ad6fa1b977d0deef14f128a3d6f9d14b4b026e3d max Wed Nov 22 07:19:50 2023 -0800 improving DAS help message, no redmine diff --git src/hg/das/das.c src/hg/das/das.c index cea00ae..80722cd 100644 --- src/hg/das/das.c +++ src/hg/das/das.c @@ -1,1114 +1,1119 @@ /* das - Distributed Annotation System server. * Needs to be called from a Web server generally. * You can spoof it from the command line by giving * it a command argument such as: * das dsn * das hg6/types segment=chr22 */ /* 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 "cheapcgi.h" #include "htmshell.h" #include "psl.h" #include "jksql.h" #include "hdb.h" #include "chromInfo.h" #include "bed.h" #include "genePred.h" #include "trackTable.h" #include "botDelay.h" /* Including the count in the types response can be very slow for large * regions and is optional. Inclusion of count if controlled by this compile- * time option. */ #define TYPES_RETURN_COUNT 0 static char *version = "1.00"; static char *database = NULL; /* DAS response codes */ #define DAS_OK 200 #define DAS_BAD_COMMAND 400 #define DAS_BAD_DATA_SOURCE 401 #define DAS_BAD_COMMAND_ARGS 402 #define DAS_BAD_REFERENCE_OBJECT 403 #define DAS_BAD_STYLESHEET 404 #define DAS_COORDINATE_ERROR 405 #define DAS_SERVER_ERROR 500 #define DAS_UNIMPLEMENTED_FEATURE 501 static void dasHead(int code, boolean justText) /* Write out very start of DAS header */ { printf("X-DAS-Version: DAS/0.95\n"); printf("X-DAS-Status: %d\n", code); if (justText) printf("Content-Type:text\n"); else printf("Content-Type:text/xml\n"); // these allow access from javascript, see http://www.w3.org/TR/cors/ printf("Access-Control-Allow-Origin: *\n"); printf("Access-Control-Expose-Headers: X-DAS-Version X-DAS-Status X-DAS-Capabilities\n"); printf("\n"); } static void dasHeader(int code) /* Write out DAS header */ { dasHead(code, FALSE); if (code != DAS_OK) exit(-1); printf("<?xml version=\"1.0\" standalone=\"no\"?>\n"); } static char dasStrand(char strand) /* convert a strand to a valid DAS strand (+,-,0) */ { if ((strand == '+') || (strand == '-')) return strand; else return '0'; } void sendHogMessage(char *hogHost) { dasHead(DAS_OK, TRUE); printf("Your host, %s, has been sending too many requests lately and is " "unfairly loading our site, impacting performance for other users. " "Please contact genome-www@soe.ucsc.edu to ask that your site " "be reenabled. Also, please consider downloading sequence and/or " "annotations in bulk -- see http://genome.ucsc.edu/downloads.html.", hogHost); exit(0); } void blockHog(char *hogHost, char *hogAddr) /* Compare host/addr to those of an abusive client that we want to block. */ { char *rhost = getenv("REMOTE_HOST"); char *raddr = getenv("REMOTE_ADDR"); if ((rhost != NULL && sameWord(rhost, hogHost)) || (raddr != NULL && sameWord(raddr, hogAddr))) { sendHogMessage(hogHost); } } static void dasHelp(char *s) /* Put up some hopefully helpful information. */ { dasHead(DAS_OK, TRUE); puts(s); exit(0); } static void dasAbout() /* Print a little info when they just hit cgi-bin/das. */ { dasHead(DAS_OK, TRUE); dasHelp("UCSC DAS Server.\n" "See http://www.biodas.org for more info on DAS.\n" "Try http://genome.ucsc.edu/cgi-bin/das/dsn for a list of databases.\n" "See our DAS FAQ (http://genome.ucsc.edu/FAQ/FAQdownloads#download23)\n" "for more information. Alternatively, we also provide query capability\n" "through our MySQL server; please see our FAQ for details\n" "(http://genome.ucsc.edu/FAQ/FAQdownloads#download29).\n\n" "Note that DAS is an inefficient protocol which does not support\n" "all types of annotation in our database. We recommend you\n" - "access the UCSC database by downloading the tab-separated files in\n" + "1) use our API at https://api.genome.ucsc.edu/\n" + "2) access the UCSC database by downloading the tab-separated files in\n" "the downloads section (http://hgdownload.soe.ucsc.edu/downloads.html)\n" - "or by using the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables)\n" - "instead of DAS in most circumstances."); + "3) use the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables)\n" + "instead of DAS in most circumstances.