08b1be37724c83f2dab17f71b5494963f34180b7
braney
  Fri Apr 24 08:16:21 2020 -0700
expand the size of a buffer in net.c to 8k instead of 2000

diff --git src/lib/net.c src/lib/net.c
index 4f8a5a5..9766bd0 100644
--- src/lib/net.c
+++ src/lib/net.c
@@ -1,2282 +1,2282 @@
 /* net.c some stuff to wrap around net communications. 
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #include "common.h"
 #include <signal.h>
 #include <errno.h>
 #include <string.h>
 #include <sys/time.h>
 #include <pthread.h>
 #include "errAbort.h"
 #include "hash.h"
 #include "net.h"
 #include "linefile.h"
 #include "base64.h"
 #include "cheapcgi.h"
 #include "https.h"
 #include "sqlNum.h"
 #include "obscure.h"
 #include "errCatch.h"
 
 /* Brought errno in to get more useful error messages */
 extern int errno;
 
 static int netStreamSocketFromAddrInfo(struct addrinfo *address)
 /* Create a socket from addrinfo structure.  
  * Complain and return something negative if can't. */
 {
 int sd = socket(address->ai_family, address->ai_socktype, address->ai_protocol);
 if (sd < 0)
     warn("Couldn't make %s socket.", familyToString(address->ai_family));
 
 return sd;
 }
 
 static int setSocketNonBlocking(int sd, boolean set)
 /* Use socket control flags to set O_NONBLOCK if set==TRUE,
  * or clear it if set==FALSE.
  * Return -1 if there are any errors, 0 if successful. */
 {
 long fcntlFlags;
 // Set or clear non-blocking
 if ((fcntlFlags = fcntl(sd, F_GETFL, NULL)) < 0) 
     {
     warn("Error fcntl(..., F_GETFL) (%s)", strerror(errno));
     return -1;
     }
 if (set)
     fcntlFlags |= O_NONBLOCK;
 else
     fcntlFlags &= (~O_NONBLOCK);
 if (fcntl(sd, F_SETFL, fcntlFlags) < 0) 
     {
     warn("Error fcntl(..., F_SETFL) (%s)", strerror(errno));
     return -1;
     }
 return 0;
 }
 
 int setReadWriteTimeouts(int sd, int seconds)
 /* Set read and write timeouts on socket sd 
  * Return -1 if there are any errors, 0 if successful. */
 {
 struct timeval timeout;      
 timeout.tv_sec = seconds;
 timeout.tv_usec = 0;
 
 if (setsockopt(sd, SOL_SOCKET, SO_RCVTIMEO, (char *)&timeout, sizeof(timeout)) < 0)
     {
     warn("setsockopt failed setting socket receive timeout\n");
     return -1;
     }
 
 if (setsockopt(sd, SOL_SOCKET, SO_SNDTIMEO, (char *)&timeout, sizeof(timeout)) < 0)
     {
     warn("setsockopt failed setting socket send timeout\n");
     return -1;
     }
 return 0;
 }
 
 
 static struct timeval tvMinus(struct timeval a, struct timeval b)
 /* Return the result of a - b; this handles wrapping of milliseconds. 
  * result.tv_usec will always be positive. 
  * result.tv_sec will be negative if b > a. */
 {
 // subtract b from a.
 if (a.tv_usec < b.tv_usec)
     {
     a.tv_usec += 1000000;
     a.tv_sec--;
     }
 a.tv_usec -= b.tv_usec;
 a.tv_sec -= b.tv_sec;
 return a;
 }
 
 int netConnectWithTimeoutOneAddr(int sd, struct addrinfo *address, long msTimeout, char *hostName, int port, struct dyString *dy)
 /* Try to connect one address with timeout or return success == 0, failure == -1 */
 {
 // Set socket to nonblocking so we can manage our own timeout time.
 if (setSocketNonBlocking(sd, TRUE) < 0)
     {
     return -1;
     }
 
 // Trying to connect with timeout
 int res;
 res = connect(sd, address->ai_addr, address->ai_addrlen);
 char ipStr[NI_MAXHOST];
 getAddrAsString6n4((struct sockaddr_storage *)address->ai_addr, ipStr, sizeof ipStr);
 if (res < 0)
     {
     if (errno == EINPROGRESS)
 	{
 	struct timeval startTime;
 	gettimeofday(&startTime, NULL);
 	struct timeval remainingTime;
 	remainingTime.tv_sec = (long) (msTimeout/1000);
 	remainingTime.tv_usec = (long) (((msTimeout/1000)-remainingTime.tv_sec)*1000000);
 	while (1) 
 	    {
 	    fd_set mySet;
 	    FD_ZERO(&mySet);
 	    FD_SET(sd, &mySet);
 	    // use tempTime (instead of using remainingTime directly) because on some platforms select() may modify the time val.
 	    struct timeval tempTime = remainingTime;
 	    res = select(sd+1, NULL, &mySet, &mySet, &tempTime);  
 	    if (res < 0) 
 		{
 		if (errno == EINTR)  // Ignore the interrupt 
 		    {
 		    // Subtract the elapsed time from remaining time since some platforms need this.
 		    struct timeval newTime;
 		    gettimeofday(&newTime, NULL);
 		    struct timeval elapsedTime = tvMinus(newTime, startTime);
 		    remainingTime = tvMinus(remainingTime, elapsedTime);
 		    if (remainingTime.tv_sec < 0)  // means our timeout has more than expired
 			{
 			remainingTime.tv_sec = 0;
 			remainingTime.tv_usec = 0;
 			}
 		    startTime = newTime;
 		    }
 		else
 		    {
 		    dyStringPrintf(dy, "Error in select() during TCP non-blocking connect %d - %s\n", errno, strerror(errno));
 		    return -1;
 		    }
 		}
 	    else if (res > 0)
 		{
 		// Socket selected for write when it is ready
 		int valOpt;
 		socklen_t lon;
 		// But check the socket for any errors
 		lon = sizeof(valOpt);
 		if (getsockopt(sd, SOL_SOCKET, SO_ERROR, (void*) (&valOpt), &lon) < 0)
 		    {
 		    warn("Error in getsockopt() %d - %s", errno, strerror(errno));
 		    return -1;
 		    }
 		// Check the value returned...
 		if (valOpt)
 		    {
 		    dyStringPrintf(dy, "Error in TCP non-blocking connect() %d - %s. Host %s IP %s port %d.\n", valOpt, strerror(valOpt), hostName, ipStr, port);
 		    return -1;
 		    }
 		break;  // OK
 		}
 	    else
 		{
 		dyStringPrintf(dy, "TCP non-blocking connect() to %s IP %s timed-out in select() after %ld milliseconds - Cancelling!", hostName, ipStr, msTimeout);
 		return -1;
 		}
 	    }
 	}
     else
 	{
 	dyStringPrintf(dy, "TCP non-blocking connect() error %d - %s", errno, strerror(errno));
 	return -1;
 	}
     }
 return 0; // OK
 }
 
 
 static int netConnectWithTimeout(char *hostName, int port, long msTimeout)
 /* In order to avoid a very long default timeout (several minutes) for hosts that will
 * not answer the port, we are forced to connect non-blocking.
 * After the connection has been established, we return to blocking mode.
 * Also closes sd if error. */
 {
 int sd;
 struct addrinfo *addressList=NULL, *address;
 char portStr[8];
 safef(portStr, sizeof portStr, "%d", port);
 
 if (hostName == NULL)
     {
     warn("NULL hostName in netConnect");
     return -1;
     }
 if (!internetGetAddrInfo6n4(hostName, portStr, &addressList))
     return -1;
 
 struct dyString *errMsg = newDyString(256);
 for (address = addressList; address; address = address->ai_next)
     {
     if ((sd = netStreamSocketFromAddrInfo(address)) < 0)
 	continue;
 
     if (netConnectWithTimeoutOneAddr(sd, address, msTimeout, hostName, port, errMsg) == 0)
 	break;
 
     close(sd);
     }
 boolean connected = (address != NULL); // one of the addresses connected successfully
 freeaddrinfo(addressList);
 
 if (!connected) 
     {
     if (!sameString(errMsg->string, ""))
 	{
 	warn("%s", errMsg->string);
 	}
     }
 dyStringFree(&errMsg);
 if (!connected)
     return -1;
 
 // Set to blocking mode again
 if (setSocketNonBlocking(sd, FALSE) < 0)
     {
     close(sd);
     return -1;
     }
 
 if (setReadWriteTimeouts(sd, DEFAULTREADWRITETTIMEOUTSEC) < 0)
     {
     close(sd);
     return -1;
     }
 
 return sd;
 
 }
 
 
 int netConnect(char *hostName, int port)
 /* Start connection with a server. */
 {
 return netConnectWithTimeout(hostName, port, DEFAULTCONNECTTIMEOUTMSEC); // 10 seconds connect timeout
 }
 
 int netMustConnect(char *hostName, int port)
 /* Start connection with server or die. */
 {
 int sd = netConnect(hostName, port);
 if (sd < 0)
    noWarnAbort();
 return sd;
 }
 
 int netMustConnectTo(char *hostName, char *portName)
 /* Start connection with a server and a port that needs to be converted to integer */
 {
 if (!isdigit(portName[0]))
     errAbort("netConnectTo: ports must be numerical, not %s", portName);
 return netMustConnect(hostName, atoi(portName));
 }
 
 int netAcceptingSocket4Only(int port, int queueSize)
 /* Create an IPV4 socket that can accept connections from 
  * only IPV4 clients on the current machine. Useful for systems with ipv6 disabled. */
 {
 struct sockaddr_in serverAddr;
 int sd;
 
 netBlockBrokenPipes();
 
