d616e51d6f1576fc2e78fab2563cf5e251fdf8be jcasper Thu Feb 20 08:50:18 2025 -0800 Whoops, missed one swap from int to long for sqlTableSize, refs #35262 diff --git src/hg/utils/blatServersCheck/blatServersCheck.c src/hg/utils/blatServersCheck/blatServersCheck.c index 854fe7d1181..e5029e30cf4 100644 --- src/hg/utils/blatServersCheck/blatServersCheck.c +++ src/hg/utils/blatServersCheck/blatServersCheck.c @@ -1,390 +1,390 @@ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ /* blatServersCheck - Check that the blatServers table value match the * actual running gfServers. */ #include "common.h" #include "options.h" #include "jksql.h" #include "hgConfig.h" #include "genoFind.h" #include "net.h" #include "hash.h" #include "obscure.h" char *database = NULL; char *host = NULL; char *user = NULL; char *password = NULL; struct sqlConnection *conn = NULL; char *blatServersTableName = "blatServers"; int timeout = 10; // default timeout in seconds char *hostFilter = NULL; // default to searching all hosts void usage() /* Explain usage and exit. */ { errAbort( "blatServersCheck - Check the blatServers table matches running gfServers\n" "usage:\n" " blatServersCheck profile\n" "profile should be from hg.conf like central or rrcentral\n" "options:\n" " -timeout=10 timeout in seconds.\n" " -host=blatx only check records with matching host.\n" " -verbose=2 can show details for each server.\n" "\n" ); } static struct optionSpec options[] = { {"timeout", OPTION_INT}, {"host", OPTION_STRING}, {"-help", OPTION_BOOLEAN}, {NULL, 0}, }; char *getCfgOption(char *config, char *setting) /* get setting for specified config */ { char temp[256]; safef(temp, sizeof(temp), "%s.%s", config, setting); char *value = cfgOption(temp); if (!value) errAbort("setting %s not found!",temp); return value; } void setSocketTimeout(int sockfd, int delayInSeconds) // put socket read timeout so it will not take forever to timeout during a read { struct timeval tv; tv.tv_sec = delayInSeconds; tv.tv_usec = 0; setsockopt(sockfd, SOL_SOCKET, SO_RCVTIMEO, (const char*)&tv, sizeof tv); setsockopt(sockfd, SOL_SOCKET, SO_SNDTIMEO, (const char*)&tv, sizeof tv); } int statusServer(char *hostName, char *portName, boolean isTrans, boolean isDynamic, char *db, struct hash *versionHash) /* Send status message to server arnd report result. * Returns -1 for connection error. * Returns -2 for error reading string. * Returns -3 for type mismatch. * Returns -4 for host mismatch. * Returns -5 for port mismatch. */ { char buf[256]; int sd = 0; int ret = 0; /* Put together command. */ sd = netConnectWithTimeout(hostName, atoi(portName), timeout * 1000); // 10 seconds connect timeout if (sd == -1) { warn("Error connecting to %s:%s", hostName, portName); return -1; } setSocketTimeout(sd, timeout); if (isDynamic) sprintf(buf, "%s%s %s %s", gfSignature(), isTrans ? "transInfo" : "untransInfo", db, db); else sprintf(buf, "%sstatus", gfSignature()); mustWriteFd(sd, buf, strlen(buf)); for (;;) { if (netGetString(sd, buf) == NULL) { warn("Error reading status information from %s:%s", hostName, portName); ret = -2; // error reading response break; } if (sameString(buf, "end")) { break; } else { verbose(2, "%s\n", buf); if (startsWith("version ", buf)) { char *hashKey = buf+strlen("version "); hashIncInt(versionHash, hashKey); // count how many with this version } if (startsWith("type ", buf)) { if (sameString(buf, "type translated") && !isTrans) { warn("type mismatch: gfServer says type translated but db says isTrans==0"); ret = -3; // type mismatch break; } if (sameString(buf, "type nucleotide") && isTrans) { warn("type mismatch: gfServer says type nucleotide but db says isTrans==1"); ret = -3; // type mismatch break; } } if (startsWith("host ", buf)) { if (!sameString(buf+strlen("host "), hostName)) { warn("host mismatch: gfServer says %s but db says db=%s", buf, hostName); ret = -4; // host mismatch break; } } if (startsWith("port ", buf)) { if (!sameString(buf+strlen("port "), portName)) { warn("port mismatch: gfServer says %s but db says port=%s", buf, portName); ret = -5; // port mismatch // probably never happens. break; } } } } close(sd); return(ret); } int getFileList(char *hostName, char *portName, char *db, struct hash *targetDbHash) /* Get and display input file list. * Returns -1 for 2bit name mismatch * Returns -2 for name mot found in targetDb, probably obsolete * Returns -3 for targetDb.seqFile does not match fileName on gfServer */ { char buf[256]; int sd = 0; int fileCount; int i; int ret = 0; char twoBitName[256]; safef(twoBitName, sizeof twoBitName, "%s.2bit", db); /* Put together