\n" + "4) alternatively, use our command line tools. They can all load data directly from a URL,\n" + "e.g. \n" + " wget https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/twoBitToFa\n" + " chmod a+x twoBitToFa\n" + " twoBitToFa https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/latest/hg38.2bit -bed=test.bed out.fa\n" + "See also the 'Data Access' section of any genome browser track with details on how to\n" + "access the annotation data using our tools or contact us by email so we can suggest the fastest way forward..\n" + ); exit(0); } static void normalHeader() /* Write normal (non-error) header. */ { dasHeader(DAS_OK); } static void earlyError(int errCode) /* Return error in early processing (before writing header) */ { dasHeader(errCode); } static char *currentUrl() /* Query environment to get current URL. WARNING: static return */ { static char url[1024]; safef(url, sizeof(url), "http://%s%s%s", getenv("SERVER_NAME"), getenv("SCRIPT_NAME"), getenv("PATH_INFO")); return url; } struct tableDef /* A table definition. */ { struct tableDef *next; /* Next in list. */ char *name; /* Name of table. */ struct slName *splitTables; /* Names of subTables. Only used if isSplit. */ char *chromField; /* Name of field chromosome is stored in. */ char *startField; /* Name of field chromosome start is in. */ char *endField; /* Name of field chromosome end is in. */ char *category; /* Category type. */ char *method; /* Category type. */ boolean hasBin; /* Has bin field. */ }; static boolean hasLogicalChromName(char *name) /* Return TRUE if name begins with "chr"*/ { return (startsWith("chr", name)); } static boolean tableIsSplit(char *table) /* Return TRUE if table is split. */ { if (!hasLogicalChromName(table)) return FALSE; if (strchr(table, '_') == NULL) return FALSE; return TRUE; } static char *skipOverChrom(char *table) /* Skip over chrN_ or chrN_random_. */ { char *e = strchr(table, '_'); if (e != NULL) { ++e; if (startsWith("random_", e)) e += 7; table = e; } return table; } static char *chromNumberToName(char *seqName) /* If seqName is a chrom number, prepend "chr". */ { char *official = NULL; char chrName[128]; safef(chrName, sizeof(chrName), "chr%s", seqName); official = hgOfficialChromName(database, chrName); if (official == NULL) official = seqName; return(official); } static boolean dasableType(char *type) /* Return TRUE if we can handle type. */ { char *dupe = cloneString(type); char *line = dupe, *word; boolean ok = TRUE; word = nextWord(&line); if (word != NULL) { if (sameString("chain", word)) ok = FALSE; else if (sameString("net", word)) ok = FALSE; else if (sameString("netAlign", word)) ok = FALSE; } freeMem(dupe); return ok; } static boolean disabledViaSettings(char *settings) // Return TRUE if this table is disabled via "tableBrowser off" in trackDb settings string. // We modify settings string (pass in a copy if you don't want it modified). { char *line; boolean disabled = FALSE; struct lineFile *lf = lineFileOnString("settings", TRUE, settings); while (!disabled && lineFileNext(lf, &line, NULL)) disabled = startsWith("tableBrowser off", line); lineFileClose(&lf); return disabled; } static struct hash *mkTrackTypeHash() /* build a hash of track name to type */ { struct sqlConnection *conn = hAllocConn(database); struct hash *hash = hashNew(10); struct slName *trackDb, *trackDbs = hTrackDbList(); for (trackDb = trackDbs; trackDb != NULL; trackDb = trackDb->next) { if (sqlTableExists(conn, trackDb->name)) { char query[128]; sqlSafef(query, sizeof(query), "select