 // ipv4 listening socket accepts ipv4 connections.
 if ((sd = socket(AF_INET, SOCK_STREAM, 0)) < 0)
     {
     errAbort("socket() failed");
     }
 
 // Allow local address reuse when server is restarted without waiting.
 int on = -1;
 if (setsockopt(sd, SOL_SOCKET, SO_REUSEADDR, (char *)&on,sizeof(on)) < 0)
     {
     errAbort("setsockopt(SO_REUSEADDR) failed");
     }
 
 ZeroVar(&serverAddr);
 serverAddr.sin_family = AF_INET;
 serverAddr.sin_port = htons(port);
 serverAddr.sin_addr.s_addr = INADDR_ANY;
 
 if (bind(sd, (struct sockaddr *)&serverAddr, sizeof(serverAddr)) < 0)
     {
     errAbort("Couldn't bind socket to %d: %s", port, strerror(errno));
     }
 
 if (listen(sd, queueSize) < 0)
     {
     errAbort("listen() failed");
     }
 
 return sd;
 }
 
 
 int netAcceptingSocket6n4(int port, int queueSize)
 /* Create an IPV6 socket that can accept connections from 
  * both IPV4 and IPV6 clients on the current machine. */
 {
 struct sockaddr_in6 serverAddr;
 int sd;
 
 netBlockBrokenPipes();
 
 // Hybrid dual stack ipv6 listening socket accepts ipv6 and ipv4 mapped connections.
 if ((sd = socket(AF_INET6, SOCK_STREAM, 0)) < 0)
     {
     errAbort("socket() failed");
     }
 
 // Allow local address reuse when server is restarted without waiting.
 int on = -1;
 if (setsockopt(sd, SOL_SOCKET, SO_REUSEADDR, (char *)&on,sizeof(on)) < 0)
     {
     errAbort("setsockopt(SO_REUSEADDR) failed");
     }
 
 // Explicitly turn off IPV6_V6ONLY which is needed on non-Linux platforms like NetBSD and Darwin.
 // This means we allow ipv4 socket connections that can have ipv4-mapped ipv6 IPs.
 int off = 0;
 if (setsockopt(sd, IPPROTO_IPV6, IPV6_V6ONLY, (void *)&off, sizeof(off)) < 0)
     {
     errAbort("setsockopt IPV6_V6ONLY off failed.");
     }
 
 ZeroVar(&serverAddr);
 serverAddr.sin6_family = AF_INET6;
 serverAddr.sin6_port   = htons(port);
 serverAddr.sin6_addr   = in6addr_any;
 if (bind(sd, (struct sockaddr *)&serverAddr, sizeof(serverAddr)) < 0)
     {
     errAbort("Couldn't bind socket to %d: %s", port, strerror(errno));
     }
 
 if (listen(sd, queueSize) < 0)
     {
     errAbort("listen() failed");
     }
 
 return sd;
 }
 
 
 int netAcceptingSocket(int port, int queueSize)
 /* Create an IPV6 socket that can accept connections from 
  * both IPV4 and IPV6 clients on the current machine.
  * OR Failover to making IPv4 Only socket if IPv6 is disabled. */
 {
 int sd = -1;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     sd = netAcceptingSocket6n4(port, queueSize);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     // if ipv6 is disabled, fall back to trying ipv4 only listen socket
     warn("%s", errCatch->message->string);
     warn("Retrying listen socket using ipv4 only.");
     sd = netAcceptingSocket4Only(port, queueSize);
     }
 errCatchFree(&errCatch);
 if (sd == -1)
   errAbort("unable to open listening socket");
 return sd;
 }
 
 int netAccept(int sd)
 /* Accept incoming connection from socket descriptor. */
 {
 socklen_t fromLen;
 return accept(sd, NULL, &fromLen);
 }
 
 int netAcceptFrom(int acceptor, struct cidr *subnet)
 /* Wait for incoming connection from socket descriptor
  * from IP address in subnet.  Subnet is something
  * returned from internetParseSubnetCidr. 
  * Subnet may be NULL. */
 {
 for (;;)
     {
     int sd = accept(acceptor, NULL, NULL);
     if (sd >= 0)
 	{
 	if (subnet == NULL)
 	    return sd;
 	else
 	    {
 	    socklen_t len;
 	    struct sockaddr_storage addr;
 	    char ipStr[INET6_ADDRSTRLEN];
 
 	    len = sizeof addr;
 	    getpeername(sd, (struct sockaddr*)&addr, &len);
 
             getAddrAsString6n4(&addr, ipStr, sizeof ipStr);
 
 	    if (!strchr(ipStr, ':'))   // convert ipv4 to ipv6-mapped
 		{
 		// prepend "::ffff:" to ipStr
 	        char temp[INET6_ADDRSTRLEN];
 		safef(temp, sizeof temp, "::ffff:%s", ipStr);
 		safecpy(ipStr, sizeof ipStr, temp);
 		}
 	    // convert back to ipv6 address.
 	    struct sockaddr_in6 clientAddr;
 	    internetIpStringToIp6(ipStr, &clientAddr.sin6_addr);
 
             // see if it is in the allowed subnet
 	    if (internetIpInSubnetCidr(&clientAddr.sin6_addr, subnet))
 		{
 		return sd;
 		}
 	    else
 		{
 		close(sd);
 		}
 	    }
 	}
     }
 }
 
 FILE *netFileFromSocket(int socket)
 /* Wrap a FILE around socket.  This should be fclose'd
  * and separately the socket close'd. */
 {
 FILE *f;
 if ((socket = dup(socket)) < 0)
    errnoAbort("Couldn't dupe socket in netFileFromSocket");
 f = fdopen(socket, "r+");
 if (f == NULL)
    errnoAbort("Couldn't fdopen socket in netFileFromSocket");
 return f;
 }
 
 static boolean plumberInstalled = FALSE;
 
 void netBlockBrokenPipes()
 /* Make it so a broken pipe doesn't kill us. */
 {
 if (!plumberInstalled)
     {
     signal(SIGPIPE, SIG_IGN);       /* Block broken pipe signals. */
     plumberInstalled = TRUE;
     }
 }
 
 ssize_t netReadAll(int sd, void *vBuf, ssize_t size)
 /* Read given number of bytes into buffer.
  * Don't give up on first read! */
 {
 char *buf = vBuf;
 ssize_t totalRead = 0;
 int oneRead;
 
 if (!plumberInstalled)
     netBlockBrokenPipes();
 while (totalRead < size)
     {
     oneRead = read(sd, buf + totalRead, size - totalRead);
     if (oneRead < 0)
 	return oneRead;
     if (oneRead == 0)
         break;
     totalRead += oneRead;
     }
 return totalRead;
 }
 
 ssize_t netMustReadAll(int sd, void *vBuf, ssize_t size)
 /* Read given number of bytes into buffer or die.
  * Don't give up if first read is short! */
 {
 ssize_t ret = netReadAll(sd, vBuf, size);
 if (ret < 0)
     errnoAbort("Couldn't finish netReadAll");
 return ret;
 }
 
 
 static void parseByteRange(char *url, ssize_t *rangeStart, ssize_t *rangeEnd, boolean terminateAtByteRange)
 /* parse the byte range information from url */
 {
 char *x;
 /* default to no byte range specified */
 *rangeStart = -1;
 *rangeEnd = -1;
 x = strrchr(url, ';');
 if (x)
     {
     if (startsWith(";byterange=", x))
 	{
 	char *y=strchr(x, '=');
 	++y;
 	char *z=strchr(y, '-');
 	if (z)
 	    {
 	    ++z;
 	    if (terminateAtByteRange)
 		*x = 0;
 	    *rangeStart = atoll(y); 
 	    if (z[0] != '\0')
 		*rangeEnd = atoll(z);
 	    }    
 	}
     }
 
 }
 
 void netHandleHostForIpv6(struct netParsedUrl *npu, struct dyString *dy)
 /* if needed, add brackets around the host name, 
  * for raw ipv6 address so it is not confused with colon port that may follow. */
 {
 boolean hostIsIpv6 = FALSE;
 if (strchr(npu->host, ':')) // Is the host really an IPV6 address?
     hostIsIpv6 = TRUE;
 if (hostIsIpv6) // surround ipv6 host with brakets []
     dyStringAppendC(dy, '[');
 dyStringAppend(dy, npu->host);
 if (hostIsIpv6) // surround ipv6 host with brakets []
     dyStringAppendC(dy, ']');
 }
 
 void netParseUrl(char *url, struct netParsedUrl *parsed)
 /* Parse a URL into components.   A full URL is made up as so:
  *   http://user:password@hostName:port/file;byterange=0-499
  * User and password may be cgi-encoded.
  * This is set up so that the http:// and the port are optional. 
  */
 {
 char *s, *t, *u, *v, *w, *br, *bl;
 char buf[MAXURLSIZE];
 
 /* Make local copy of URL. */
 if (strlen(url) >= sizeof(buf))
     errAbort("Url too long: '%s'", url);
 strcpy(buf, url);
 url = buf;
 
