9fa9d885584e6f007336ff740b1aad5621eb19fd angie Fri Sep 11 15:56:17 2015 -0700 If the current table doesn't have hti, getIdField tries to get hti for the current track -- except that's a problem when the track is a composite track yet has a type for which we expect to have a bigDataFileOrUrl. So if the current track is a composite, don't try. Test case: Table Browser, hg19, group = Variation, track = 1000G Ph3 Accsbl; before fix, page fails trying to query the non-existent table for composite. diff --git src/hg/hgTables/hgTables.c src/hg/hgTables/hgTables.c index 618d734..a4c2e6c 100644 --- src/hg/hgTables/hgTables.c +++ src/hg/hgTables/hgTables.c @@ -1,1823 +1,1823 @@ /* hgTables - Main and utility functions for table browser. */ /* Copyright (C) 2014 The Regents of the University of California * See README in this or parent directory for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "memalloc.h" #include "obscure.h" #include "htmshell.h" #include "cheapcgi.h" #include "cart.h" #include "cartTrackDb.h" #include "textOut.h" #include "jksql.h" #include "hdb.h" #include "web.h" #include "hui.h" #include "hCommon.h" #include "hgColors.h" #include "trackDb.h" #include "botDelay.h" #include "grp.h" #include "customTrack.h" #include "pipeline.h" #include "hgFind.h" #include "hgTables.h" #include "joiner.h" #include "bedCart.h" #include "hgMaf.h" #include "gvUi.h" #include "wikiTrack.h" #include "trackHub.h" #include "hubConnect.h" #include "hgConfig.h" #include "udc.h" #include "chromInfo.h" #include "knetUdc.h" #include "trashDir.h" void usage() /* Explain usage and exit. */ { errAbort( "hgTables - Get table data associated with tracks and intersect tracks\n" "usage:\n" " hgTables XXX\n" "options:\n" " -xxx=XXX\n" ); } /* Global variables. */ struct cart *cart; /* This holds cgi and other variables between clicks. */ struct hash *oldVars; /* The cart before new cgi stuff added. */ char *genome; /* Name of genome - mouse, human, etc. */ char *database; /* Current genome database - hg17, mm5, etc. */ char *freezeName; /* Date of assembly. */ struct grp *fullGroupList; /* List of all groups. */ struct grp *curGroup; /* Currently selected group. */ struct trackDb *fullTrackList; /* List of all tracks in database. */ struct hash *fullTableToTdbHash; /* All tracks and subtracks keyed by tdb->table field. */ struct trackDb *curTrack; /* Currently selected track. */ char *curTable; /* Currently selected table. */ struct joiner *allJoiner; /* Info on how to join tables. */ static struct pipeline *compressPipeline = (struct pipeline *)NULL; char *gsTemp = NULL; int saveStdout = -1; /* --------------- HTML Helpers ----------------- */ void hPrintSpaces(int count) /* Print a number of non-breaking spaces. */ { int i; for (i=0; i<count; ++i) hPrintf(" "); } static void stripHtmlTags(char *text) /* remove HTML tags from text string, replacing in place by moving * the text up to take their place */ { char *s = text; char *e = text; char c = *text; for ( ; c != 0 ; ) { c = *s++; if (c == 0) /* input string is NULL, or it ended with '>' without any * opening '>' */ { *e = 0; break; } /* stays in the while loop for adjacent tags <TR><TD> ... etc */ while (c == '<' && c != 0) { s = strchr(s,'>'); if (s != NULL) { if (*s == '>') ++s; /* skip closing bracket > */ c = *s++; /* next char after the closing bracket > */ } else c = 0; /* no closing bracket > found, end of string */ } *e++ = c; /* copies all text outside tags, including ending NULL */ } } void writeHtmlCell(char *text) /* Write out a cell in an HTML table, making text not too big, * and stripping html tags and breaking spaces.... */ { int maxLen = 128; int len = strlen(text); char *extra = ""; if (len > maxLen) { len = maxLen; extra = " ..."; } char *s = cloneStringZ(text,len); char *r; stripHtmlTags(s); eraseTrailingSpaces(s); r = replaceChars(s, " ", " "); hPrintf("<TD>%s%s</TD>", r, extra); freeMem(s); freeMem(r); } static void earlyAbortHandler(char *format, va_list args) { // provide more explicit message when we run out of memory (#5147). popWarnHandler(); if(strstr(format, "needLargeMem:") || strstr(format, "carefulAlloc:")) format = "Region selected is too large for calculation. Please specify a smaller region or try limiting to fewer data points."; vaWarn(format, args); if(isErrAbortInProgress()) noWarnAbort(); } static void errAbortHandler(char *format, va_list args) { // provide more explicit message when we run out of memory (#5147). if(strstr(format, "needLargeMem:") || strstr(format, "carefulAlloc:")) htmlVaWarn("Region selected is too large for calculation. Please specify a smaller region or try limiting to fewer data points.", args); else { // call previous handler popWarnHandler(); vaWarn(format, args); } if(isErrAbortInProgress()) noWarnAbort(); } static void vaHtmlOpen(char *format, va_list args) /* Start up a page that will be in html format. */ { puts("Content-Type:text/html\n"); cartVaWebStart(cart, database, format, args); pushWarnHandler(errAbortHandler); } void htmlOpen(char *format, ...) /* Start up a page that will be in html format. */ { va_list args; va_start(args, format); vaHtmlOpen(format, args); va_end(args); } void htmlClose() /* Close down html format page. */ { popWarnHandler(); cartWebEnd(); } void explainWhyNoResults(FILE *f) /* Put up a little explanation to user of why they got nothing. */ { if (f == NULL) f = stdout; fprintf(f, "# No results"); if (identifierFileName() != NULL) fprintf(f, " matching identifier list"); if (anyFilter()) fprintf(f, " passing filter"); if (!fullGenomeRegion()) fprintf(f, " in given region"); if (anyIntersection()) fprintf(f, " after intersection"); fprintf(f, ".