tableName,type,settings from %s", trackDb->name); struct sqlResult *sr = sqlGetResult(conn, query); char **row; while ((row = sqlNextRow(sr)) != NULL) { if (dasableType(row[1]) && !disabledViaSettings(row[2]) && (hashLookup(hash, row[0]) == NULL)) hashAdd(hash, row[0], NULL); } sqlFreeResult(&sr); } } slFreeList(&trackDbs); hFreeConn(&conn); return hash; } static boolean dasableTrack(char *name) /* Return TRUE if track can be put into DAS format. */ { static struct hash *types = NULL; if (types == NULL) types = mkTrackTypeHash(); return hashLookup(types, name) != NULL; } static struct hash *mkSkipTableHash() /* build hash of big tables that we don't actually want to serve. */ { struct hash *skips = hashNew(0); hashAdd(skips, "all_est", NULL); hashAdd(skips, "all_mrna", NULL); hashAdd(skips, "refFlat", NULL); hashAdd(skips, "simpleRepeat", NULL); hashAdd(skips, "ctgPos", NULL); hashAdd(skips, "gold", NULL); hashAdd(skips, "clonePos", NULL); hashAdd(skips, "gap", NULL); hashAdd(skips, "rmsk", NULL); hashAdd(skips, "estPair", NULL); hashAdd(skips, "altGraphX", NULL); return skips; } static boolean skipTable(char *name) /* should big tables be skipped. */ { static struct hash *skips = NULL; if (skips == NULL) skips = mkSkipTableHash(); return hashLookup(skips, name) != NULL; } static struct tableDef *getTables() /* Get all tables. */ { struct sqlConnection *conn = hAllocConn(database); struct hash *hash = newHash(0); struct tableDef *tdList = NULL, *td; struct sqlResult *sr; char **row; char *table, *root; boolean isSplit, hasBin; char chromField[32], startField[32], endField[32]; char query[1024]; sqlSafef(query, sizeof query, "show tables"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { table = root = row[0]; if (hFindFieldsAndBin(database, table, chromField, startField, endField, &hasBin)) { isSplit = tableIsSplit(table); if (isSplit) root = skipOverChrom(table); if (!skipTable(root) && dasableTrack(root)) { if ((td = hashFindVal(hash, root)) == NULL) { AllocVar(td); slAddHead(&tdList, td); hashAdd(hash, root, td); td->name = cloneString(root); td->chromField = cloneString(chromField); td->startField = cloneString(startField); td->endField = cloneString(endField); td->hasBin = hasBin; if (stringIn("snp", root) || stringIn("Snp", root)) { td->category = "variation"; } else if (stringIn("est", root) || stringIn("Est", root) || stringIn("mrna", root) || stringIn("Mrna", root)) { td->category = "transcription"; td->method = "BLAT"; } else if (sameString("txStart", startField) || stringIn("rnaGene", root)) { td->category = "transcription"; } else if (stringIn("mouse", root) || stringIn("Mouse", root) || stringIn("fish", root) || stringIn("Fish", root)) { td->category = "similarity"; if (startsWith("blat", root)) td->method = "BLAT"; else if (sameString("exoMouse", root)) td->method = "Exonerate"; else if (sameString("exoMouse", root)) td->method = "Exofish"; } else if (sameString("gap", root) || sameString("gold", root) || sameString("gl", root) || sameString("clonePos", root)) { td->category = "structural"; td->method = "GigAssembler"; } else td->category = "other"; } if (isSplit) { struct slName *sln = newSlName(table); slAddHead(&td->splitTables, sln); } } } } sqlFreeResult(&sr); hFreeConn(&conn); hashFree(&hash); slReverse(&tdList); return tdList; } static struct hash *hashOfTracks() /* Get list of tracks and put into hash keyed by tableName*/ { struct hash *trackHash = newHash(7); struct trackTable *ttList = hGetTracks(database), *tt; for (tt = ttList; tt != NULL; tt = tt->next) hashAdd(trackHash, tt->tableName, tt); return trackHash; } struct segment /* A subset of a sequence. */ { struct segment *next; /* Next in list. */ char *seq; /* Name of sequence, often a chromosome. */ int start; /* Zero based start. */ int end; /* Base after end. */ boolean