 /* Find out protocol - default to http. */
 s = trimSpaces(url);
 s = stringIn("://", url);
 if (s == NULL)
     {
     strcpy(parsed->protocol, "http");
     s = url;
     }
 else
     {
     *s = 0;
     tolowers(url);
     safecpy(parsed->protocol, sizeof(parsed->protocol), url);
     s += 3;
     }
 
 /* Split off file part. */
 parsed->byteRangeStart = -1;  /* default to no byte range specified */
 parsed->byteRangeEnd = -1;
 u = strchr(s, '/');
 if (u == NULL)
     strcpy(parsed->file, "/");
 else
     {
 
     parseByteRange(u, &parsed->byteRangeStart, &parsed->byteRangeEnd, TRUE);
 
     if (sameWord(parsed->protocol,"http") ||
         sameWord(parsed->protocol,"https"))
 	{
 	// http servers expect the URL request to be URL-encoded already.
 	/* need to encode spaces, but not ! other characters */
 	char *t=replaceChars(u," ","%20");
 	safecpy(parsed->file, sizeof(parsed->file), t);
 	freeMem(t);
 	}
 
     *u = 0; // terminate the host:port string
 
     if (sameWord(parsed->protocol,"ftp"))
 	{
 	++u; // that first slash is not considered part of the ftp path 
 	// decode now because the FTP server does NOT expect URL-encoding.
 	cgiDecodeFull(u,parsed->file,strlen(u));  // decodes %FF but not +
 	}
 
     }
 
 /* Split off user part */
 v = strchr(s, '@');
 if (v == NULL)
     {
     if (sameWord(parsed->protocol,"http") ||
         sameWord(parsed->protocol,"https"))
 	{
 	strcpy(parsed->user, "");
 	strcpy(parsed->password, "");
 	}
     if (sameWord(parsed->protocol,"ftp"))
 	{
 	strcpy(parsed->user, "anonymous");
 	strcpy(parsed->password, "x@genome.ucsc.edu");
 	}
     }
 else
     {
     *v = 0;
     /* split off password part */
     w = strchr(s, ':');
     if (w == NULL)
 	{
 	safecpy(parsed->user, sizeof(parsed->user), s);
 	strcpy(parsed->password, "");
 	}
     else
 	{
 	*w = 0;
 	safecpy(parsed->user, sizeof(parsed->user), s);
 	safecpy(parsed->password, sizeof(parsed->password), w+1);
 	}
     
     cgiDecode(parsed->user,parsed->user,strlen(parsed->user));
     cgiDecode(parsed->password,parsed->password,strlen(parsed->password));
     s = v+1;
     }
 
 
 // Whenever IPv6 address : port are provided,
 // the address MUST be surrounded by square brackets like [IPv6-address]:port
 // because without the square brackets, we cannot tell if the trailing bit
 // is end end of an IPv6 address, or port number.
 
 int blCount = countChars(s, '[');
 int brCount = countChars(s, ']');
 
 // double-check any stray brackets
 if ((brCount != blCount) || (brCount > 1))
     errAbort("badly formed url, stray square brackets in IPv6 address");
 
 /* Save port if it's there.  If not default to 80. */
 bl = strchr(s, '['); // IPV6 address in url surrounded by brackets []
 br = strrchr(s, ']'); // IPV6 address in url surrounded by brackets []
 
 if (!br != !bl)  // logical XOR
     errAbort("badly formed url, unbalanced square brackets around IPv6 address.");
 
 if (!br && isIpv6Address(s))  // host looks like IPv6 address but no brackets.
     errAbort("badly formed url, should be protocol://[IPv6-address]:port/. Put square brackets around literal IPv6 address.");
 
 // trim off the brackets around the ipv6 host name
 if (br)
     {
     // expecting *s == [
     if (*s != '[')
 	errAbort("badly formed url %s, expected [ at start of ipv6 address", s);
     ++s;    // skip [
     *br = 0; // erase ]
     t = br+1;
     char c = *t;
     if (c == 0)
 	t = NULL;
     else if (c != ':')
 	errAbort("badly formed url %s, stray characters after ] at end of ipv6 address", s);
     }
 else
     {
     t = strrchr(s, ':');
     }
 
 if (br && !isIpv6Address(s))  // host has brackets but does not look like IPv6 address.
     errAbort("badly formed url, brackets found, but not valid literal IPv6 address.");
 
 if (t) // the port was explicitly provided
     {
     *t++ = 0;
     if (!isdigit(t[0]))
 	errAbort("Non-numeric port name %s", t);
     safecpy(parsed->port, sizeof(parsed->port), t);
     }
 else // get default port for each protocol
     {  
     if (sameWord(parsed->protocol,"http"))
 	strcpy(parsed->port, "80");
     if (sameWord(parsed->protocol,"https"))
 	strcpy(parsed->port, "443");
     if (sameWord(parsed->protocol,"ftp"))
 	strcpy(parsed->port, "21");
     }
 
 /* What's left is the host. */
 safecpy(parsed->host, sizeof(parsed->host), s);
 }
 
 char *urlFromNetParsedUrl(struct netParsedUrl *npu)
 /* Build URL from netParsedUrl structure */
 {
 struct dyString *dy = newDyString(512);
 
 dyStringAppend(dy, npu->protocol);
 dyStringAppend(dy, "://");
 if (npu->user[0] != 0)
     {
     char *encUser = cgiEncode(npu->user);
     dyStringAppend(dy, encUser);
     freeMem(encUser);
     if (npu->password[0] != 0)
 	{
 	dyStringAppend(dy, ":");
 	char *encPassword = cgiEncode(npu->password);
 	dyStringAppend(dy, encPassword);
 	freeMem(encPassword);
 	}
     dyStringAppend(dy, "@");
     }
 
 netHandleHostForIpv6(npu, dy);
 
 /* do not include port if it is the default */
 if (!(
  (sameString(npu->protocol, "ftp"  ) && sameString("21", npu->port)) ||
  (sameString(npu->protocol, "http" ) && sameString("80", npu->port)) ||
  (sameString(npu->protocol, "https") && sameString("443",npu->port))
     ))
     {
     dyStringAppend(dy, ":");
     dyStringAppend(dy, npu->port);
     }
 dyStringAppend(dy, npu->file);
 if (npu->byteRangeStart != -1)
     {
     dyStringPrintf(dy, ";byterange=%lld-", (long long)npu->byteRangeStart);
     if (npu->byteRangeEnd != -1)
 	dyStringPrintf(dy, "%lld", (long long)npu->byteRangeEnd);
     }
 
 /* Clean up and return handle. */
 return dyStringCannibalize(&dy);
 }
 
 int netWaitForData(int sd, int microseconds)
 /* Wait for descriptor to have some data to read, up to given number of
  * microseconds.  Returns amount of data there or zero if timed out. */
 {
 struct timeval tv;
 fd_set set;
 int readyCount;
 
 for (;;)
     {
     if (microseconds >= 1000000)
 	{
 	tv.tv_sec = microseconds/1000000;
 	tv.tv_usec = microseconds%1000000;
 	}
     else
 	{
 	tv.tv_sec = 0;
 	tv.tv_usec = microseconds;
 	}
     FD_ZERO(&set);
     FD_SET(sd, &set);
     readyCount = select(sd+1, &set, NULL, NULL, &tv);
     if (readyCount < 0) 
 	{
 	if (errno == EINTR)	/* Select interrupted, not timed out. */
 	    continue;
     	else 
     	    warn("select failure %s", strerror(errno));
     	}
     else
 	{
     	return readyCount;	/* Zero readyCount indicates time out */
 	}
     }
 }
 
 static boolean readReadyWait(int sd, int microseconds)
 /* Wait for descriptor to have some data to read, up to given number of
  * number of microseconds.  Returns true if there is data, false if timed out. */
 {
 int readyCount = netWaitForData(sd, microseconds);
 return readyCount > 0;	/* Zero readyCount indicates time out */
 }
 
 static void sendFtpCommandOnly(int sd, char *cmd)
 /* send command to ftp server */
 {   
 mustWriteFd(sd, cmd, strlen(cmd));
 }
 
 #define NET_FTP_TIMEOUT 1000000
 
 static boolean receiveFtpReply(int sd, char *cmd, struct dyString **retReply, int *retCode)
 /* send command to ftp server and check resulting reply code, 
  * warn and return FALSE if not desired reply.  If retReply is non-NULL, store reply text there. */
 {
 char *startLastLine = NULL;
 struct dyString *rs = newDyString(4*1024);
 while (1)
     {
     int readSize = 0;
     while (1)
 	{
 	char buf[4*1024];
 	if (!readReadyWait(sd, NET_FTP_TIMEOUT))
 	    {
 	    warn("ftp server response timed out > %d microsec", NET_FTP_TIMEOUT);
 	    return FALSE;
 	    }
 	if ((readSize = read(sd, buf, sizeof(buf))) == 0)
 	    break;
 
 	dyStringAppendN(rs, buf, readSize);
 	if (endsWith(rs->string,"\n"))
 	    break;
 	}
 	