\n"); } char *curTableLabel() /* Return label for current table - track short label if it's a track */ { if (curTrack != NULL && sameString(curTrack->table, curTable)) return curTrack->shortLabel; else return curTable; } char *getScriptName() /* returns script name from environment or hardcoded for command line */ { char *script = cgiScriptName(); if (script != NULL) return script; else return hgTablesName(); } void textOpen() /* Start up page in text format. (No need to close this). * In case of pipeline output to a compressor, it is closed * at main() exit. */ { char *fileName = cartUsualString(cart, hgtaOutFileName, ""); char *compressType = cartUsualString(cart, hgtaCompressType, textOutCompressNone); if (doGenomeSpace()) { char hgsid[64]; struct tempName tn; safef(hgsid, sizeof(hgsid), "%s", cartSessionId(cart)); trashDirFile(&tn, "genomeSpace", hgsid, ".tmp"); gsTemp = cloneString(tn.forCgi); fileName = gsTemp; } compressPipeline = textOutInit(fileName, compressType, &saveStdout); } void dbOverrideFromTable(char buf[256], char **pDb, char **pTable) /* If *pTable includes database, overrider *pDb with it, using * buf to hold string. */ { char *s; safef(buf, 256, "%s", *pTable); s = strchr(buf, '.'); if (s != NULL) { *pDb = buf; *s++ = 0; *pTable = s; } } boolean fullGenomeRegion() /* Return TRUE if region is full genome. */ { char *regionType = cartUsualString(cart, hgtaRegionType, "genome"); return sameString(regionType, "genome"); } static int regionCmp(const void *va, const void *vb) /* Compare to sort based on chrom,start */ { const struct region *a = *((struct region **)va); const struct region *b = *((struct region **)vb); int dif; dif = chrStrippedCmp(a->chrom, b->chrom); if (dif == 0) dif = a->start - b->start; return dif; } static struct region *getRegionsFullGenomeLocal() /* get all the chrom ranges for a local database */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct region *region, *regionList = NULL; sr = sqlGetResult(conn, "NOSQLINJ select chrom,size from chromInfo"); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(region); region->chrom = cloneString(row[0]); region->end = sqlUnsigned(row[1]); region->fullChrom = TRUE; region->name = NULL; /* unused for full chrom */ slAddHead(®ionList, region); } slSort(®ionList, regionCmp); sqlFreeResult(&sr); hFreeConn(&conn); return regionList; } static struct region *getRegionsFullGenomeHub() /* get all the chrom ranges for a hub database */ { struct chromInfo *ci = trackHubAllChromInfo(database); struct region *region, *regionList = NULL; AllocVar(region); for(; ci; ci = ci->next) { AllocVar(region); region->chrom = cloneString(ci->chrom); region->end = ci->size; region->fullChrom = TRUE; region->name = NULL; /* unused for full chrom */ slAddHead(®ionList, region); } slSort(®ionList, regionCmp); return regionList; } struct region *getRegionsFullGenome() /* Get a region list that covers all of each chromosome. */ { if (trackHubDatabase(database)) return getRegionsFullGenomeHub(); return getRegionsFullGenomeLocal(); } struct region *getEncodeRegions() /* Get encode regions from encodeRegions table. */ { struct sqlConnection *conn = hAllocConn(database); struct sqlResult *sr; char **row; struct region *list = NULL, *region; sr = sqlGetResult(conn, "NOSQLINJ select chrom,chromStart,chromEnd,name from encodeRegions order by name desc"); while ((row = sqlNextRow(sr)) != NULL) { AllocVar(region); region->chrom = cloneString(row[0]); region->start = atoi(row[1]); region->end = atoi(row[2]); region->name = cloneString(row[3]); /* encode region name */ slAddHead(&list, region); } sqlFreeResult(&sr); hFreeConn(&conn); return list; } boolean searchPosition(char *range, struct region *region) /* Try and fill in region via call to hgFind. Return FALSE * if it can't find a single position. */ { struct hgPositions *hgp = NULL; char retAddr[512]; char position[512]; safef(retAddr, sizeof(retAddr), "%s", getScriptName()); hgp = findGenomePosWeb(database, range, ®ion->chrom, ®ion->start, ®ion->end, cart, TRUE, retAddr); if (hgp != NULL && hgp->singlePos != NULL) { safef(position, sizeof(position), "%s:%d-%d", region->chrom, region->start+1, region->end); cartSetString(cart, hgtaRange, position); return TRUE; } else if (region->start == 0) /* Confusing way findGenomePosWeb says pos not found. */ { cartSetString(cart, hgtaRange, hDefaultPos(database)); return FALSE; } else return FALSE; } boolean lookupPosition() /* Look up position (aka range) if need be. Return FALSE if it puts * up multiple positions. */ { char *range = cartUsualString(cart, hgtaRange, ""); boolean isSingle = TRUE; range = trimSpaces(range); if (range[0] != 0) { struct region r; isSingle = searchPosition(range, &r); if (!isSingle) { // In case user manually edits the browser location as described in #13009, // revert the position. If they instead choose from the list as we expect, // that will set the position to their choice. char *lastPosition = cartUsualString(cart, "lastPosition", hDefaultPos(database)); cartSetString(cart, "position", lastPosition); } } else { cartSetString(cart, hgtaRange, hDefaultPos(database)); } return isSingle; } struct region *getRegions() /* Consult cart to get list of regions to work on. */ { char *regionType = cartUsualString(cart, hgtaRegionType, "genome"); struct region *regionList = NULL, *region; if (sameString(regionType, hgtaRegionTypeGenome)) { regionList = getRegionsFullGenome(); } else if (sameString(regionType, hgtaRegionTypeRange)) { char *range = cartString(cart, hgtaRange); boolean parseOk = FALSE; regionList = AllocVar(region); if (! strchr(range, ':')) parseOk = ((region->chrom = hgOfficialChromName(database, range)) != NULL); else parseOk = hgParseChromRange(database, range, ®ion->chrom, ®ion->start, ®ion->end); if (! parseOk) { errAbort("Bad position %s, please enter something else in position box", range); } region->name = NULL; /* unused for range */ } else if (sameString(regionType, hgtaRegionTypeEncode)) { regionList = getEncodeRegions(); } else if (sameString(regionType, hgtaRegionTypeUserRegions) && (NULL != userRegionsFileName())) { regionList = getUserRegions(userRegionsFileName()); } else { regionList = getRegionsFullGenome(); } return regionList; } char *getRegionName() /* Get a name for selected region. Don't free this. */ { char *region = cartUsualString(cart, hgtaRegionType, "genome"); if (sameString(region, "range")) region = cartUsualString(cart, hgtaRange, "n/a"); return region; } struct sqlResult *regionQuery(struct sqlConnection *conn, char *table, char *fields, struct region *region, boolean isPositional, char *extraWhere) /* Construct and execute query for table on region. Returns NULL if * table doesn't exist (e.g. missing split table for region->chrom). */ { struct sqlResult *sr; if (isPositional) { /* Check for missing split tables before querying: */ char *db = sqlGetDatabase(conn); struct hTableInfo *hti = hFindTableInfo(db, region->chrom, table); if (hti == NULL) return NULL; else if (hti->isSplit) { char fullTableName[256]; safef(fullTableName, sizeof(fullTableName), "%s_%s", region->chrom, table); if (!sqlTableExists(conn, fullTableName)) return NULL; } if (region->fullChrom) /* Full chromosome. */ { sr = hExtendedChromQuery(conn, table, region->chrom, extraWhere, FALSE, fields, NULL); } else { sr = hExtendedRangeQuery(conn, table, region->chrom, region->start, region->end, extraWhere, TRUE, fields, NULL); } } else { struct dyString *query = dyStringNew(0); sqlDyStringPrintf(query, "select %-s from %s", sqlCkIl(fields), table); if (extraWhere) { dyStringAppend(query, " where "); dyStringAppend(query, extraWhere); } sr = sqlGetResult(conn, query->string); dyStringFree(&query); } return sr; } char *getDbTable(char *db, char *table) /* If table already contains its real database as a dot-prefix, then * return a clone of table; otherwise alloc and return db.table . */ { if (sameString(table, WIKI_TRACK_TABLE)) { char dbTable[256]; safef(dbTable, sizeof(dbTable), "%s.%s", wikiDbName(), WIKI_TRACK_TABLE); return cloneString(dbTable); } else if (strchr(table, '.') != NULL) return cloneString(table); else { char dbTable[256]; safef(dbTable, sizeof(dbTable), "%s.%s", db, table); return cloneString(dbTable); } } char *connectingTableForTrack(char *rawTable) /* Return table name to use with all.joiner for track. * You can freeMem this when done. */ { return cloneString(rawTable); } char *chromTable(struct sqlConnection *conn, char *table) /* Get chr1_table if it exists, otherwise table. * You can freeMem this when done. */ { if (isHubTrack(table)) return cloneString(table); else { char *chrom = hDefaultChrom(database); if (sqlTableExists(conn, table)) return cloneString(table); else { char buf[256]; safef(buf, sizeof(buf), "%s_%s", chrom, table); return cloneString(buf); } } } struct hTableInfo *hubTrackTableInfo(struct trackDb *tdb) /* Given trackDb entry for a hub track, wrap table info around it. */ { struct hTableInfo *hti = NULL; if (tdb->subtracks == NULL) { if (startsWithWord("bigBed", tdb->type) || startsWithWord("bigGenePred", tdb->type)) hti = bigBedToHti(tdb->table, NULL); else if (startsWithWord("bam", tdb->type)) hti = bamToHti(tdb->table); else if (startsWithWord("vcfTabix", tdb->type)) hti = vcfToHti(tdb->table, TRUE); } if (hti == NULL) { AllocVar(hti); hti->rootName = cloneString(tdb->track); hti->isPos = TRUE; hti->type = cloneString(tdb->type); } return hti; } struct hTableInfo *maybeGetHti(char *db, char *table, struct sqlConnection *conn) /* Return primary table info, but don't abort if table not there. Conn should be open to db. */ { struct hTableInfo *hti = NULL; boolean isTabix = FALSE; if (isHubTrack(table)) { struct trackDb *tdb = hashMustFindVal(fullTableToTdbHash, table); hti = hubTrackTableInfo(tdb); } else if (isBigBed(database, table, curTrack, ctLookupName)) hti = bigBedToHti(table, conn); else if (isBamTable(table)) hti = bamToHti(table); else if (isVcfTable(table, &isTabix)) { boolean isTabix = trackIsType(database, table, curTrack, "vcfTabix", ctLookupName); hti = vcfToHti(table, isTabix); } else if (isCustomTrack(table)) { struct customTrack *ct = ctLookupName(table); hti = ctToHti(ct); } else if (sameWord(table, WIKI_TRACK_TABLE)) { hti = wikiHti(); } else { char *track; if (startsWith("chrN_", table)) track = table + strlen("chrN_"); else track = table; hti = hFindTableInfo(db, NULL, track); } return(hti); } struct hTableInfo *getHti(char *db, char *table, struct sqlConnection *conn) /* Return primary table info. */ { struct hTableInfo *hti = maybeGetHti(db, table, conn); if (hti == NULL) { errAbort("Could not find table info for table %s in db %s", table, db); } return(hti); } struct hTableInfo *getHtiOnDb(char *db, char *table) /* Return primary table info. */ { struct sqlConnection *conn = hAllocConn(db); struct hTableInfo *hti = getHti(db, table, conn); hFreeConn(&conn); return hti; } struct hTableInfo *maybeGetHtiOnDb(char *db, char *table) /* Return primary table info, but don't abort if table not there. */ { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = hAllocConn(db); struct hTableInfo *hti = maybeGetHti(db, table, conn); hFreeConn(&conn); return hti; } boolean isPositional(char *db, char *table) /* Return TRUE if it looks to be a positional table. */ { boolean result = FALSE; struct sqlConnection *conn = hAllocConn(db); if (sqlTableExists(conn, "chromInfo")) { char chromName[64]; struct hTableInfo *hti; sqlQuickQuery(conn, "NOSQLINJ select chrom from chromInfo limit 1", chromName, sizeof(chromName)); hti = hFindTableInfo(db, chromName, table); if (hti != NULL) { result = htiIsPositional(hti); } } hFreeConn(&conn); return result; } boolean isSqlStringType(char *type) /* Return TRUE if type is a stringish SQL type. */ { return strstr(type, "char") || strstr(type, "text") || strstr(type, "blob"); } boolean isSqlEnumType(char *type) /* Return TRUE if type is an enum. */ { return startsWith("enum", type); } boolean isSqlSetType(char *type) /* Return TRUE if type is a set. */ { return startsWith("set", type); } boolean isSqlNumType(char *type) /* Return TRUE if it is a numerical SQL type. */ { return strstr(type, "int") || strstr(type, "float") || strstr(type, "double"); } boolean isSqlIntType(char *type) /* Return TRUE if it is an integer SQL type. */ { return (strstr(type, "int") != NULL); } struct sqlFieldType *sqlFieldTypeNew(char *name, char *type) /* Create a new sqlFieldType */ { struct sqlFieldType *ft; AllocVar(ft); ft->name = cloneString(name); ft->type = cloneString(type); return ft; } void sqlFieldTypeFree(struct sqlFieldType **pFt) /* Free resources used by sqlFieldType */ { struct sqlFieldType *ft = *pFt; if (ft != NULL) { freeMem(ft->name); freeMem(ft->type); freez(pFt); } } void sqlFieldTypeFreeList(struct sqlFieldType **pList) /* Free a list of dynamically allocated sqlFieldType's */ { struct sqlFieldType *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; sqlFieldTypeFree(&el); } *pList = NULL; } struct sqlFieldType *sqlListFieldsAndTypes(struct sqlConnection *conn, char *table) /* Get list of fields including their names and types. The type currently is just * a MySQL type string. */ { struct sqlFieldType *ft, *list = NULL; char query[512]; struct sqlResult *sr; char **row; sqlSafef(query, sizeof(query), "describe %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { ft = sqlFieldTypeNew(row[0], row[1]); slAddHead(&list, ft); } sqlFreeResult(&sr); slReverse(&list); return list; } static struct trackDb *findTrackInGroup(char *name, struct trackDb *trackList, struct grp *group) /* Find named track that is in group (NULL for any group). * Return NULL if can't find it. */ { struct trackDb *track; if (group != NULL && sameString(group->name, "all")) group = NULL; for (track = trackList; track != NULL; track = track->next) { if (sameString(name, track->track) && (group == NULL || sameString(group->name, track->grp))) return track; if (track->subtracks) { struct trackDb *subtrack = findTrackInGroup(name, track->subtracks, group); if (subtrack != NULL) return subtrack; } } return NULL; } struct trackDb *findTrack(char *name, struct trackDb *trackList) /* Find track, or return NULL if can't find it. */ { return findTrackInGroup(name, trackList, NULL); } struct trackDb *mustFindTrack(char *name, struct trackDb *trackList) /* Find track or squawk and die. */ { struct trackDb *track = findTrack(name, trackList); if (track == NULL) { if (isCustomTrack(name)) errAbort("Can't find custom track %s. " "If it's been 8 hours since you accessed this track you " "may just need to upload it again.", name); else errAbort("Track %s doesn't exist in database %s.", name, database); } return track; } struct trackDb *findSelectedTrack(struct trackDb *trackList, struct grp *group, char *varName) /* Find selected track - from CGI variable if possible, else * via various defaults. */ { char *name = cartOptionalString(cart, varName); struct trackDb *track = NULL; if (name != NULL) { track = findTrackInGroup(name, trackList, group); } if (track == NULL) { if (group == NULL || sameString(group->name, "all")) track = trackList; else { for (track = trackList; track != NULL; track = track->next) if (sameString(track->grp, group->name)) break; } } return track; } static struct grp *findGroup(struct grp *groupList, char *name) /* Return named group in list, or NULL if not found. */ { struct grp *group; for (group = groupList; group != NULL; group = group->next) if (sameString(name, group->name)) return group; return NULL; } struct grp *findSelectedGroup(struct grp *groupList, char *cgiVar) /* Find user-selected group if possible. If not then * go to various levels of defaults. */ { char *defaultGroup = "genes"; char *name = cartUsualString(cart, cgiVar, defaultGroup); struct grp *group = findGroup(groupList, name); if (group == NULL) group = findGroup(groupList, defaultGroup); if (group == NULL) group = groupList; return group; } static char *findSelectedTable(struct trackDb *track, char *var) /* Find selected table. Default to main track table if none * found. */ { if (track == NULL) return cartString(cart, var); else if (isCustomTrack(track->table)) return track->table; else { struct slName *tableList = cartTrackDbTablesForTrack(database, track, TRUE); char *table = cartUsualString(cart, var, tableList->name); if (slNameInList(tableList, table)) return table; return tableList->name; } } void addWhereClause(struct dyString *query, boolean *gotWhere) /* Add where clause to query. If already have a where clause * add 'and' to it. */ { if (*gotWhere) { dyStringAppend(query, " and "); } else { dyStringAppend(query, " where "); *gotWhere = TRUE; } } boolean htiIsPositional(struct hTableInfo *hti) /* Return TRUE if hti looks like it's from a positional table. */ { return isCustomTrack(hti->rootName) || hti->isPos; #ifdef OLD ((hti->startField[0] && hti->endField[0]) && (hti->chromField[0] || sameString(hti->rootName, "gl"))); #endif /* OLD */ } char *getIdField(char *db, struct trackDb *track, char *table, struct hTableInfo *hti) /* Get ID field for table, or NULL if none. FreeMem result when done */ { char *idField = NULL; if (hti != NULL && hti->nameField[0] != 0) idField = cloneString(hti->nameField); -else if (track != NULL) +else if (track != NULL && !tdbIsComposite(track)) { struct hTableInfo *trackHti = maybeGetHtiOnDb(db, track->table); if (trackHti != NULL && isCustomTrack(table)) idField = cloneString(trackHti->nameField); else if (hti != NULL && trackHti != NULL && trackHti->nameField[0] != 0) { struct joinerPair *jp, *jpList; jpList = joinerRelate(allJoiner, db, track->table); for (jp = jpList; jp != NULL; jp = jp->next) { if (sameString(jp->a->field, trackHti->nameField)) { if ( sameString(jp->b->database, db) && sameString(jp->b->table, table) ) { idField = cloneString(jp->b->field); break; } } } joinerPairFreeList(&jpList); } } /* If we haven't found the answer but this looks like a non-positional table, * use the first field. */ if (idField == NULL && !isCustomTrack(table) && (hti == NULL || !hti->isPos)) { struct sqlConnection *conn = track ? hAllocConnTrack(db, track) : hAllocConn(db); struct slName *fieldList = sqlListFields(conn, table); if (fieldList == NULL) errAbort("getIdField: Can't find fields of table %s", table); idField = cloneString(fieldList->name); slFreeList(&fieldList); hFreeConn(&conn); } return idField; } int countTableColumns(struct sqlConnection *conn, char *table) /* Count columns in table. */ { char *splitTable = chromTable(conn, table); int count = sqlCountColumnsInTable(conn, splitTable); freez(&splitTable); return count; } #if defined(__GNUC__) static void hOrFPrintf(FILE *f, char *format, ...) __attribute__((format(printf, 2, 3))); #endif static void hOrFPrintf(FILE *f, char *format, ...) /* fprintf if f is non-null, else hPrintf. */ { va_list(args); va_start(args, format); if (f != NULL) { vfprintf(f, format, args); if (ferror(f)) noWarnAbort(); } else hvPrintf(format, args); va_end(args); } static void itemRgbDataOut(FILE *f, char **row, int lastCol, int itemRgbCol) /* display bed data, show "reserved" column as r,g,b */ { int colIx; int rgb; /* Print up to itemRgbCol */ for (colIx = 0; (colIx < itemRgbCol) && (colIx < lastCol); ++colIx) hOrFPrintf(f, "%s\t", row[colIx]); /* Print out the itemRgbCol column */ rgb = atoi(row[itemRgbCol]); hOrFPrintf(f, "%d,%d,%d", (rgb & 0xff0000) >> 16, (rgb & 0xff00) >> 8, (rgb & 0xff)); /* Print the rest if there are any */ if (itemRgbCol < lastCol) { hOrFPrintf(f, "\t"); for (colIx = itemRgbCol+1; colIx < lastCol; ++colIx) hOrFPrintf(f, "%s\t", row[colIx]); hOrFPrintf(f, "%s\n", row[lastCol]); } else hOrFPrintf(f, "\n"); /* itemRgbCol was the last column */ } static int itemRgbHeader(FILE *f, struct sqlResult *sr, int lastCol) /* print out bed header, recognize "reserved" column, return which * column it is, or -1 if not found */ { int colIx; int ret = -1; char *field = sqlFieldName(sr); for (colIx = 0; colIx < lastCol; ++colIx) { if (sameWord("reserved",field)) { hOrFPrintf(f, "itemRgb\t"); ret = colIx; } else hOrFPrintf(f, "%s\t", field); field = sqlFieldName(sr); } if (sameWord("reserved",field)) { hOrFPrintf(f, "itemRgb\n"); ret = lastCol; } else hOrFPrintf(f, "%s\n", field); return(ret); } void doTabOutDb( char *db, char *dbVarName, char *table, char *tableVarName, FILE *f, struct sqlConnection *conn, char *fields) /* Do tab-separated output on fields of a single table. */ { struct region *regionList = getRegions(); struct region *region; struct hTableInfo *hti = NULL; struct dyString *fieldSpec = newDyString(256); struct hash *idHash = NULL; int outCount = 0; boolean isPositional; int fieldCount; char *idField; boolean showItemRgb = FALSE; int itemRgbCol = -1; /* -1 means not found */ boolean printedColumns = FALSE; struct trackDb *tdb = findTdbForTable(db, curTrack, table, ctLookupName); hti = getHti(db, table, conn); idField = getIdField(db, curTrack, table, hti); showItemRgb=bedItemRgb(tdb); /* should we expect itemRgb instead of "reserved" */ /* If they didn't pass in a field list assume they want all fields. */ if (fields != NULL) { dyStringAppend(fieldSpec, sqlCkIl(fields)); fieldCount = countChars(fields, ',') + 1; } else { dyStringAppend(fieldSpec, "*"); fieldCount = countTableColumns(conn, table); } /* If can find id field for table then get * uploaded list of identifiers, create identifier hash * and add identifier column to end of result set. */ char *identifierFilter = NULL; if (idField != NULL) { idHash = identifierHash(db, table); if (idHash != NULL) { identifierFilter = identifierWhereClause(idField, idHash); if (isEmpty(identifierFilter)) { dyStringAppendC(fieldSpec, ','); dyStringAppend(fieldSpec, sqlCkId(idField)); } } } isPositional = htiIsPositional(hti); /* Loop through each region. */ for (region = regionList; region != NULL; region = region->next) { struct sqlResult *sr; char **row; int colIx, lastCol = fieldCount-1; char *filter = filterClause(dbVarName, tableVarName, region->chrom, identifierFilter); sr = regionQuery(conn, table, fieldSpec->string, region, isPositional, filter); if (sr == NULL) continue; /* First time through print column names. */ if (! printedColumns) { // Show only the SQL filter built from filter page options, not identifierFilter, // because identifierFilter can get enormous (like 126kB for 12,500 rsIDs). char *filterNoIds = filterClause(dbVarName, tableVarName, region->chrom, NULL); if (filterNoIds != NULL) hOrFPrintf(f, "#filter: %s\n", filterNoIds); hOrFPrintf(f, "#"); if (showItemRgb) { itemRgbCol = itemRgbHeader(f, sr, lastCol); if (itemRgbCol == -1) showItemRgb = FALSE; /* did not find "reserved" */ } else { for (colIx = 0; colIx < lastCol; ++colIx) hOrFPrintf(f, "%s\t", sqlFieldName(sr)); hOrFPrintf(f, "%s\n", sqlFieldName(sr)); } printedColumns = TRUE; } while ((row = sqlNextRow(sr)) != NULL) { if (idHash == NULL || isNotEmpty(identifierFilter) || hashLookup(idHash, row[fieldCount])) { if (showItemRgb) itemRgbDataOut(f, row, lastCol, itemRgbCol); else { for (colIx = 0; colIx < lastCol; ++colIx) hOrFPrintf(f, "%s\t", row[colIx]); hOrFPrintf(f, "%s\n", row[lastCol]); } ++outCount; } } sqlFreeResult(&sr); if (!isPositional) break; /* No need to iterate across regions in this case. */ freez(&filter); } /* Do some error diagnostics for user. */ if (outCount == 0) explainWhyNoResults(f); hashFree(&idHash); } void doTabOutTable( char *db, char *table, FILE *f, struct sqlConnection *conn, char *fields) /* Do tab-separated output on fields of a single table. */ { boolean isTabix = FALSE; if (isBigBed(database, table, curTrack, ctLookupName)) bigBedTabOut(db, table, conn, fields, f); else if (isBamTable(table)) bamTabOut(db, table, conn, fields, f); else if (isVcfTable(table, &isTabix)) vcfTabOut(db, table, conn, fields, f, isTabix); else if (isCustomTrack(table)) { doTabOutCustomTracks(db, table, conn, fields, f); } else