wholeThing; /* TRUE if user requested whole sequence. */ char *seqName; /* Name of sequence in external DAS world */ }; static struct segment *segmentNew(char *seq, int start, int end, boolean wholeThing, char *seqName) /* Make a new segment. */ { struct segment *segment; AllocVar(segment); segment->seq = cloneString(seq); segment->start = start; segment->end = end; segment->wholeThing = wholeThing; segment->seqName = cloneString(seqName); return segment; } static struct segment *dasSegmentList(boolean mustExist) /* Get a DAS segment list from either segment or ref parameters. * Call this before you write out header so it can return errors * properly if parameters are malformed. */ { struct slName *segList, *seg; struct segment *segmentList = NULL, *segment; char *seq, *seqName; int start=0, end=0; boolean wholeThing; segList = cgiStringList("segment"); if (segList != NULL) { /* Handle new format (post 0.995 spec) lists. */ for (seg = segList; seg != NULL; seg = seg->next) { char *parts[3]; int partCount; wholeThing = FALSE; partCount = chopString(seg->name, ":,", parts, ArraySize(parts)); seqName = parts[0]; seq = chromNumberToName(seqName); if (partCount == 1) { start = 0; end = hChromSize(database, seq); wholeThing = TRUE; } else if (partCount == 3) { if (!isdigit(parts[1][0]) || !isdigit(parts[2][0])) earlyError(DAS_BAD_COMMAND_ARGS); start = atoi(parts[1])-1; end = atoi(parts[2]); if (start > end) earlyError(DAS_COORDINATE_ERROR); } else { earlyError(DAS_BAD_COMMAND_ARGS); } segment = segmentNew(seq, start, end, wholeThing, seqName); slAddHead(&segmentList, segment); } slReverse(&segmentList); } else { /* Handle old format (pre 0.995 spec) lists. */ seqName = cgiOptionalString("ref"); wholeThing = TRUE; if (seqName == NULL) { if (mustExist) earlyError(DAS_BAD_COMMAND_ARGS); else { return NULL; } } seq = chromNumberToName(seqName); if (cgiVarExists("start")) { start = cgiInt("start")-1; wholeThing = FALSE; } else start = 0; if (cgiVarExists("stop")) { end = cgiInt("stop"); wholeThing = FALSE; } else end = hChromSize(database, seq); if (start > end) earlyError(DAS_COORDINATE_ERROR); segmentList = segmentNew(seq, start, end, wholeThing, seqName); } /* Check all segments are chromosomes. */ for (segment = segmentList; segment != NULL; segment = segment->next) { if (hgOfficialChromName(database, segment->seq) == NULL) earlyError(DAS_BAD_REFERENCE_OBJECT); } return segmentList; } struct filters /* hash tables of filter values. */ { struct hash *type; // type filters, or NULL if no filters struct hash *category; // category filters, or NULL if no filters }; static struct hash *filtersFromCgiVar(char *cgiVar) /* build hash of filters from a cgiVar name */ { struct slName *nList = cgiStringList(cgiVar), *n; if (nList == NULL) return NULL; // no filters struct hash *filters = hashNew(10); for (n = nList; n != NULL; n = n->next) hashStore(filters, n->name); return filters; } static struct filters *filtersNew() /* construct filters for type and category */ { struct filters *filters; AllocVar(filters); filters->type = filtersFromCgiVar("type"); filters->category = filtersFromCgiVar("category"); return filters; } static boolean catTypeFilter(struct filters *filters, char *cat, char *type) /* Combined category/type filter. */ { /* spec doesn't says if both category and type results a AND or OR, so we * treat it as an AND, as this seems more usefully. */ if ((filters->category != NULL) && (filters->type != NULL)) return (hashLookup(filters->category,cat) != NULL) && (hashLookup(filters->type, type) != NULL); if (filters->category != NULL) return (hashLookup(filters->category,cat) != NULL); if (filters->type != NULL) return (hashLookup(filters->type, type) != NULL); return TRUE; } static boolean tableDefFilter(struct tableDef *td) /* determine if a tableDef has the required information