44ccfacbe3a3d4b300f80d48651c77837a4b571e galt Tue Apr 26 11:12:02 2022 -0700 SQL INJECTION Prevention Version 2 - this improves our methods by making subclauses of SQL that get passed around be both easy and correct to use. The way that was achieved was by getting rid of the obscure and not well used functions sqlSafefFrag and sqlDyStringPrintfFrag and replacing them with the plain versions of those functions, since these are not needed anymore. The new version checks for NOSQLINJ in unquoted %-s which is used to include SQL clauses, and will give an error the NOSQLINJ clause is not present, and this will automatically require the correct behavior by developers. sqlDyStringPrint is a very useful function, however because it was not enforced, users could use various other dyString functions and they operated without any awareness or checking for SQL correct use. Now those dyString functions are prohibited and it will produce an error if you try to use a dyString function on a SQL string, which is simply detected by the presence of the NOSQLINJ prefix. diff --git src/hg/hgTables/hgTables.c src/hg/hgTables/hgTables.c index 3a0df73..60071c9 100644 --- src/hg/hgTables/hgTables.c +++ src/hg/hgTables/hgTables.c @@ -1,1809 +1,1815 @@ /* hgTables - Main and utility functions for table browser. */ /* Copyright (C) 2014 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 "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" #include "genbank.h" #include "windowsToAscii.h" #include "chromAlias.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; static boolean issueBotWarning = FALSE; 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); // hgBotDelay(); function is now in earlyBotCheck() at the start of main() } 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. */ { // hgBotDelay function is now in earlyBotCheck() at the start of main(), and in // this case, the issueBotWarning flag is ignored to avoid any output here // hgBotDelayNoWarn(); // delay but suppress warning at 10-20 sec delay level because this is not html output. char *fileName = textOutSanitizeHttpFileName(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"); } boolean isNoGenomeDisabled(char *db, char *table) /* Return TRUE if table (or a track with which it is associated) has 'tableBrowser noGenome' * and region is genome. */ { return (fullGenomeRegion() && cartTrackDbIsNoGenome(db, table)); } void checkNoGenomeDisabled(char *db, char *table) /* Before producing output, make sure that the URL hasn't been hacked to make a * genome-wide query on a noGenome table. */ { if (isNoGenomeDisabled(db, table)) errAbort("Can't do genome-wide query on %s. " "Please go back and choose a position range.", table); } 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"); +char query[1024]; +sqlSafef(query, sizeof query, "select chrom,size from chromInfo"); +sr = sqlGetResult(conn, query); 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"); +char query[1024]; +sqlSafef(query, sizeof query, "select chrom,chromStart,chromEnd,name from encodeRegions order by name desc"); +sr = sqlGetResult(conn, query); 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; } struct hgPositions *lookupPosition(struct dyString *dyWarn) /* Look up position (aka range) if need be. Return a container of matching tables and positions. * Warnings/errors are appended to dyWarn. */ { char *range = windowsToAscii(cloneString(cartUsualString(cart, hgtaRange, ""))); range = trimSpaces(range); if (isEmpty(range)) range = hDefaultPos(database); struct hgPositions *hgp = hgFindSearch(cart, &range, NULL, NULL, NULL, getScriptName(), dyWarn); cartSetString(cart, hgtaRange, range); return hgp; } boolean isRegionWholeGenome() /* Return TRUE if the current region is the whole genome. */ { char *regionType = cartString(cart, hgtaRegionType); if (regionType == NULL) return TRUE; if (sameString(regionType, hgtaRegionTypeGenome)) return TRUE; return FALSE; } 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); + sqlCkIl(fieldsSafe,fields) + sqlDyStringPrintf(query, "select %-s from %s", fieldsSafe, table); if (extraWhere) { - dyStringAppend(query, " where "); - dyStringAppend(query, extraWhere); + sqlDyStringPrintf(query, " where %-s", 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) || startsWithWord("bigNarrowPeak", tdb->type)) hti = bigBedToHti(tdb->table, NULL); else if (startsWithWord("longTabix", tdb->type)) hti = longTabixToHti(tdb->table); else if (startsWithWord("bam", tdb->type)) hti = bamToHti(tdb->table); else if (startsWithWord("vcfTabix", tdb->type)) hti = vcfToHti(tdb->table, TRUE); else if (sameWord("hic", tdb->type)) hti = hicToHti(tdb->table); } 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 (isBigWigTable(table)) hti = bigWigToHti(table); else if (isLongTabixTable(table)) hti = longTabixToHti(table); 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 (isHicTable(table)) hti = hicToHti(table); 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)); + char query[1024]; + sqlSafef(query, sizeof query, "select chrom from chromInfo limit 1"); + sqlQuickQuery(conn, query, 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); } 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 composite track if given a subtrack name (e.g. hg19 refGene track to // hg38 refSeqComposite, #19920) return track; } } 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 "); + sqlDyStringPrintf(query, " and "); } else { - dyStringAppend(query, " where "); + sqlDyStringPrintf(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 && !