     /* find the start of the last line in the buffer */
     startLastLine = rs->string+strlen(rs->string)-1;
     if (startLastLine >= rs->string)
 	if (*startLastLine == '\n') 
 	    --startLastLine;
     while ((startLastLine >= rs->string) && (*startLastLine != '\n'))
 	--startLastLine;
     ++startLastLine;
 	
     if (strlen(startLastLine)>4)
       if (
 	isdigit(startLastLine[0]) &&
 	isdigit(startLastLine[1]) &&
 	isdigit(startLastLine[2]) &&
 	startLastLine[3]==' ')
 	break;
 	
     if (readSize == 0)
 	break;  // EOF
     /* must be some text info we can't use, ignore it till we get status code */
     }
 
 int reply = atoi(startLastLine);
 if ((reply < 200) || (reply > 399))
     {
     warn("ftp server error on cmd=[%s] response=[%s]",cmd,rs->string);
     return FALSE;
     }
     
 if (retReply)
     *retReply = rs;
 else
     dyStringFree(&rs);
 if (retCode)
     *retCode = reply;
 return TRUE;
 }
 
 static boolean sendFtpCommand(int sd, char *cmd, struct dyString **retReply, int *retCode)
 /* send command to ftp server and check resulting reply code, 
  * warn and return FALSE if not desired reply.  If retReply is non-NULL, store reply text there. */
 {   
 sendFtpCommandOnly(sd, cmd);
 return receiveFtpReply(sd, cmd, retReply, retCode);
 }
 
 static int parsePasvPort(char *rs)
 /* parse PASV reply to get the port and return it */
 {
 char *words[7];
 int wordCount;
 char *rsStart = strchr(rs,'(');
 char *rsEnd = strchr(rs,')');
 int result = 0;
 rsStart++;
 *rsEnd=0;
 wordCount = chopString(rsStart, ",", words, ArraySize(words));
 if (wordCount != 6)
     errAbort("PASV reply does not parse correctly");
 result = atoi(words[4])*256+atoi(words[5]);    
 return result;
 }    
 
 
 static long long parseFtpSIZE(char *rs)
 /* parse reply to SIZE and return it */
 {
 char *words[3];
 int wordCount;
 char *rsStart = rs;
 long long result = 0;
 wordCount = chopString(rsStart, " ", words, ArraySize(words));
 if (wordCount != 2)
     errAbort("SIZE reply does not parse correctly");
 result = atoll(words[1]);    
 return result;
 }    
 
 
 static time_t parseFtpMDTM(char *rs)
 /* parse reply to MDTM and return it
  * 200 YYYYMMDDhhmmss */
 {
 char *words[3];
 int wordCount = chopString(rs, " ", words, ArraySize(words));
 if (wordCount != 2)
     errAbort("MDTM reply should have 2 words but has %d", wordCount);
 #define EXPECTED_MDTM_FORMAT "YYYYmmddHHMMSS"
 if (strlen(words[1]) < strlen(EXPECTED_MDTM_FORMAT))
     errAbort("MDTM reply word [%s] shorter than " EXPECTED_MDTM_FORMAT, words[1]);
 // man strptime ->
 // "There should be whitespace or other alphanumeric characters between any two field descriptors."
 // There are no separators in the MDTM timestamp, so make a spread-out version for strptime:
 char spread[] = "YYYY mm dd HH MM SS";
 char *from = words[1];
 char *to = spread;
 *to++ = *from++;
 *to++ = *from++;
 *to++ = *from++;
 *to++ = *from++;
 *to++ = '-';
 *to++ = *from++;
 *to++ = *from++;
 *to++ = '-';
 *to++ = *from++;
 *to++ = *from++;
 *to++ = ' ';
 *to++ = *from++;
 *to++ = *from++;
 *to++ = ':';
 *to++ = *from++;
 *to++ = *from++;
 *to++ = ':';
 *to++ = *from++;
 *to++ = *from++;
 *to++ = 0;
 struct tm tm;
 if (strptime(spread, "%Y-%m-%d %H:%M:%S", &tm) == NULL)
     errAbort("unable to parse MDTM string [%s]", spread);
 // Not set by strptime(); tells mktime() to determine whether daylight saving time is in effect:
 tm.tm_isdst = -1;
 time_t t = mktime(&tm);
 if (t == -1)
     errAbort("mktime failed while parsing strptime'd MDTM string [%s]", words[1]);
 return t;
 }    
 
 
 static int openFtpControlSocket(char *host, int port, char *user, char *password)
 /* Open a socket to host,port; authenticate anonymous ftp; set type to I; 
  * return socket desc or -1 if there was an error. */
 {
 int sd = netConnect(host, port);
 if (sd < 0)
     return -1;
 
 /* First read the welcome msg */
 if (readReadyWait(sd, NET_FTP_TIMEOUT))
     sendFtpCommand(sd, "", NULL, NULL);
 
 char cmd[256];
 int retCode = 0;
 safef(cmd,sizeof(cmd),"USER %s\r\n", user);
 if (!sendFtpCommand(sd, cmd, NULL, &retCode))
     {
     close(sd);
     return -1;
     }
 
 if (retCode == 331)
     {
     safef(cmd,sizeof(cmd),"PASS %s\r\n", password);
     if (!sendFtpCommand(sd, cmd, NULL, NULL))
 	{
 	close(sd);
 	return -1;
 	}
     }
 
 if (!sendFtpCommand(sd, "TYPE I\r\n", NULL, NULL))
     {
     close(sd);
     return -1;
     }
 /* 200 Type set to I */
 /* (send the data as binary, so can support compressed files) */
 return sd;
 }
 
 boolean netGetFtpInfo(char *url, long long *retSize, time_t *retTime)
 /* Return date in UTC and size of ftp url file */
 {
 /* Parse the URL and connect. */
 struct netParsedUrl npu;
 netParseUrl(url, &npu);
 if (!sameString(npu.protocol, "ftp"))
     errAbort("netGetFtpInfo: url (%s) is not for ftp.", url);
 
 if (sameString(npu.file,"/"))
     {
     *retSize = 0;
     *retTime = time(NULL);
     return TRUE;
     }
 
 int sd = openFtpControlSocket(npu.host, atoi(npu.port), npu.user, npu.password);
 if (sd < 0)
     return FALSE;
 char cmd[256];
 safef(cmd,sizeof(cmd),"SIZE %s\r\n", npu.file);
 struct dyString *rs = NULL;
 if (!sendFtpCommand(sd, cmd, &rs, NULL))
     {
     close(sd);
     return FALSE;
     }
 *retSize = parseFtpSIZE(rs->string);
 /* 200 12345 */
 dyStringFree(&rs);
 
 safef(cmd,sizeof(cmd),"MDTM %s\r\n", npu.file);
 if (!sendFtpCommand(sd, cmd, &rs, NULL))
     {
     close(sd);
     return FALSE;
     }
 *retTime = parseFtpMDTM(rs->string);
 /* 200 YYYYMMDDhhmmss */
 dyStringFree(&rs);
 close(sd);   
 return TRUE;
 }
 
 struct netConnectFtpParams
 /* params to pass to thread */
 {
 pthread_t thread;
 int pipefd[2];
 int sd;
 int sdata; 
 struct netParsedUrl npu;
 };
 
 static void *sendFtpDataToPipeThread(void *threadParams)
 /* This is to be executed by the child process after the fork in netGetOpenFtpSockets.
  * It keeps the ftp control socket alive while reading from the ftp data socket
  * and writing to the pipe to the parent process, which closes the ftp sockets
  * and reads from the pipe. */
 {
 
 struct netConnectFtpParams *params = threadParams;
 
 pthread_detach(params->thread);  // this thread will never join back with it's progenitor
 
 char buf[32768];
 int rd = 0;
 long long dataPos = 0; 
 if (params->npu.byteRangeStart != -1)
     dataPos = params->npu.byteRangeStart;
 while((rd = read(params->sdata, buf, 32768)) > 0) 
     {
     if (params->npu.byteRangeEnd != -1 && (dataPos + rd) > params->npu.byteRangeEnd)
 	rd = params->npu.byteRangeEnd - dataPos + 1;
     int wt = write(params->pipefd[1], buf, rd);
     if (wt == -1 && params->npu.byteRangeEnd != -1)
 	{
 	// errAbort in child process is messy; let reader complain if
 	// trouble.  If byterange was open-ended, we will hit this point
 	// when the parent stops reading and closes the pipe.
 	errnoWarn("error writing ftp data to pipe");
 	break;
 	}
     dataPos += rd;
     if (params->npu.byteRangeEnd != -1 && dataPos >= params->npu.byteRangeEnd)
 	break;	    
     }
 if (rd == -1)
     // Again, avoid abort in child process.
     errnoWarn("error reading ftp socket");
 close(params->pipefd[1]);  /* we are done with it */
 close(params->sd);
 close(params->sdata);
 return NULL;
 }
 
 static int netGetOpenFtpSockets(char *url, int *retCtrlSd)
 /* Return a socket descriptor for url data (url can end in ";byterange:start-end)",
  * or -1 if error.
  * If retCtrlSd is non-null, keep the control socket alive and set *retCtrlSd.
  * Otherwise, create a pipe and fork to keep control socket alive in the child 
  * process until we are done fetching data. */
 {
 char cmd[256];
 