to use the track */ { return isNotEmpty(td->chromField) && isNotEmpty(td->startField) && isNotEmpty(td->endField); } static boolean trackFilter(struct filters *filters, struct tableDef *td) /* do track filtering. */ { return tableDefFilter(td) && catTypeFilter(filters, td->category, td->name); } static void doDsn(struct slName *dbList) /* dsn - DSN Server for DAS. */ { struct slName *db; normalHeader(); printf( "<!DOCTYPE DASDSN SYSTEM \"http://www.biodas.org/dtd/dasdsn.dtd\">\n" "<DASDSN>\n"); for (db = dbList; db != NULL; db = db->next) { char *freeze = hFreezeFromDb(db->name); char *organism = hOrganism(db->name); if (! hDbIsActive(db->name)) continue; printf(" <DSN>\n"); printf(" <SOURCE id=\"%s\" version=\"%s\">%s at UCSC</SOURCE>\n", db->name, version, freeze); printf(" <DESCRIPTION>%s %s Genome at UCSC</DESCRIPTION>\n", organism, freeze); printf(" <MAPMASTER>http://genome.ucsc.edu:80/cgi-bin/das/%s</MAPMASTER>\n", db->name); printf(" </DSN>\n"); } printf("</DASDSN>\n"); } static int countFeatures(struct tableDef *td, struct segment *segmentList) /* Count all the features in a given segment. */ { struct segment *segment; int acc = 0; struct sqlConnection *conn = hAllocConn(database); char chrTable[256]; char query[512]; struct slName *n; if (segmentList == NULL) { if (td->splitTables == NULL) { sqlSafef(query, sizeof query, "select count(*) from %s", td->name); acc = sqlQuickNum(conn, query); } else { for (n = td->splitTables; n != NULL; n = n->next) { sqlSafef(query, sizeof query, "select count(*) from %s", n->name); acc += sqlQuickNum(conn, query); } } } else { for (segment = segmentList; segment != NULL; segment = segment->next) { if (segment->wholeThing) { if (td->splitTables == NULL) { sqlSafef(query, sizeof query, "select count(*) from %s where %s = '%s'", td->name, td->chromField, segment->seq); acc += sqlQuickNum(conn, query); } else { sprintf(chrTable, "%s_%s", segment->seq, td->name); if (sqlTableExists(conn, chrTable)) { sqlSafef(query, sizeof query, "select count(*) from %s", chrTable); acc += sqlQuickNum(conn, query); } } } else { if (td->splitTables == NULL) { sqlSafef(query, sizeof query, "select count(*) from %s where %s = '%s' and %s < %d and %s > %d", td->name, td->chromField, segment->seq, td->startField, segment->end, td->endField, segment->start); acc += sqlQuickNum(conn, query); } else { sprintf(chrTable, "%s_%s", segment->seq, td->name); if (sqlTableExists(conn, chrTable)) { sqlSafef(query, sizeof query, "select count(*) from %s where %s < %d and %s > %d", chrTable, td->startField, segment->end, td->endField, segment->start); acc += sqlQuickNum(conn, query); } } } } } hFreeConn(&conn); return acc; } static void doTypes() /* Handle a types request. */ { struct segment *segment, *segmentList = dasSegmentList(FALSE); struct tableDef *tdList = getTables(), *td; struct filters *filters = filtersNew(); normalHeader(); printf("<!DOCTYPE DASTYPES SYSTEM \"http://www.biodas.org/dtd/dastypes.dtd\">\n"); printf("<DASTYPES>\n"); printf("<GFF version=\"1.2\" href=\"%s\">\n", currentUrl()); for (segment = segmentList;;) { if (segment == NULL) printf("<SEGMENT version=\"%s\">\n", version); else printf("<SEGMENT id=\"%s\" start=\"%d\" stop=\"%d\" version=\"%s\">\n", segment->seqName, segment->start+1, segment->end, version); for (td = tdList; td != NULL; td = td->next) { if (trackFilter(filters, td)) { printf("<TYPE id=\"%s\" category=\"%s\"", td->name, td->category); if (td->method != NULL) printf(" method=\"%s\"", td->method); if (TYPES_RETURN_COUNT) printf(">%d</TYPE>\n", countFeatures(td, segment)); else printf("/>\n"); } } printf("</SEGMENT>\n"); if (segment == NULL || segment->next == NULL) break; segment = segment->next; } printf("</GFF>\n"); printf("</DASTYPES>\n"); } static void dasPrintType(struct tableDef *td, struct trackTable *tt) /* Print out from <TYPE> to </TYPE> inside a feature. */ { char *description = (tt != NULL ? tt->shortLabel : td->name); printf(" <TYPE id=\"%s\" category=\"%s\" reference=\"no\">%s</TYPE>\n", td->name, td->category, description); } static void dasOutGp(struct genePred *gp, struct tableDef *td, struct trackTable *tt) /* Write out DAS info on a gene prediction. */ { int i; for (i=0; i<gp->exonCount; ++i) { int start = gp->exonStarts[i]; int end = gp->exonEnds[i]; printf( "<FEATURE id=\"%s.