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, NULL); 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, char outSep) /* 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 dyString *fieldSpec = dyStringNew(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)); + dyStringAppend(fieldSpec, 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)); + dyStringAppend(fieldSpec, 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) { if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%s", sqlFieldName(sr)); if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%c", outSep); } if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%s", sqlFieldName(sr)); if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "\n"); } 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) { if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%s", row[colIx]); if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%c", outSep); } if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "%s", row[lastCol]); if (outSep == ',') hOrFPrintf(f, "\""); hOrFPrintf(f, "\n"); } ++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, char outSep) /* 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, outSep); else if (isLongTabixTable(table)) longTabixTabOut(db, table, conn, fields, f, outSep); else if (isBamTable(table)) bamTabOut(db, table, conn, fields, f, outSep); else if (isVcfTable(table, &isTabix)) vcfTabOut(db, table, conn, fields, f, isTabix); else if (isHicTable(table)) hicTabOut(db, table, conn, fields, f, outSep); else if (isCustomTrack(table)) { doTabOutCustomTracks(db, table, conn, fields, f, outSep); } else doTabOutDb(db, db, table, table, f, conn, fields, outSep); } 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 (isLongTabixTable(table)) fieldList = getLongTabixFields(6); else if (isHalTable(table)) fieldList = getBedFields(6); else if (isBamTable(table)) fieldList = bamGetFields(table); else if (isVcfTable(table, NULL)) fieldList = vcfGetFields(table); else if (isHicTable(table)) fieldList = hicGetFields(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("barChart", type) || sameWord("interact", 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(); char sep = sameString(cartUsualString(cart, hgtaOutSep, outTab), outTab) ? '\t' : ','; if (sameWord(table, WIKI_TRACK_TABLE)) sepOutSelectedFields(wikiDbName(), table, NULL, fullTableFields(wikiDbName(), table), sep); else sepOutSelectedFields(database, table, NULL, fullTableFields(database, table), sep); } 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 = ""; +char query[1024]; +sqlSafef(query, sizeof query, "%s", ""); if (cartVarExists(cart, hgtaMetaStatus)) { printf("Table status for database %s\n", database); - query = NOSQLINJ "SHOW TABLE STATUS"; + sqlSafef(query, sizeof query, "SHOW TABLE STATUS"); } else if (cartVarExists(cart, hgtaMetaVersion)) { - query = NOSQLINJ "SELECT @@VERSION"; + sqlSafef(query, sizeof query, "SELECT @@VERSION"); } else if (cartVarExists(cart, hgtaMetaDatabases)) { - query = NOSQLINJ "SHOW DATABASES"; + sqlSafef(query, sizeof query, "SHOW DATABASES"); } else if (cartVarExists(cart, hgtaMetaTables)) { - query = NOSQLINJ "SHOW TABLES"; + sqlSafef(query, sizeof query, "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; 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; } checkNoGenomeDisabled(database, table); 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); 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; 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); // Try to deal with virt chrom position used by hgTracks. if (startsWith( MULTI_REGION_CHROM, cartUsualString(cart, "position", "")) || startsWith(OLD_MULTI_REGION_CHROM, cartUsualString(cart, "position", ""))) cartSetString(cart, "position", cartUsualString(cart, "nonVirtPosition", "")); /* Set up global variables. */ allJoiner = joinerRead("all.joiner"); getDbGenomeClade(cart, &database, &genome, &clade, oldVars); chromAliasSetup(database); freezeName = hFreezeFromDb(database); initGenbankTableNames(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(); struct dyString *dyWarn = dyStringNew(0); boolean noShort = (cartOptionalString(cart, "noShort") != NULL); // is this the second page of results char *range = windowsToAscii(cloneString(cartUsualString(cart, hgtaRange, ""))); struct hgPositions *hgp = lookupPosition(dyWarn); if (hgp->singlePos && isEmpty(dyWarn->string) && !noShort) { if (cartUsualBoolean(cart, hgtaDoGreatOutput, FALSE)) doGetGreatOutput(dispatch); else dispatch(); } else { cartWebStartHeader(cart, database, "Table Browser"); if (isNotEmpty(dyWarn->string)) { if (noShort) // we're on the second page of results hgp->posCount = 0; // hgFindSearch gives us a bogus hgp if the warn string is set else warn("%s", dyWarn->string); } if ((hgp->posCount > 1) || noShort) // if we're on the second page we want to put out HTML even if there are no results. { hgPositionsHtml(database, hgp, hgTablesName(), cart); cartSetString(cart, hgtaRange, range); // we need to reset the position because lookupPosition above trashes it } else { struct sqlConnection *conn = NULL; if (!trackHubDatabase(database)) conn = curTrack ? hAllocConnTrack(database, curTrack) : hAllocConn(database); mainPageAfterOpen(conn); hFreeConn(&conn); } cartWebEnd(); } textOutClose(&compressPipeline, &saveStdout); if (doGenomeSpace()) { if (gsTemp) { cartSetString(cart, "gsTemp", gsTemp); char *workUrl = NULL; startBackgroundWork("./hgTables backgroundExec=gsSendToDM", &workUrl); htmlOpen("Uploading Output to GenomeSpace"); jsInlineF( "setTimeout(function(){location = 'hgTables?backgroundStatus=%s';},2000);\n", // was 10000? cgiEncode(workUrl)); htmlClose(); fflush(stdout); gsTemp = NULL; } } /* Save variables. */ cartCheckout(&cart); } int main(int argc, char *argv[]) /* Process command line. */ { long enteredMainTime = clock1000(); issueBotWarning = earlyBotCheck(enteredMainTime, "hgTables", 0.0, 0, 0, "html"); pushCarefulMemHandler(LIMIT_2or6GB); htmlPushEarlyHandlers(); /* Make errors legible during initialization. */ cgiSpoof(&argc, argv); hgTables(); cgiExitTime("hgTables", enteredMainTime); return 0; }