doTabOutDb(db, db, table, table, f, conn, fields); } struct slName *fullTableFields(char *db, char *table) /* Return list of fields in db.table.field format. */ { char dtBuf[256]; struct sqlConnection *conn=NULL; struct slName *fieldList = NULL, *dtfList = NULL, *field, *dtf; if (isBigBed(database, table, curTrack, ctLookupName)) { if (!trackHubDatabase(database)) conn = hAllocConn(db); fieldList = bigBedGetFields(table, conn); hFreeConn(&conn); } else if (isHalTable(table)) fieldList = getBedFields(6); else if (isBamTable(table)) fieldList = bamGetFields(table); else if (isVcfTable(table, NULL)) fieldList = vcfGetFields(table); else if (isCustomTrack(table)) { struct customTrack *ct = ctLookupName(table); char *type = ct->dbTrackType; if (type != NULL) { conn = hAllocConn(CUSTOM_TRASH); if (startsWithWord("maf", type) || startsWithWord("makeItems", type) || sameWord("bedDetail", type) || sameWord("pgSnp", type)) fieldList = sqlListFields(conn, ct->dbTableName); hFreeConn(&conn); } if (fieldList == NULL) fieldList = getBedFields(ct->fieldCount); } else { char *splitTable; dbOverrideFromTable(dtBuf, &db, &table); conn = hAllocConn(db); splitTable = chromTable(conn, table); fieldList = sqlListFields(conn, splitTable); freez(&splitTable); hFreeConn(&conn); } for (field = fieldList; field != NULL; field = field->next) { char buf[256]; safef(buf, sizeof(buf), "%s.%s.%s", db, table, field->name); dtf = slNameNew(buf); slAddHead(&dtfList, dtf); } slReverse(&dtfList); slFreeList(&fieldList); return dtfList; } void doOutPrimaryTable(char *table, struct sqlConnection *conn) /* Dump out primary table. */ { if (anySubtrackMerge(database, table)) errAbort("Can't do all fields output when subtrack merge is on. " "Please go back and select another output type (BED or custom track is good), or clear the subtrack merge."); if (anyIntersection()) errAbort("Can't do all fields output when intersection is on. " "Please go back and select another output type (BED or custom track is good), or clear the intersection."); textOpen(); if (sameWord(table, WIKI_TRACK_TABLE)) tabOutSelectedFields(wikiDbName(), table, NULL, fullTableFields(wikiDbName(), table)); else tabOutSelectedFields(database, table, NULL, fullTableFields(database, table)); } void ensureVisibility(char *db, char *table, struct trackDb *tdb) /* Check track visibility; if hide, print out CGI to set it to pack or full. */ { enum trackVisibility vis = tvHide; char *cartVis = cartOptionalString(cart, table); if (isNotEmpty(cartVis)) vis = hTvFromString(cartVis); else { if (tdb == NULL) tdb = hTrackDbForTrackAndAncestors(db, table); if (tdb != NULL) { cartVis = cartOptionalString(cart, tdb->track); if (isNotEmpty(cartVis)) vis = hTvFromString(cartVis); else vis = tdb->visibility; } } if (vis == tvHide) { enum trackVisibility openVis = tvFull; if (tdb != NULL) { if (tdb->canPack) openVis = tvPack; hPrintf("&%s=%s", table, hStringFromTv(openVis)); if (!sameString(table, tdb->track)) hPrintf("&%s_sel=1", table); } else hPrintf("&%s=%s", table, hStringFromTv(openVis)); } } void doOutHyperlinks(char *table, struct sqlConnection *conn) /* Output as genome browser hyperlinks. */ { char *table2 = cartOptionalString(cart, hgtaIntersectTrack); int outputPad = cartUsualInt(cart, hgtaOutputPad,0); struct region *region, *regionList = getRegions(); char posBuf[64]; int count = 0; htmlOpen("Hyperlinks to Genome Browser"); for (region = regionList; region != NULL; region = region->next) { struct lm *lm = lmInit(64*1024); struct bed *bedList, *bed; bedList = cookedBedList(conn, table, region, lm, NULL); for (bed = bedList; bed != NULL; bed = bed->next) { char *name; int start = max(0,bed->chromStart+1-outputPad); int end = min(hChromSize(database, bed->chrom),bed->chromEnd+outputPad); safef(posBuf, sizeof(posBuf), "%s:%d-%d", bed->chrom, start, end); /* Construct browser anchor URL with tracks we're looking at open. */ if (doGalaxy()) { char *s, *script = hgTracksName(); s = strstr(script, "cgi-bin"); hPrintf("<A HREF=\"http://%s/%s?db=%s", cgiServerNamePort(), s, database); } else hPrintf("<A HREF=\"%s?db=%s", hgTracksName(), database); hPrintf("&position=%s", posBuf); ensureVisibility(database, table, curTrack); if (table2 != NULL) { struct trackDb *tdb2 = findTrack(table2, fullTrackList); ensureVisibility(database, table2, tdb2); } hPrintf("\" TARGET=_blank>"); name = bed->name; if (bed->name == NULL) name = posBuf; if (sameString(name, posBuf)) hPrintf("%s", posBuf); else { char *tmp = htmlEncode(name); hPrintf("%s at %s", tmp, posBuf); freeMem(tmp); } hPrintf("</A><BR>\n"); ++count; } lmCleanup(&lm); } if (count == 0) hPrintf(NO_RESULTS); htmlClose(); } /* Remove any meta data variables from the cart. (Copied from above!) */ void removeMetaData() { cartRemove(cart, "hgta_metaStatus"); cartRemove(cart, "hgta_metaVersion"); cartRemove(cart, "hgta_metaDatabases"); cartRemove(cart, "hgta_metaTables"); } void doMetaData(struct sqlConnection *conn) /* Get meta data for a database. */ { puts("Content-Type:text/plain\n"); char *query = ""; if (cartVarExists(cart, hgtaMetaStatus)) { printf("Table status for database %s\n", database); query = "NOSQLINJ SHOW TABLE STATUS"; } else if (cartVarExists(cart, hgtaMetaVersion)) { query = "NOSQLINJ SELECT @@VERSION"; } else if (cartVarExists(cart, hgtaMetaDatabases)) { query = "NOSQLINJ SHOW DATABASES"; } else if (cartVarExists(cart, hgtaMetaTables)) { query = "NOSQLINJ SHOW TABLES"; } struct sqlResult *sr; char **row; char *sep=""; int c = 0; int numCols = 0; sr = sqlGetResult(conn, query); numCols = sqlCountColumns(sr); char *field; while ((field = sqlFieldName(sr)) != NULL) printf("%s \t", field); printf("\n"); while ((row = sqlNextRow(sr)) != NULL) { sep=""; for (c=0;c<numCols;++c) { printf("%s%s",sep,row[c]); sep = "\t"; } fprintf(stdout, "\n"); } sqlFreeResult(&sr); removeMetaData(); } void dispatch(); void doTopSubmit(struct sqlConnection *conn) /* Respond to submit