 /* Parse the URL and connect. */
 struct netParsedUrl npu;
 struct netParsedUrl pxy;
 netParseUrl(url, &npu);
 if (!sameString(npu.protocol, "ftp"))
     errAbort("netGetOpenFtpSockets: url (%s) is not for ftp.", url);
 
 boolean noProxy = checkNoProxy(npu.host);
 char *proxyUrl = getenv("ftp_proxy");
 if (noProxy)
     proxyUrl = NULL;
 
 int sd = -1;
 if (proxyUrl)
     {
     netParseUrl(proxyUrl, &pxy);
     if (!sameString(pxy.protocol, "ftp"))
         errAbort("Unknown proxy protocol %s in %s. Should be ftp.", pxy.protocol, proxyUrl);
     char proxyUser[4096];
     safef(proxyUser, sizeof proxyUser, "%s@%s:%s", npu.user, npu.host, npu.port);
     sd = openFtpControlSocket(pxy.host, atoi(pxy.port), proxyUser, npu.password);
     char *logProxy = getenv("log_proxy");
     if (sameOk(logProxy,"on"))
 	verbose(1, "%s as %s via proxy %s\n", url, proxyUser, proxyUrl);
     }
 else
     {
     sd = openFtpControlSocket(npu.host, atoi(npu.port), npu.user, npu.password);
     }
 
 if (sd == -1)
     return -1;
 
 struct dyString *rs = NULL;
 if (!sendFtpCommand(sd, "PASV\r\n", &rs, NULL))
     {
     close(sd);
     return -1;
     }
 /* 227 Entering Passive Mode (128,231,210,81,222,250) */
 
 if (npu.byteRangeStart != -1)
     {
     safef(cmd,sizeof(cmd),"REST %lld\r\n", (long long) npu.byteRangeStart);
     if (!sendFtpCommand(sd, cmd, NULL, NULL))
 	{
 	close(sd);
 	return -1;
 	}
     }
 
 /* RETR for files, LIST for directories ending in / */
 safef(cmd,sizeof(cmd),"%s %s\r\n",((npu.file[strlen(npu.file)-1]) == '/') ? "LIST" : "RETR", npu.file);
 sendFtpCommandOnly(sd, cmd);
 
 int sdata = -1;
 if (proxyUrl)
     sdata = netConnect(pxy.host, parsePasvPort(rs->string));
 else
     sdata = netConnect(npu.host, parsePasvPort(rs->string));
 dyStringFree(&rs);
 if (sdata < 0)
     {
     close(sd);
     return -1;
     }
 
 int secondsWaited = 0;
 while (TRUE)
     {
     if (secondsWaited >= 10)
 	{
 	warn("ftp server error on cmd=[%s] timed-out waiting for data or error", cmd);
 	close(sd);
 	close(sdata);
 	return -1;
 	}
     if (readReadyWait(sdata, NET_FTP_TIMEOUT))
 	break;   // we have some data
     if (readReadyWait(sd, 0)) /* wait in microsec */
 	{
 	// this can see an error like bad filename
 	if (!receiveFtpReply(sd, cmd, NULL, NULL))
 	    {
 	    close(sd);
 	    close(sdata);
 	    return -1;
 	    }
 	}
     ++secondsWaited;
     }
 
 if (retCtrlSd != NULL)
     {
     *retCtrlSd = sd;
     return sdata;
     }
 else
     {
     /* Because some FTP servers will kill the data connection
      * as soon as the control connection closes,
      * we have to develop a workaround using a partner thread. */
     fflush(stdin);
     fflush(stdout);
     fflush(stderr);
 
     struct netConnectFtpParams *params;
     AllocVar(params);
     params->sd = sd;
     params->sdata = sdata;
     params->npu = npu;
     /* make a pipe (fds go in pipefd[0] and pipefd[1])  */
     if (pipe(params->pipefd) != 0)
 	errAbort("netGetOpenFtpSockets: failed to create pipe: %s", strerror(errno));
     int rc;
     rc = pthread_create(&params->thread, NULL, sendFtpDataToPipeThread, (void *)params);
     if (rc)
 	{
 	errAbort("Unexpected error %d from pthread_create(): %s",rc,strerror(rc));
 	}
 
     return params->pipefd[0];
     }
 }
 
 
 int connectNpu(struct netParsedUrl npu, char *url, boolean noProxy)
 /* Connect using NetParsedUrl. */
 {
 int sd = -1;
 if (sameString(npu.protocol, "http"))
     {
     sd = netConnect(npu.host, atoi(npu.port));
     }
 else if (sameString(npu.protocol, "https"))
     {
     sd = netConnectHttps(npu.host, atoi(npu.port), noProxy);
     }
 else
     {
     errAbort("netHttpConnect: url (%s) is not for http.", url);
     return -1;  /* never gets here, fixes compiler complaint */
     }
 return sd;
 }
 
 void setAuthorization(struct netParsedUrl npu, char *authHeader, struct dyString *dy)
 /* Set the specified authorization header with BASIC auth base64-encoded user and password */
 {
 if (!sameString(npu.user,""))
     {
     char up[256];
     char *b64up = NULL;
     safef(up, sizeof(up), "%s:%s", npu.user, npu.password);
     b64up = base64Encode(up, strlen(up));
     dyStringPrintf(dy, "%s: Basic %s\r\n", authHeader, b64up);
     freez(&b64up);
     }
 }
 
 boolean checkNoProxy(char *host)
 /* See if host endsWith element on no_proxy list. Elements are comma-separated. */
 {
 char *list = cloneString(getenv("no_proxy"));
 if (!list)
     return FALSE;
 replaceChar(list, ',', ' ');
 char *word;
 while((word=nextWord(&list)))
     {
     if (endsWith(host, word))
 	return TRUE;
     }
 return FALSE;
 }
 
 int netHttpConnect(char *url, char *method, char *protocol, char *agent, char *optionalHeader)
 /* Parse URL, connect to associated server on port, and send most of
  * the request to the server.  If specified in the url send user name
  * and password too.  Typically the "method" will be "GET" or "POST"
  * and the agent will be the name of your program or
  * library. optionalHeader may be NULL or contain additional header
  * lines such as cookie info. 
  * Proxy support via hg.conf httpProxy or env var http_proxy
  * Return data socket, or -1 if error.*/
 {
 struct netParsedUrl npu;
 struct netParsedUrl pxy;
 struct dyString *dy = newDyString(512);
 int sd = -1;
 /* Parse the URL and connect. */
 netParseUrl(url, &npu);
 
 boolean noProxy = checkNoProxy(npu.host);
 char *proxyUrl = getenv("http_proxy");
 if (sameString(npu.protocol, "https"))
     proxyUrl = NULL;
 if (noProxy)
     proxyUrl = NULL;
 if (proxyUrl)
     {
     netParseUrl(proxyUrl, &pxy);
     if (!sameString(pxy.protocol, "http"))
 	errAbort("Unknown proxy protocol %s in %s.", pxy.protocol, proxyUrl);
     sd = connectNpu(pxy, url, noProxy);
     char *logProxy = getenv("log_proxy");
     if (sameOk(logProxy,"on"))
 	verbose(1, "%s via proxy %s\n", url, proxyUrl);
     }
 else
     {
     sd = connectNpu(npu, url, noProxy);
     }
 if (sd < 0)
     return -1;
 
 /* Ask remote server for a file. */
 char *urlForProxy = NULL;
 if (proxyUrl)
     {
     /* trim off the byterange part at the end of url because proxy does not understand it. */
     urlForProxy = cloneString(url);
     char *x = strrchr(urlForProxy, ';');
     if (x && startsWith(";byterange=", x))
 	*x = 0;
     }
 dyStringPrintf(dy, "%s %s %s\r\n", method, proxyUrl ? urlForProxy : npu.file, protocol);
 freeMem(urlForProxy);
 dyStringPrintf(dy, "User-Agent: %s\r\n", agent);
 
 dyStringPrintf(dy, "Host: ");
 netHandleHostForIpv6(&npu, dy);
 
 boolean portIsDefault = FALSE;
 /* do not need the 80 since it is the default */
 if (sameString(npu.protocol, "http" ) && sameString("80", npu.port))
     portIsDefault = TRUE;
 if (sameString(npu.protocol, "https" ) && sameString("443", npu.port))
     portIsDefault = TRUE;
 if (!portIsDefault)
     {
     dyStringAppendC(dy, ':');
     dyStringAppend(dy, npu.port);
     }
 dyStringPrintf(dy, "\r\n");
 
 setAuthorization(npu, "Authorization", dy);
 if (proxyUrl)
     setAuthorization(pxy, "Proxy-Authorization", dy);
 dyStringAppend(dy, "Accept: */*\r\n");
 if (npu.byteRangeStart != -1)
     {
     if (npu.byteRangeEnd != -1)
 	dyStringPrintf(dy, "Range: bytes=%lld-%lld\r\n"
 		       , (long long)npu.byteRangeStart
 		       , (long long)npu.byteRangeEnd);
     else
 	dyStringPrintf(dy, "Range: bytes=%lld-\r\n"
 		       , (long long)npu.byteRangeStart);
     }
 
 if (optionalHeader)
     dyStringAppend(dy, optionalHeader);
 
 /* finish off the header with final blank line */
 dyStringAppend(dy, "\r\n");
 
 mustWriteFd(sd, dy->string, dy->stringSize);
 
