } +else { showAliPlaces(pslTn.forCgi, faTn.forCgi, NULL, serve->db, qType, tType, organism, feelingLucky); } if(!feelingLucky) cartWebEnd(); gfFileCacheFree(&tFileCache); } void askForSeq(char *organism, char *db) /* Put up a little form that asks for sequence. * Call self.... */ { /* ignore struct serverTable* return, but can error out if not found */ findServer(db, FALSE);