button on top level page. * This basically just dispatches based on output type. */ { char *output = cartString(cart, hgtaOutputType); char *trackName = NULL; char *table = cartString(cart, hgtaTable); struct trackDb *track = NULL; hgBotDelay(); if (!sameString(curGroup->name, "allTables")) { trackName = cartString(cart, hgtaTrack); track = mustFindTrack(trackName, fullTrackList); } else { struct trackDb *cTdb = NULL; track = hTrackDbForTrack(database, table); cTdb = hCompositeTrackDbForSubtrack(database, track); if (cTdb) track = cTdb; } if (track != NULL) { if (sameString(track->table, "gvPos") && !cartVarExists(cart, "gvDisclaimer")) { /* display disclaimer and add flag to cart, program exits from here */ htmlStart("Table Browser"); gvDisclaimer(); } else if (sameString(track->table, "gvPos") && sameString(cartString(cart, "gvDisclaimer"), "Disagree")) { cartRemove(cart, "gvDisclaimer"); cartRemove(cart, hgtaDoTopSubmit); cartSetString(cart, hgtaDoMainPage, "return to table browser"); dispatch(); return; } } if (doGenomeSpace()) { if (!checkGsReady()) return; } if (doGreat()) verifyGreatFormat(output); if (sameString(output, outPrimaryTable)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else doOutPrimaryTable(table, conn); } else if (sameString(output, outSelectedFields)) doOutSelectedFields(table, conn); else if (sameString(output, outSequence)) doOutSequence(conn); else if (sameString(output, outMicroarrayNames)) doOutMicroarrayNames(track); else if (sameString(output, outBed)) doOutBed(table, conn); else if (sameString(output, outCustomTrack)) doOutCustomTrack(table, conn); else if (sameString(output, outPalOptions)) doOutPalOptions( conn); else if (sameString(output, outGff)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else doOutGff(table, conn, TRUE); } else if (sameString(output, outHyperlinks)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else doOutHyperlinks(table, conn); } else if (sameString(output, outWigData)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else doOutWigData(track, table, conn); } else if (sameString(output, outWigBed)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else if (doGreat() && !cgiOptionalString(hgtaDoGreatQuery)) doGreatTopLevel(); else doOutWigBed(track, table, conn); } else if (sameString(output, outMaf)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else if (isHalTable(table)) doHalMaf(track, table, conn); else doOutMaf(track, table, conn); } else if (sameString(output, outChromGraphData)) { if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoTopSubmit, "get output"); else doOutChromGraphDataCt(track, table); } else errAbort("Don't know how to handle %s output yet", output); } void dispatch() /* Scan for 'do' variables and dispatch to appropriate page-generator. * By default head to the main page. */ { struct hashEl *varList; struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = curTrack ? hAllocConnTrack(database, curTrack) : hAllocConn(database); pushWarnHandler(earlyAbortHandler); /* only allows view table schema function for CGB or GSID servers for the time being */ if (hIsCgbServer() || hIsGsidServer()) { if (cartVarExists(cart, hgtaDoSchema)) { doSchema(conn); } else { if (cartVarExists(cart, hgtaDoValueRange)) { doValueRange(cartString(cart, hgtaDoValueRange)); } else { if (cartVarExists(cart, hgtaDoValueHistogram)) { doValueHistogram(cartString(cart, hgtaDoValueHistogram)); } else { errAbort("Sorry, currently only the \"View Table Schema\" function of the Table Browser is available on this server."); } } } } else if (cartVarExists(cart, hgtaDoTest)) doTest(); else if (cartVarExists(cart, hgtaDoMainPage)) doMainPage(conn); else if (cartVarExists(cart, hgtaDoSchema)) doSchema(conn); else if (cartVarExists(cart, hgtaDoTopSubmit)) doTopSubmit(conn); else if (cartVarExists(cart, hgtaDoSummaryStats)) doSummaryStats(conn); else if (cartVarExists(cart, hgtaDoIntersectPage)) doIntersectPage(conn); else if (cartVarExists(cart, hgtaDoPalOut)) doGenePredPal(conn); else if (cartVarExists(cart, hgtaDoPal)) doOutPalOptions( conn); else if (cartVarExists(cart, hgtaDoClearIntersect)) doClearIntersect(conn); else if (cartVarExists(cart, hgtaDoIntersectMore)) doIntersectMore(conn); else if (cartVarExists(cart, hgtaDoIntersectSubmit)) doIntersectSubmit(conn); else if (cartVarExists(cart, hgtaDoCorrelatePage)) doCorrelatePage(conn); else if (cartVarExists(cart, hgtaDoClearCorrelate)) doClearCorrelate(conn); else if (cartVarExists(cart, hgtaDoClearContinueCorrelate)) doClearContinueCorrelate(conn); else if (cartVarExists(cart, hgtaDoCorrelateMore)) doCorrelateMore(conn); else if (cartVarExists(cart, hgtaDoCorrelateSubmit)) doCorrelateSubmit(conn); else if (cartVarExists(cart, hgtaDoPasteIdentifiers)) doPasteIdentifiers(conn); else if (cartVarExists(cart, hgtaDoClearPasteIdentifierText)) doClearPasteIdentifierText(conn); /* Respond to clear within paste identifier page. */ else if (cartVarExists(cart, hgtaDoPastedIdentifiers)) doPastedIdentifiers(conn); else if (cartVarExists(cart, hgtaDoUploadIdentifiers)) doUploadIdentifiers(conn); else if (cartVarExists(cart, hgtaDoClearIdentifiers)) doClearIdentifiers(conn); else if (cartVarExists(cart, hgtaDoFilterPage)) doFilterPage(conn); else if (cartVarExists(cart, hgtaDoFilterMore)) doFilterMore(conn); else if (cartVarExists(cart, hgtaDoFilterSubmit)) doFilterSubmit(conn); else if (cartVarExists(cart, hgtaDoClearFilter)) doClearFilter(conn); else if (cartVarExists(cart, hgtaDoSchemaTable)) { doTableSchema( cartString(cart, hgtaDoSchemaDb), cartString(cart, hgtaDoSchemaTable), conn); } else if (cartVarExists(cart, hgtaDoValueHistogram)) doValueHistogram(cartString(cart, hgtaDoValueHistogram)); else if (cartVarExists(cart, hgtaDoValueRange)) doValueRange(cartString(cart, hgtaDoValueRange)); else if (cartVarExists(cart, hgtaDoSelectFieldsMore)) doSelectFieldsMore(); else if (cartVarExists(cart, hgtaDoPrintSelectedFields)) doPrintSelectedFields(); else if (cartVarExists(cart, hgtaDoGalaxySelectedFields)) sendParamsToGalaxy(hgtaDoPrintSelectedFields, "get output"); else if ((varList = cartFindPrefix(cart, hgtaDoClearAllFieldPrefix)) != NULL) doClearAllField(varList->name + strlen(hgtaDoClearAllFieldPrefix)); else if ((varList = cartFindPrefix(cart, hgtaDoSetAllFieldPrefix)) != NULL) doSetAllField(varList->name + strlen(hgtaDoSetAllFieldPrefix)); else if (cartVarExists(cart, hgtaDoGenePredSequence)) doGenePredSequence(conn); else if (cartVarExists(cart, hgtaDoGenomicDna)) if (doGalaxy() && !cgiOptionalString(hgtaDoGalaxyQuery)) sendParamsToGalaxy(hgtaDoGenomicDna, "submit"); else doGenomicDna(conn); else if (cartVarExists(cart, hgtaDoGetBed) || cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) doGetBed(conn); else if (cartVarExists(cart, hgtaDoGetCustomTrackTb)) doGetCustomTrackTb(conn); else if (cartVarExists(cart, hgtaDoGetCustomTrackGb)) doGetCustomTrackGb(conn); else if (cartVarExists(cart, hgtaDoGetCustomTrackFile)) doGetCustomTrackFile(conn); else if (cartVarExists(cart, hgtaDoRemoveCustomTrack)) doRemoveCustomTrack(conn); else if (cartVarExists(cart, hgtaDoClearSubtrackMerge)) doClearSubtrackMerge(conn); /* Hack but I don't know what else to do now: hCompositeUi makes a hidden * var for hgtaDoSubtrackMergePage, so that javascript can submit and it will * look like that button was pressed. However when the real submit button is * pressed, it will look like both were pressed... so check the real submit * button first (and check doMainPage before this too, for "cancel"!): */ else if (cartVarExists(cart, hgtaDoSubtrackMergeSubmit)) doSubtrackMergeSubmit(conn); else if (cartVarExists(cart, hgtaDoSubtrackMergePage)) doSubtrackMergePage(conn); else if (cartVarExists(cart, hgtaDoSetUserRegions)) doSetUserRegions(conn); else if (cartVarExists(cart, hgtaDoSubmitUserRegions)) doSubmitUserRegions(conn); else if (cartVarExists(cart, hgtaDoClearSetUserRegionsText)) doClearSetUserRegionsText(conn); else if (cartVarExists(cart, hgtaDoClearUserRegions)) doClearUserRegions(conn); else if (cartVarExists(cart, hgtaDoMetaData)) doMetaData(conn); else if (cartVarExists(cart, hgtaDoGsLogin)) { doGsLogin(conn); dispatch(); } else /* Default - put up initial page. */ doMainPage(conn); cartRemovePrefix(cart, hgtaDo); hFreeConn(&conn); } char *excludeVars[] = {"Submit", "submit", NULL}; static void rAddTablesToHash(struct trackDb *tdbList, struct hash *hash) /* Add tracks in list to hash, keyed by tdb->table*/ { struct trackDb *tdb; for (tdb = tdbList; tdb != NULL; tdb = tdb->next) { hashAdd(hash, tdb->table, tdb); if (tdb->subtracks) rAddTablesToHash(tdb->subtracks, hash); } } void initGroupsTracksTables() /* Get list of groups that actually have something in them, prepare hashes * containing all tracks and all tables. Set global variables that correspond * to the group, track, and table specified in the cart. */ { cartTrackDbInit(cart, &fullTrackList, &fullGroupList, TRUE); fullTableToTdbHash = hashNew(0); rAddTablesToHash(fullTrackList, fullTableToTdbHash); curTrack = findSelectedTrack(fullTrackList, NULL, hgtaTrack); // if there isn't a current track, then use the default group if (curTrack != NULL) curGroup = findSelectedGroup(fullGroupList, hgtaGroup); else curGroup = fullGroupList; if (sameString(curGroup->name, "allTables")) curTrack = NULL; curTable = findSelectedTable(curTrack, hgtaTable); if (curTrack == NULL) { struct trackDb *tdb = hTrackDbForTrack(database, curTable); struct trackDb *cTdb = hCompositeTrackDbForSubtrack(database, tdb); if (cTdb) curTrack = cTdb; else curTrack = tdb; } } void hgTables() /* hgTables - Get table data associated with tracks and intersect tracks. * Here we set up cart and some global variables, dispatch the command, * and put away the cart when it is done. */ { char *clade = NULL; setUdcCacheDir(); oldVars = hashNew(10); /* Sometimes we output HTML and sometimes plain text; let each outputter * take care of headers instead of using a fixed cart*Shell(). */ cart = cartAndCookieNoContent(hUserCookie(), excludeVars, oldVars); /* Set up global variables. */ allJoiner = joinerRead("all.joiner"); getDbGenomeClade(cart, &database, &genome, &clade, oldVars); freezeName = hFreezeFromDb(database); int timeout = cartUsualInt(cart, "udcTimeout", 300); if (udcCacheTimeout() < timeout) udcSetCacheTimeout(timeout); knetUdcInstall(); char *backgroundStatus = cartUsualString(cart, "backgroundStatus", NULL); if (backgroundStatus) { getBackgroundStatus(backgroundStatus); exit(0); } char *backgroundExec = cgiUsualString("backgroundExec", NULL); if (sameOk(backgroundExec,"gsSendToDM")) { gsSendToDM(); exit(0); } /* Init track and group lists and figure out what page to put up. */ initGroupsTracksTables(); if (lookupPosition()) { if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) doGetGreatOutput(dispatch); else dispatch(); } else { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = curTrack ? hAllocConnTrack(database, curTrack) : hAllocConn(database); webPushErrHandlersCartDb(cart, database); mainPageAfterOpen(conn); hFreeConn(&conn); webPopErrHandlers(); } textOutClose(&compressPipeline, &saveStdout); if (doGenomeSpace()) { if (gsTemp) { cartSetString(cart, "gsTemp", gsTemp); char *workUrl = NULL; startBackgroundWork("./hgTables backgroundExec=gsSendToDM", &workUrl); htmlOpen("Uploading Output to GenomeSpace"); puts("<script type=\"text/JavaScript\">"); puts("<!--"); printf("setTimeout(\"location = 'hgTables?backgroundStatus=%s';\",2000);\n", cgiEncode(workUrl)); // was 10000? puts("-->"); puts("</script>"); gsTemp = NULL; } } /* Save variables. */ cartCheckout(&cart); } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); pushCarefulMemHandler(LIMIT_2or6GB); htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ cgiSpoof(&argc, argv); hgTables(); cgiExitTime("hgTables", enteredMainTime); return 0; }