 /* Clean up and return handle. */
 dyStringFree(&dy);
 return sd;
 }
 
 
 int netOpenHttpExt(char *url, char *method, char *optionalHeader)
 /* Return a file handle that will read the url.  optionalHeader
  * may by NULL or may contain cookies and other info.  */
 {
 return netHttpConnect(url, method, "HTTP/1.0", "genome.ucsc.edu/net.c", optionalHeader);
 }
 
 static int netGetOpenHttp(char *url)
 /* Return a file handle that will read the url.  */
 {
 return netOpenHttpExt(url, "GET", NULL);
 }
 
 int netUrlHeadExt(char *url, char *method, struct hash *hash)
 /* Go get head and return status.  Return negative number if
  * can't get head. If hash is non-null, fill it with header
  * lines with upper cased keywords for case-insensitive lookup, 
  * including hopefully CONTENT-TYPE: . */
 {
 int sd = netOpenHttpExt(url, method, NULL);
 int status = EIO;
 if (sd >= 0)
     {
     char *line, *word;
     struct lineFile *lf = lineFileAttach(url, TRUE, sd);
 
     if (lineFileNext(lf, &line, NULL))
 	{
 	if (startsWith("HTTP/", line))
 	    {
 	    word = nextWord(&line);
 	    word = nextWord(&line);
 	    if (word != NULL && isdigit(word[0]))
 	        {
 		status = atoi(word);
 		if (hash != NULL)
 		    {
 		    while (lineFileNext(lf, &line, NULL))
 		        {
 			word = nextWord(&line);
 			if (word == NULL)
 			    break;
 			hashAdd(hash, strUpper(word), cloneString(skipLeadingSpaces(line)));
 			}
 		    }
 		}
 	    }
 	}
     lineFileClose(&lf);
     }
 else
     status = errno;
 return status;
 }
 
 
 int netUrlHead(char *url, struct hash *hash)
 /* Go get head and return status.  Return negative number if
  * can't get head. If hash is non-null, fill it with header
  * lines with upper cased keywords for case-insensitive lookup, 
  * including hopefully CONTENT-TYPE: . */
 {
 return netUrlHeadExt(url, "HEAD", hash);
 }
 
 
 int netUrlFakeHeadByGet(char *url, struct hash *hash)
 /* Use GET with byteRange as an alternate method to HEAD. 
  * Return status. */
 {
 char rangeUrl[MAXURLSIZE];
 safef(rangeUrl, sizeof(rangeUrl), "%s;byterange=0-0", url);
 int status = netUrlHeadExt(rangeUrl, "GET", hash);
 return status;
 }
 
 
 int netUrlOpenSockets(char *url, int *retCtrlSocket)
 /* Return socket descriptor (low-level file handle) for read()ing url data,
  * or -1 if error. 
  * If retCtrlSocket is non-NULL and url is FTP, set *retCtrlSocket
  * to the FTP control socket which is left open for a persistent connection.
  * close(result) (and close(*retCtrlSocket) if applicable) when done. 
  * If url is missing :// then it's just treated as a file. */
 {
 if (stringIn("://", url) == NULL)
     return open(url, O_RDONLY);
 else
     {
     if (startsWith("http://",url) || startsWith("https://",url))
 	return netGetOpenHttp(url);
     else if (startsWith("ftp://",url))
 	return netGetOpenFtpSockets(url, retCtrlSocket);
     else    
 	errAbort("Sorry, can only netUrlOpen http, https and ftp currently, not '%s'", url);
     }
 return -1;    
 }
 
 int netUrlOpen(char *url)
 /* Return socket descriptor (low-level file handle) for read()ing url data,
  * or -1 if error.  Just close(result) when done. */
 {
 return netUrlOpenSockets(url, NULL);
 }
 
 struct dyString *netSlurpFile(int sd)
 /* Slurp file into dynamic string and return. */
 {
 char buf[4*1024];
 int readSize;
 struct dyString *dy = newDyString(4*1024);
 
 /* Slurp file into dy and return. */
 while ((readSize = read(sd, buf, sizeof(buf))) > 0)
     dyStringAppendN(dy, buf, readSize);
 return dy;
 }
 
 struct dyString *netSlurpUrl(char *url)
 /* Go grab all of URL and return it as dynamic string. */
 {
 int sd = netUrlOpen(url);
 if (sd < 0)
     errAbort("netSlurpUrl: failed to open socket for [%s]", url);
 struct dyString *dy = netSlurpFile(sd);
 close(sd);
 return dy;
 }
 
 static void parseContentRange(char *x, ssize_t *rangeStart, ssize_t *rangeEnd)
 /* parse the content range information from response header value 
 	"bytes 763400000-763400112/763400113"
  */
 {
 /* default to no byte range specified */
 *rangeStart = -1;
 *rangeEnd = -1;
 if (startsWith("bytes ", x))
     {
     char *y=strchr(x, ' ');
     ++y;
     char *z=strchr(y, '-');
     if (z)
 	{
 	++z;
 	*rangeStart = atoll(y); 
 	if (z[0] != '\0')
 	    *rangeEnd = atoll(z);
 	}    
     }
 
 }
 
 
 boolean netSkipHttpHeaderLinesWithRedirect(int sd, char *url, char **redirectedUrl)
 /* Skip http header lines. Return FALSE if there's a problem.
  * The input is a standard sd or fd descriptor.
  * This is meant to be able work even with a re-passable stream handle,
  * e.g. can pass it to the pipes routines, which means we can't
  * attach a linefile since filling its buffer reads in more than just the http header.
  * Handles 300, 301, 302, 303, 307, 308 http redirects by setting *redirectedUrl to
  * the new location. */
 {
-char buf[2000];
+char buf[8192];
 char *line = buf;
 int maxbuf = sizeof(buf);
 int i=0;
 char c = ' ';
 int nread = 0;
 char *sep = NULL;
 char *headerName = NULL;
 char *headerVal = NULL;
 boolean redirect = FALSE;
 boolean byteRangeUsed = (strstr(url,";byterange=") != NULL);
 ssize_t byteRangeStart = -1;
 ssize_t byteRangeEnd = -1;
 boolean foundContentRange = FALSE;
 ssize_t contentRangeStart = -1;
 ssize_t contentRangeEnd = -1;
 
 boolean mustUseProxy = FALSE;  /* User must use proxy 305 error*/
 char *proxyLocation = NULL;
 boolean mustUseProxyAuth = FALSE;  /* User must use proxy authentication 407 error*/
 
 if (byteRangeUsed)
     {
     parseByteRange(url, &byteRangeStart, &byteRangeEnd, FALSE);
     }
 
 while(TRUE)
     {
     i = 0;
     while (TRUE)
 	{
 	nread = read(sd, &c, 1);  /* one char at a time, but http headers are small */
 	if (nread != 1)
 	    {
 	    if (nread == -1)
 		{
 		if (errno == EINTR)
 		    continue;
     		warn("Error (%s) reading http header on %s", strerror(errno), url);
 		}
 	    else if (nread == 0)
     		warn("Error unexpected end of input reading http header on %s", url);
 	    else
     		warn("Error reading http header on %s", url);
 	    return FALSE;  /* err reading descriptor */
 	    }
 	if (c == 10)
 	    break;
 	if (c != 13)
     	    buf[i++] = c;
 	if (i >= maxbuf)
 	    {
 	    warn("http header line too long > %d chars.",maxbuf);
 	    return FALSE;
 	    }
 	}
     buf[i] = 0;  /* add string terminator */
 
     if (sameString(line,""))
 	{
 	break; /* End of Header found */
 	}
     if (startsWith("HTTP/", line))
         {
 	char *code;
 	nextWord(&line);  // version
 	code = nextWord(&line);
 	if (code == NULL)
 	    {
 	    warn("Strange http header on %s", url);
 	    return FALSE;
 	    }
 	if (sameString(code, "301")
 	 || sameString(code, "302")
 	 || sameString(code, "307")
 	 || sameString(code, "308")
 	   )
 	    {
 	    redirect = TRUE;
 	    }
 	else if (sameString(code, "305"))
 	    {
 	    mustUseProxy = TRUE;
 	    }
 	else if (sameString(code, "407"))
 	    {
 	    mustUseProxyAuth = TRUE;
 	    }
 	else if (byteRangeUsed 
 	    /* hack for Apache bug 2.2.20 and 2.2.21 2011-10-21 should be OK to remove after one year. */
 		&& !(sameString(code, "200") && byteRangeStart == 0 && byteRangeEnd == -1))  
 	    {
 	    if (!sameString(code, "206"))
 		{
 		if (sameString(code, "200"))
 		    warn("Byte-range request was ignored by server. ");
 		warn("Expected Partial Content 206. %s: %s %s. rangeStart=%lld rangeEnd=%lld", 
 		    url, code, line, (long long)byteRangeStart, (long long)byteRangeEnd);
 		return FALSE;
 		}
 	    }
 	else if (sameString(code, "404"))
 	    {
 	    warn("404 file not found on %s", url);
 	    return FALSE;
 	    }
 	else if (!sameString(code, "200"))
 	    {
 	    warn("Expected 200 %s: %s %s", url, code, line);
 	    return FALSE;
 	    }
 	line = buf;  /* restore it */
 	}
     headerName = line;
     sep = strchr(line,':');
     if (sep)
 	{
 	*sep = 0;
 	headerVal = skipLeadingSpaces(++sep);
 	}
     else
 	{
 	headerVal = NULL;
 	}
     if (sameWord(headerName,"Location"))
 	{
 	if (redirect)
 	    *redirectedUrl = cloneString(headerVal);
 	if (mustUseProxy)
 	    proxyLocation = cloneString(headerVal);
 	}
     if (sameWord(headerName,"Content-Range"))
 	{
 	if (byteRangeUsed)
 	    {
 	    foundContentRange = TRUE;
 	    parseContentRange(headerVal, &contentRangeStart, &contentRangeEnd);	
     	    if ((contentRangeStart != byteRangeStart) ||
 		(byteRangeEnd != -1 && (contentRangeEnd != byteRangeEnd)))
 		{
 		char bre[256];
 		safef(bre, sizeof bre, "%lld", (long long)byteRangeEnd);
 		if (byteRangeEnd == -1)
 		    bre[0] = 0;
 		warn("Found Content-Range: %s. Expected bytes %lld-%s. Improper caching of 206 reponse byte-ranges?",
 		    headerVal, (long long) byteRangeStart, bre);
     		return FALSE;
 		}
 	    }
 	}
     }
 if (mustUseProxy ||  mustUseProxyAuth)
     {
     warn("%s: %s error. Use Proxy%s. Location = %s", url, 
 	mustUseProxy ? "" : " Authentication", 
 	mustUseProxy ? "305" : "407", 
 	proxyLocation ? proxyLocation : "not given");
     return FALSE;
     }
 if (byteRangeUsed && !foundContentRange && !redirect
 	    /* hack for Apache bug 2.2.20 and 2.2.21 2011-10-21 should be OK to remove after one year. */
 		&& !(byteRangeStart == 0 && byteRangeEnd == -1))  
     {
     char bre[256];
     safef(bre, sizeof bre, "%lld", (long long)byteRangeEnd);
     if (byteRangeEnd == -1)
 	bre[0] = 0;
     warn("Expected response header Content-Range: %lld-%s", (long long) byteRangeStart, bre);
     return FALSE;
     }
 