%s.%d.%d\" label=\"%s\">\n", gp->name, gp->chrom, gp->txStart, i, gp->name); dasPrintType(td, tt); if (td->method != NULL) printf(" <METHOD id=\"id\">%s</METHOD>\n", td->method); else printf(" <METHOD></METHOD>\n"); printf(" <START>%d</START>\n", start+1); printf(" <END>%d</END>\n", end); printf(" <SCORE>-</SCORE>\n"); printf(" <ORIENTATION>%c</ORIENTATION>\n", dasStrand(gp->strand[0])); printf(" <PHASE>-</PHASE>\n"); printf(" <GROUP id=\"%s.%s.%d\">\n", gp->name, gp->chrom, gp->txStart); printf(" <LINK href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?position=%s:%d-%d&db=%s\">Link to UCSC Browser</LINK>\n", gp->chrom, gp->txStart, gp->txEnd, database); printf(" </GROUP>\n"); printf("</FEATURE>\n"); } } static void dasOutGpSegment(struct sqlResult *sr, int rowOffset, struct tableDef *td, struct trackTable *tt) /* output genePreds resulting from query */ { char **row; while ((row = sqlNextRow(sr)) != NULL) { struct genePred *gp = genePredLoad(row+rowOffset); dasOutGp(gp, td, tt); genePredFree(&gp); } } static void dasOutPsl(struct psl *psl, struct tableDef *td, struct trackTable *tt) /* Write out DAS info on a psl alignment. */ { int i; int score = 1000 - pslCalcMilliBad(psl, TRUE); for (i=0; i<psl->blockCount; ++i) { int s = psl->tStarts[i]; int e = s + psl->blockSizes[i]; int qStart, qEnd; int start,end; if (psl->strand[1] == '-') { start = psl->tSize - e; end = psl->tSize - s; } else { start = s; end = e; } s = psl->qStarts[i]; e = s + psl->blockSizes[i]; if (psl->strand[0] == '-') { qStart = psl->qSize - e; qEnd = psl->qSize - s; } else { qStart = s; qEnd = e; } printf( "<FEATURE id=\"%s.%s.%d.%d\" label=\"%s\">\n", psl->qName, psl->tName, psl->tStart, i, psl->qName); dasPrintType(td, tt); if (td->method != NULL) printf(" <METHOD id=\"id\">%s</METHOD>\n", td->method); else printf(" <METHOD></METHOD>\n"); printf(" <START>%d</START>\n", start+1); printf(" <END>%d</END>\n", end); printf(" <SCORE>%d</SCORE>\n", score); printf(" <ORIENTATION>%c</ORIENTATION>\n", dasStrand(psl->strand[0])); printf(" <PHASE>-</PHASE>\n"); printf(" <GROUP id=\"%s.%s.%d\">\n", psl->qName, psl->tName, psl->tStart); printf(" <LINK href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?position=%s:%d-%d&db=%s\">Link to UCSC Browser</LINK>\n", psl->tName, psl->tStart, psl->tEnd, database); printf(" <TARGET id=\"%s\" start=\"%d\" stop=\"%d\">%s</TARGET>\n", psl->qName, qStart+1, qEnd, psl->qName); printf(" </GROUP>\n"); printf("</FEATURE>\n"); } } static void dasOutPslSegment(struct sqlResult *sr, int rowOffset, struct tableDef *td, struct trackTable *tt) /* output psls resulting from query */ { char **row; while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row+rowOffset); dasOutPsl(psl, td, tt); pslFree(&psl); } } static void dasOutBed(char *chrom, int start, int end, char *name, char *score, char *strand, struct tableDef *td, struct trackTable *tt) /* Write out a generic one. */ { printf("<FEATURE id=\"%s.%s.%d\" label=\"%s\">\n", name, chrom, start, name); dasPrintType(td, tt); if (td->method != NULL) printf(" <METHOD id=\"id\">%s</METHOD>\n", td->method); else printf(" <METHOD></METHOD>\n"); printf(" <START>%d</START>\n", start+1); printf(" <END>%d</END>\n", end); printf(" <SCORE>%s</SCORE>\n", score); printf(" <ORIENTATION>%c</ORIENTATION>\n", dasStrand(strand[0])); printf(" <PHASE>-</PHASE>\n"); printf(" <GROUP id=\"%s.