command. */ sd = netConnectWithTimeout(hostName, atoi(portName), timeout * 1000); // 10 seconds connect timeout setSocketTimeout(sd, timeout); sprintf(buf, "%sfiles", gfSignature()); mustWriteFd(sd, buf, strlen(buf)); /* Get count of files, and then each file name. */ if (netGetString(sd, buf) != NULL) { fileCount = atoi(buf); for (i=0; i<fileCount; ++i) // could have multiples if .nib used? { char *fileName = netRecieveString(sd, buf); //printf("%s\n", fileName); verbose(2, "%s\n", fileName); // if .nib, cannot confirm the name. if (endsWith(fileName,".nib")) { // DO NOTHING FOR NIBS } else if (strstr(db, "Kg")) { struct hashEl *hel = hashLookup(targetDbHash, db); if (hel == NULL) { warn("db %s not found in targetDb.name, probably obsolete", db); ret = -2; // name mot found in targetDb, probably obsolete break; } else { char *seqFile = hel->val; if (!endsWith(seqFile, fileName)) { warn("targetDb.seqFile %s does not match fileName=%s on gfServer", seqFile, twoBitName); ret = -3; // targetSeq fileName mistmatch break; } } } else { if (!sameString(fileName, twoBitName)) { warn("2bit name mismatch fileName=%s twoBitName=%s", fileName, twoBitName); ret = -1; // 2bit name mismatch break; } } } } close(sd); return ret; } void getTargetDb(struct sqlConnection *conn, struct hash *targetDbHash) /* read targetDb table into hash */ { struct sqlResult *sr; char **row; char query[256]; sqlSafef(query,sizeof(query), "select name, seqFile from targetDb"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *name = row[0]; char *seqFile = row[1]; struct hashEl *hel = hashLookup(targetDbHash, name); if (hel == NULL) { hashAdd(targetDbHash, name, cloneString(seqFile)); } else { warn("duplicate targetDb.name found %s", name); } } sqlFreeResult(&sr); } void blatServersCheck(char *config) /* Check blatServers table against running gfServers */ { struct hash *hash = hashNew(12); struct hash *versionHash = hashNew(6); struct hash *targetDbHash = hashNew(6); char hashKey[256]; /* get connection info */ database = getCfgOption(config, "db" ); host = getCfgOption(config, "host" ); user = getCfgOption(config, "user" ); password = getCfgOption(config, "password"); conn = sqlConnectRemote(host, user, password, database); getTargetDb(conn, targetDbHash); struct sqlResult *sr; char **row; char query[256]; long totalRows = 0; verbose(1, "-------------------\n"); verbose(1, "Reading table %s\n", blatServersTableName); totalRows = sqlTableSize(conn, blatServersTableName); -verbose(1,"totalRows=%d\n", totalRows); +verbose(1,"totalRows=%ld\n", totalRows); verbose(1,"\n"); if (totalRows==0) { errAbort("table %s is empty!", blatServersTableName); } int errCount = 0; sqlSafef(query,sizeof(query), "select db, host, port, isTrans, dynamic from %s order by db,port", blatServersTableName); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { char *db = row[0]; char *host = row[1]; char *portStr = row[2]; unsigned int port = sqlUnsigned(portStr); unsigned int trans = sqlUnsigned(row[3]); unsigned int dynamic = sqlUnsigned(row[4]); boolean isTrans = (trans == 1); boolean isDynamic = (dynamic == 1); if (hostFilter && !sameString(hostFilter, host)) continue; // skip int res = statusServer(host, portStr, isTrans, isDynamic, db, versionHash); int res2 = 0; if (res != -1) // if not a connection error, proceed. { res2 = getFileList(host, portStr, db, targetDbHash); } safef(hashKey, sizeof hashKey, "%s:%s", host, portStr); struct hashEl *hel = hashLookup(hash, hashKey); if (hel == NULL) { hashAdd(hash, hashKey, NULL); } else { if (!isDynamic) warn("duplicate host:port %s found", hashKey); } if ((res != 0) || (res2 != 0) || ((hel != NULL) && !isDynamic)) { ++errCount; verbose(1, "db=%s host=%s port=%d isTrans=%d res=%d res2=%d\n\n", db, host, port, trans, res, res2); } else { verbose(2, "db=%s host=%s port=%d isTrans=%d res=%d res2=%d\n\n", db, host, port, trans, res, res2); } } sqlFreeResult(&sr); sqlDisconnect(&conn); // Show a count of how many servers were of each gfServer version struct hashEl *el, *list = hashElListHash(versionHash); slSort(&list, hashElCmp); verbose(1, "version count\n"); verbose(1, "-------------\n"); for (el = list; el != NULL; el = el->next) { verbose(1, "%s %d\n", el->name, ptToInt(el->val)); } hashElFreeList(&list); verbose(1, "\n"); if (errCount > 0) errAbort("error count=%d", errCount); } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if ((argc != 2) || optionExists("-help")) usage(); timeout = optionInt("timeout", timeout); hostFilter = optionVal("host", hostFilter); blatServersCheck(argv[1]); printf("No errors found!\n"); return 0; }