 return TRUE;
 }
 
 char *transferParamsToRedirectedUrl(char *url, char *newUrl)
 /* Transfer password, byteRange, and any other parameters from url to newUrl and return result.
  * freeMem result. */
 {
 struct netParsedUrl npu, newNpu;
 /* Parse the old URL to make parts available for graft onto the redirected url. */
 /* This makes redirection work with byterange urls and user:password@ */
 netParseUrl(url, &npu);
 netParseUrl(newUrl, &newNpu);
 if (npu.byteRangeStart != -1)
     {
     newNpu.byteRangeStart = npu.byteRangeStart;
     newNpu.byteRangeEnd = npu.byteRangeEnd;
     }
 if ((npu.user[0] != 0) && (newNpu.user[0] == 0))
     {
     safecpy(newNpu.user,     sizeof newNpu.user,     npu.user);
     safecpy(newNpu.password, sizeof newNpu.password, npu.password);
     }
 return urlFromNetParsedUrl(&newNpu);
 }
 
 boolean netSkipHttpHeaderLinesHandlingRedirect(int sd, char *url, int *redirectedSd, char **redirectedUrl)
 /* Skip http headers lines, returning FALSE if there is a problem.  Generally called as
  *    netSkipHttpHeaderLine(sd, url, &sd, &url);
  * where sd is a socket (file) opened with netUrlOpen(url), and url is in dynamic memory.
  * If the http header indicates that the file has moved, then it will update the *redirectedSd and
  * *redirectedUrl with the new socket and URL, first closing sd.
  * If for some reason you want to detect whether the forwarding has occurred you could
  * call this as:
  *    char *newUrl = NULL;
  *    int newSd = 0;
  *    netSkipHttpHeaderLine(sd, url, &newSd, &newUrl);
  *    if (newUrl != NULL)
  *          // Update sd with newSd, free url if appropriate and replace it with newUrl, etc.
  *          //  free newUrl when finished.
  * This routine handles up to 5 steps of redirection.
  * The logic to this routine is also complicated a little to make it work in a pipe, which means we
  * can't attach a lineFile since filling the lineFile buffer reads in more than just the http header. */
 {
 int redirectCount = 0;
 while (TRUE)
     {
     /* url needed for err msgs, and to return redirect location */
     char *newUrl = NULL;
     boolean success = netSkipHttpHeaderLinesWithRedirect(sd, url, &newUrl);
     if (success && !newUrl) /* success after 0 to 5 redirects */
         {
 	if (redirectCount > 0)
 	    {
 	    *redirectedSd = sd;
 	    *redirectedUrl = url;
 	    }
 	else
 	    {
 	    *redirectedSd = -1;
 	    *redirectedUrl = NULL;
 	    }
 	return TRUE;
 	}
     close(sd);
     if (success)
 	{
 	/* we have a new url to try */
 	++redirectCount;
 	if (redirectCount > 5)
 	    {
 	    warn("code 30x redirects: exceeded limit of 5 redirects, %s", newUrl);
 	    success = FALSE;
 	    }
 	else if (!startsWith("http://",newUrl) 
               && !startsWith("https://",newUrl))
 	    {
 	    warn("redirected to non-http(s): %s", newUrl);
 	    success = FALSE;
 	    }
 	else 
 	    {
 	    newUrl = transferParamsToRedirectedUrl(url, newUrl);		
 	    sd = netUrlOpen(newUrl);
 	    if (sd < 0)
 		{
 		warn("Couldn't open %s", newUrl);
 		success = FALSE;
 		}
 	    }
 	}
     if (redirectCount > 1)
 	freeMem(url);
     if (!success)
 	{  /* failure after 0 to 5 redirects */
 	if (redirectCount > 0)
 	    freeMem(newUrl);
 	return FALSE;
 	}
     url = newUrl;
     }
 return FALSE;
 }
 
 struct lineFile *netLineFileMayOpen(char *url)
 /* Return a lineFile attached to url. http skips header.
  * Supports some compression formats.  Prints warning message, but
  * does not abort, just returning NULL if there's a problem. */
 {
 int sd = netUrlOpen(url);
 if (sd < 0)
     {
     warn("Couldn't open %s", url);
     return NULL;
     }
 else
     {
     struct lineFile *lf = NULL;
     char *newUrl = NULL;
     int newSd = 0;
     if (startsWith("http://",url) || startsWith("https://",url))
 	{  
 	if (!netSkipHttpHeaderLinesHandlingRedirect(sd, url, &newSd, &newUrl))
 	    {
 	    return NULL;
 	    }
 	if (newUrl != NULL)
 	    {
     	    /*  Update sd with newSd, replace it with newUrl, etc. */
 	    sd = newSd;
 	    url = newUrl;
 	    }
 	}
     char *urlDecoded = cloneString(url);
     cgiDecode(url, urlDecoded, strlen(url));
     boolean isCompressed =
 	(endsWith(urlDecoded,".gz") ||
    	 endsWith(urlDecoded,".Z")  ||
 	 endsWith(urlDecoded,".bz2"));
     freeMem(urlDecoded);
     if (isCompressed)
 	{
 	lf = lineFileDecompressFd(url, TRUE, sd);
            /* url needed only for compress type determination */
 	}
     else
 	{
 	lf = lineFileAttach(url, TRUE, sd);
 	}
     if (newUrl) 
 	freeMem(newUrl); 
     return lf;
     }
 }
 
 int netUrlMustOpenPastHeader(char *url)
 /* Get socket descriptor for URL.  Process header, handling any forwarding and
  * the like.  Do errAbort if there's a problem, which includes anything but a 200
  * return from http after forwarding. */
 {
 int sd = netUrlOpen(url);
 if (sd < 0)
     noWarnAbort();
 int newSd = 0;
 if (startsWith("http://",url) || startsWith("https://",url))
     {  
     char *newUrl = NULL;
     if (!netSkipHttpHeaderLinesHandlingRedirect(sd, url, &newSd, &newUrl))
 	noWarnAbort();
     if (newUrl != NULL)
 	{
 	sd = newSd;
 	freeMem(newUrl); 
 	}
     }
 return sd;
 }
 
 struct lineFile *netLineFileSilentOpen(char *url)
 /* Open a lineFile on a URL.  Just return NULL without any user
  * visible warning message if there's a problem. */
 {
 pushSilentWarnHandler();
 struct lineFile *lf = netLineFileMayOpen(url);
 popWarnHandler();
 return lf;
 }
 
 char *netReadTextFileIfExists(char *url)
 /* Read entire URL and return it as a string.  URL should be text (embedded zeros will be
  * interpreted as end of string).  If the url doesn't exist or has other problems,
  * returns NULL. */
 {
 struct lineFile *lf = netLineFileSilentOpen(url);
 if (lf == NULL)
     return NULL;
 char *text = lineFileReadAll(lf);
 lineFileClose(&lf);
 return text;
 }
 
 struct lineFile *netLineFileOpen(char *url)
 /* Return a lineFile attached to url.  This one
  * will skip any headers.   Free this with
  * lineFileClose(). */
 {
 struct lineFile *lf = netLineFileMayOpen(url);
 if (lf == NULL)
     noWarnAbort();
 return lf;
 }
 
 boolean netSendString(int sd, char *s)
 /* Send a string down a socket - length byte first. */
 {
 int length = strlen(s);
 UBYTE len;
 
 if (length > 255)
     errAbort("Trying to send a string longer than 255 bytes (%d bytes)", length);
 len = length;
 if (write(sd, &len, 1)<0)
     {
     warn("Couldn't send string to socket");
     return FALSE;
     }
 if (write(sd, s, length)<0)
     {
     warn("Couldn't send string to socket");
     return FALSE;
     }
 return TRUE;
 }
 
 boolean netSendLongString(int sd, char *s)
 /* Send a long string down socket: two bytes for length. */
 {
 unsigned length = strlen(s);
 UBYTE b[2];
 