%s.%d\">\n", name, chrom, start); printf(" <LINK href=\"http://genome.ucsc.edu/cgi-bin/hgTracks?position=%s:%d-%d&db=%s\">Link to UCSC Browser</LINK>\n", chrom, start, end, database); printf(" </GROUP>\n"); printf("</FEATURE>\n"); } static void dasOutBedSegment(struct sqlResult *sr, char *table, struct tableDef *td, struct trackTable *tt) /* output BEDs and BED like tables resulting from query */ { char **row; int chromIx = sqlFieldColumn(sr, "chrom"); int chromStartIx = sqlFieldColumn(sr, "chromStart"); int chromEndIx = sqlFieldColumn(sr, "chromEnd"); int nameIx = sqlFieldColumn(sr, "name"); int scoreIx = sqlFieldColumn(sr, "score"); int strandIx = sqlFieldColumn(sr, "strand"); if (nameIx == -1) nameIx = sqlFieldColumn(sr, "contig"); if (scoreIx == -1) scoreIx = sqlFieldColumn(sr, "gcPpt"); if (scoreIx == -1) scoreIx = sqlFieldColumn(sr, "dataValue"); // bedGraph while ((row = sqlNextRow(sr)) != NULL) { char *chrom = (chromIx >= 0) ? row[chromIx] : "-"; char *chromStart = (chromStartIx >= 0) ? row[chromStartIx] : "0"; char *chromEnd = (chromEndIx >= 0) ? row[chromEndIx] : "0"; char *name = (nameIx >= 0 ? row[nameIx] : td->name); char *score = (scoreIx >= 0 ? row[scoreIx] : "-"); char *strand = (strandIx >= 0 ? row[strandIx] : "0"); dasOutBed(chrom, sqlUnsigned(chromStart), sqlUnsigned(chromEnd), name, score, strand, td, tt); } } static void writeSegmentFeaturesTable(struct segment *segment, struct tableDef *td, struct hash *trackHash, struct sqlConnection *conn) /* write segments features for a table */ { int rowOffset; boolean hasBin; char table[HDB_MAX_TABLE_STRING]; verbose(2, "track %s\n", td->name); if (!hFindSplitTable(database, segment->seq, td->name, table, sizeof table, &hasBin)) errAbort("track %s not found", td->name); // horrible hack because hFindSplitTable and hRangeQuery don't really seem to // handle est->all_est/mrna->all_mrna right, but markd fears modifying that // code if (sameString(td->name, "mrna")) safecpy(table, sizeof(table), "all_mrna"); else if (sameString(td->name, "est")) safecpy(table, sizeof(table), "all_est"); struct trackTable *tt = hashFindVal(trackHash, td->name); struct sqlResult *sr = hRangeQuery(conn, table, segment->seq, segment->start, segment->end, NULL, &rowOffset); // FIXME: should use trackDb to determine type, as field names are // not always unique. if (sameString(td->startField, "tStart") && (sqlFieldColumn(sr, "qStart") >= 0)) { dasOutPslSegment(sr, rowOffset, td, tt); } else if (sameString(td->startField, "txStart")) { dasOutGpSegment(sr, rowOffset, td, tt); } else if (sameString(td->startField, "chromStart")) { dasOutBedSegment(sr, table, td, tt); } sqlFreeResult(&sr); } static void writeSegmentFeatures(struct segment *segment, struct filters *filters, struct tableDef *tdList, struct hash *trackHash, struct sqlConnection *conn) /* write features for a segment */ { /* Print segment header. */ printf( "<SEGMENT id=\"%s\" start=\"%d\" stop=\"%d\" version=\"%s\" label=\"%s\">\n", segment->seqName, segment->start+1, segment->end, version, segment->seqName); /* Query database and output features. */ struct tableDef *td; for (td = tdList; td != NULL; td = td->next) { if (trackFilter(filters, td)) writeSegmentFeaturesTable(segment, td, trackHash, conn); } printf("</SEGMENT>\n"); } static void doFeatures() /* features - DAS Annotation Feature Server. */ { struct segment *segmentList = dasSegmentList(TRUE), *segment; struct hash *trackHash = hashOfTracks(); struct tableDef *tdList = getTables(); struct filters *filters = filtersNew(); struct sqlConnection *conn = hAllocConn(database); /* Write out DAS features header. */ normalHeader(); printf( "<!DOCTYPE DASGFF SYSTEM \"http://www.biodas.org/dtd/dasgff.dtd\">\n" "<DASGFF>\n" "<GFF version=\"1.0\" href=\"%s\">\n", currentUrl()); for (segment = segmentList; segment != NULL; segment = segment->next) writeSegmentFeatures(segment, filters, tdList, trackHash, conn); /* Write out DAS footer. */ printf("</GFF></DASGFF>\n"); /* Clean up. */ freeHash(&trackHash); hFreeConn(&conn); } static void doEntryPoints() /* Handle entry points request. */ { struct sqlConnection *conn; struct sqlResult *sr; char **row; struct chromInfo *ci; normalHeader(); conn = hAllocConn(database); printf("<!DOCTYPE DASEP SYSTEM \"http://www.biodas.org/dtd/dasep.dtd\">\n"); printf("<DASEP>\n"); printf("<ENTRY_POINTS href=\"%s\" version=\"7.00\">\n", currentUrl()); char query[1024]; sqlSafef(query, sizeof query, "select * from chromInfo"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { ci = chromInfoLoad(row); /* "chr"-less chromosome ID for clients such as Ensembl: */ if (startsWith("chr", ci->chrom)) printf(" <SEGMENT id=\"%s\" start=\"%d\" stop=\"%d\" orientation=\"+\" subparts=\"no\">%s</SEGMENT>\n", ci->chrom+3, 1, ci->size, ci->chrom+3); else printf(" <SEGMENT id=\"%s\" start=\"%d\" stop=\"%d\" orientation=\"+\" subparts=\"no\">%s</SEGMENT>\n", ci->chrom, 1, ci->size, ci->chrom); chromInfoFree(&ci); } printf("</ENTRY_POINTS>\n"); printf("</DASEP>\n"); } static void doDna() /* Handle request for DNA. */ { struct segment *segmentList = dasSegmentList(TRUE), *segment; int size = 0; struct dnaSeq *seq; int i, oneSize, lineSize = 50; /* Write header. */ normalHeader(); printf("<!DOCTYPE DASDNA SYSTEM \"http://www.biodas.org/dtd/dasdna.dtd\">\n"); printf("<DASDNA>\n"); /* Write each sequence. */ for (segment = segmentList; segment != NULL; segment = segment->next) { printf("<SEQUENCE id=\"%s\" start=\"%d\" stop=\"%d\" version=\"%s\">\n", segment->seqName, segment->start+1, segment->end, version); printf("<DNA length=\"%d\">\n", segment->end - segment->start); /* Write out DNA. */ seq = hDnaFromSeq(database, segment->seq, segment->start, segment->end, dnaLower); if (seq == NULL) errAbort("Couldn't fetch %s\n", segment->seq); size = seq->size; for (i=0; i<size; i += oneSize) { oneSize = size - i; if (oneSize > lineSize) oneSize = lineSize; mustWrite(stdout, seq->dna+i, oneSize); fputc('\n', stdout); } printf("</DNA>\n"); printf("</SEQUENCE>\n"); } /* Write footer. */ printf("</DASDNA>\n"); } static void dispatch(char *dataSource, char *command) /* Dispatch a dase command. */ { struct slName *dbList = hDbList(); if (sameString(dataSource, "dsn")) { doDsn(dbList); } else if (slNameFind(dbList, dataSource) != NULL && hDbIsActive(dataSource)) { database = dataSource; if (sameString(command, "entry_points")) doEntryPoints(); else if (sameString(command, "dna")) doDna(); else if (sameString(command, "types")) doTypes(); else if (sameString(command, "features")) doFeatures(); else earlyError(DAS_UNIMPLEMENTED_FEATURE); } else earlyError(DAS_BAD_DATA_SOURCE); } static void das(char *pathInfo) /* das - Das Server. */ { static char *parts[3]; int partCount; if (pathInfo == NULL) dasAbout(); pathInfo = cloneString(pathInfo); partCount = chopString(pathInfo, "/", parts, ArraySize(parts)); if (partCount < 1) dasAbout(); if (partCount == 1 && !sameString(parts[0], "dsn")) { dasHelp("Expecting dsn or database/command in the URL after das.\n" "Try das/dsn for a list of databases.\n" "Try das/database/types for a list of available annotations.\n"); } dispatch(parts[0], parts[1]); } int main(int argc, char *argv[]) /* Process command line. */ { char *path = getenv("PATH_INFO"); cgiSpoof(&argc, argv); if (cgiVarExists("verbose")) verboseSetLevel(cgiInt("verbose")); if (argc == 2) path = argv[1]; -/* Temporary measure to shut down abusive clients */ -#if 0 - blockHog("pix39.systemsbiology.net", "198.107.152.39"); -#endif int delay = hgBotDelayTimeFrac(0.03); if (delay > 2000) { char *hogHost = getenv("REMOTE_ADDR"); sendHogMessage(hogHost); } sleep1000(delay); das(path); return 0; }