 if (length >= 64*1024)
     {
     warn("Trying to send a string longer than 64k bytes (%d bytes)", length);
     return FALSE;
     }
 b[0] = (length>>8);
 b[1] = (length&0xff);
 if (write(sd, b, 2) < 0)
     {
     warn("Couldn't send long string to socket");
     return FALSE;
     }
 if (write(sd, s, length)<0)
     {
     warn("Couldn't send long string to socket");
     return FALSE;
     }
 return TRUE;
 }
 
 boolean netSendHugeString(int sd, char *s)
 /* Send a long string down socket: four bytes for length. */
 {
 unsigned long length = strlen(s);
 unsigned long l = length;
 UBYTE b[4];
 int i;
 for (i=3; i>=0; --i)
     {
     b[i] = l & 0xff;
     l >>= 8;
     }
 if (write(sd, b, 4) < 0)
     {
     warn("Couldn't send huge string to socket");
     return FALSE;
     }
 if (write(sd, s, length) < 0)
     {
     warn("Couldn't send huge string to socket");
     return FALSE;
     }
 return TRUE;
 }
 
 
 char *netGetString(int sd, char buf[256])
 /* Read string into buf and return it.  If buf is NULL
  * an internal buffer will be used. Print warning message
  * and return NULL if any problem. */
 {
 static char sbuf[256];
 UBYTE len = 0;
 int length;
 int sz;
 if (buf == NULL) buf = sbuf;
 sz = netReadAll(sd, &len, 1);
 if (sz == 0)
     return NULL;
 if (sz < 0)
     {
     warn("Couldn't read string length");
     return NULL;
     }
 length = len;
 if (length > 0)
     if (netReadAll(sd, buf, length) < 0)
 	{
 	warn("Couldn't read string body");
 	return NULL;
 	}
 buf[length] = 0;
 return buf;
 }
 
 char *netGetLongString(int sd)
 /* Read string and return it.  freeMem
  * the result when done. */
 {
 UBYTE b[2];
 char *s = NULL;
 int length = 0;
 int sz;
 b[0] = b[1] = 0;
 sz = netReadAll(sd, b, 2);
 if (sz == 0)
     return NULL;
 if (sz < 0)
     {
     warn("Couldn't read long string length");
     return NULL;
     }
 length = (b[0]<<8) + b[1];
 s = needMem(length+1);
 if (length > 0)
     if (netReadAll(sd, s, length) < 0)
 	{
 	warn("Couldn't read long string body");
 	return NULL;
 	}
 s[length] = 0;
 return s;
 }
 
 char *netGetHugeString(int sd)
 /* Read string and return it.  freeMem
  * the result when done. */
 {
 UBYTE b[4];
 char *s = NULL;
 unsigned long length = 0;
 int sz, i;
 sz = netReadAll(sd, b, 4);
 if (sz == 0)
     return NULL;
 if (sz < 4)
     {
     warn("Couldn't read huge string length");
     return NULL;
     }
 for (i=0; i<4; ++i)
     {
     length <<= 8;
     length += b[i];
     }
 s = needMem(length+1);
 if (length > 0)
     {
     if (netReadAll(sd, s, length) < 0)
 	{
 	warn("Couldn't read huge string body");
 	return NULL;
 	}
     }
 s[length] = 0;
 return s;
 }
 
 
 char *netRecieveString(int sd, char buf[256])
 /* Read string into buf and return it.  If buf is NULL
  * an internal buffer will be used. Abort if any problem. */
 {
 char *s = netGetString(sd, buf);
 if (s == NULL)
      noWarnAbort();   
 return s;
 }
 
 char *netRecieveLongString(int sd)
 /* Read string and return it.  freeMem
  * the result when done. Abort if any problem*/
 {
 char *s = netGetLongString(sd);
 if (s == NULL)
      noWarnAbort();   
 return s;
 }
 
 char *netRecieveHugeString(int sd)
 /* Read string and return it.  freeMem
  * the result when done. Abort if any problem*/
 {
 char *s = netGetHugeString(sd);
 if (s == NULL)
      noWarnAbort();   
 return s;
 }
 
 
 struct lineFile *netHttpLineFileMayOpen(char *url, struct netParsedUrl **npu)
 /* Parse URL and open an HTTP socket for it but don't send a request yet. */
 {
 int sd;
 struct lineFile *lf;
 
 /* Parse the URL and try to connect. */
 AllocVar(*npu);
 netParseUrl(url, *npu);
 if (!sameString((*npu)->protocol, "http"))
     errAbort("netHttpLineFileMayOpen: url (%s) is not for http.", url);
 sd = netConnect((*npu)->host, atoi((*npu)->port));
 if (sd < 0)
     return NULL;
 
 /* Return handle. */
 lf = lineFileAttach(url, TRUE, sd);
 return lf;
 } /* netHttpLineFileMayOpen */
 
 
 void netHttpGet(struct lineFile *lf, struct netParsedUrl *npu,
 		boolean keepAlive)
 /* Send a GET request, possibly with Keep-Alive. */
 {
 struct dyString *dy = newDyString(512);
 
 /* Ask remote server for the file/query. */
 dyStringPrintf(dy, "GET %s HTTP/1.1\r\n", npu->file);
 dyStringPrintf(dy, "User-Agent: genome.ucsc.edu/net.c\r\n");
 
 dyStringPrintf(dy, "Host: ");
 netHandleHostForIpv6(npu, dy);
 dyStringAppendC(dy, ':');
 dyStringAppend(dy, npu->port);
 dyStringPrintf(dy, "\r\n");
 
 if (!sameString(npu->user,""))
     {
     char up[256];
     char *b64up = NULL;
     safef(up,sizeof(up), "%s:%s", npu->user, npu->password);
     b64up = base64Encode(up, strlen(up));
     dyStringPrintf(dy, "Authorization: Basic %s\r\n", b64up);
     freez(&b64up);
     }
 dyStringAppend(dy, "Accept: */*\r\n");
 if (keepAlive)
   {
     dyStringAppend(dy, "Connection: Keep-Alive\r\n");
     dyStringAppend(dy, "Connection: Persist\r\n");
   }
 else
     dyStringAppend(dy, "Connection: close\r\n");
 dyStringAppend(dy, "\r\n");
 mustWriteFd(lf->fd, dy->string, dy->stringSize);
 /* Clean up. */
 dyStringFree(&dy);
 } /* netHttpGet */
 
 int netHttpGetMultiple(char *url, struct slName *queries, void *userData,
 		       void (*responseCB)(void *userData, char *req,
 					  char *hdr, struct dyString *body))
 /* Given an URL which is the base of all requests to be made, and a 
  * linked list of queries to be appended to that base and sent in as 
  * requests, send the requests as a batch and read the HTTP response 
  * headers and bodies.  If not all the requests get responses (i.e. if 
  * the server is ignoring Keep-Alive or is imposing a limit), try again 
  * until we can't connect or until all requests have been served. 
  * For each HTTP response, do a callback. */
 {
   struct slName *qStart;
   struct slName *qPtr;
   struct lineFile *lf;
   struct netParsedUrl *npu;
   struct dyString *dyQ    = newDyString(512);
   struct dyString *body;
   char *base;
   char *hdr;
   int qCount;
   int qTotal;
   int numParseFailures;
   int contentLength;
   boolean chunked;
   boolean done;
   boolean keepAlive;
 
   /* Find out how many queries we'll need to do so we know how many times 
    * it's OK to run into end of file in case server ignores Keep-Alive. */
   qTotal = 0;
   for (qPtr = queries;  qPtr != NULL;  qPtr = qPtr->next)
     {
       qTotal++;
     }
 
   done = FALSE;
   qCount = 0;
   numParseFailures = 0;
   qStart = queries;
   while ((! done) && (qStart != NULL))
     {
       lf = netHttpLineFileMayOpen(url, &npu);
       if (lf == NULL)
 	{
 	  done = TRUE;
 	  break;
 	}
       base = cloneString(npu->file);
       /* Send all remaining requests with keep-alive. */
       for (qPtr = qStart;  qPtr != NULL;  qPtr = qPtr->next)
 	{
 	  dyStringClear(dyQ);
 	  dyStringAppend(dyQ, base);
 	  dyStringAppend(dyQ, qPtr->name);
 	  strcpy(npu->file, dyQ->string);
 	  keepAlive = (qPtr->next == NULL) ? FALSE : TRUE;
 	  netHttpGet(lf, npu, keepAlive);
 	}
       /* Get as many responses as we can; call responseCB() and 
        * advance qStart for each. */
       for (qPtr = qStart;  qPtr != NULL;  qPtr = qPtr->next)
         {
 	  if (lineFileParseHttpHeader(lf, &hdr, &chunked, &contentLength))
 	    {
 	      body = lineFileSlurpHttpBody(lf, chunked, contentLength);
 	      dyStringClear(dyQ);
 	      dyStringAppend(dyQ, base);
 	      dyStringAppend(dyQ, qPtr->name);
 	      responseCB(userData, dyQ->string, hdr, body);
 	      qStart = qStart->next;
 	      qCount++;
 	    }
 	  else
 	    {
 	      if (numParseFailures++ > qTotal) {
 		done = TRUE;
 	      }
 	      break;
 	    }
 	}
     }
 
   return qCount;
 } /* netHttpMultipleQueries */
 
 boolean hasProtocol(char *urlOrPath)
 /* Return TRUE if it looks like it has http://, ftp:// etc. */
 {
 return stringIn("://", urlOrPath) != NULL;
 }