a13302691fc41d6ff9a561685f4af33ef2921d51
galt
  Wed May 24 14:32:19 2017 -0700
Problem discovered handle leak. Reported by Jonathan. We just need to close it ourselves at the end since we use BIO_noclose flag. This is good for future if we someday re-use a connection.

diff --git src/lib/https.c src/lib/https.c
index 5bf8b6a..fdfe924 100644
--- src/lib/https.c
+++ src/lib/https.c
@@ -1,487 +1,490 @@
 /* Connect via https. */
 
 /* Copyright (C) 2012 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "openssl/ssl.h"
 #include "openssl/err.h"
 
 #include <sys/socket.h>
 #include <unistd.h>
 #include <pthread.h>
 #include <signal.h>
 
 #include "common.h"
 #include "internet.h"
 #include "errAbort.h"
 #include "net.h"
 
 
 static pthread_mutex_t *mutexes = NULL;
  
 static unsigned long openssl_id_callback(void)
 {
 return ((unsigned long)pthread_self());
 }
  
 static void openssl_locking_callback(int mode, int n, const char * file, int line)
 {
 if (mode & CRYPTO_LOCK)
     pthread_mutex_lock(&mutexes[n]);
 else
     pthread_mutex_unlock(&mutexes[n]);
 }
  
 void openssl_pthread_setup(void)
 {
 int i;
 int numLocks = CRYPTO_num_locks();
 AllocArray(mutexes, numLocks);
 for (i = 0;  i < numLocks;  i++)
     pthread_mutex_init(&mutexes[i], NULL);
 CRYPTO_set_id_callback(openssl_id_callback);
 CRYPTO_set_locking_callback(openssl_locking_callback);
 }
  
 
 struct netConnectHttpsParams
 /* params to pass to thread */
 {
 pthread_t thread;
 char *hostName;
 int port;
 boolean noProxy;
 int sv[2]; /* the pair of socket descriptors */
 };
 
 static void xerrno(char *msg)
 {
 fprintf(stderr, "%s : %s\n", strerror(errno), msg); fflush(stderr);
 }
 
 static void xerr(char *msg)
 {
 fprintf(stderr, "%s\n", msg); fflush(stderr);
 }
 
 void openSslInit()
 /* do only once */
 {
 static boolean done = FALSE;
 static pthread_mutex_t osiMutex = PTHREAD_MUTEX_INITIALIZER;
 pthread_mutex_lock( &osiMutex );
 if (!done)
     {
     SSL_library_init();
     ERR_load_crypto_strings();
     ERR_load_SSL_strings();
     OpenSSL_add_all_algorithms();
     openssl_pthread_setup();
     done = TRUE;
     }
 pthread_mutex_unlock( &osiMutex );
 }
 
 
 void *netConnectHttpsThread(void *threadParam)
 /* use a thread to run socket back to user */
 {
 /* child */
 
 struct netConnectHttpsParams *params = threadParam;
 
 pthread_detach(params->thread);  // this thread will never join back with it's progenitor
 
 int fd=0;
 char *proxyUrl = getenv("https_proxy");
 if (params->noProxy)
     proxyUrl = NULL;
 char *connectHost;
 int connectPort;
 
-BIO *sbio=NULL, *ssbio=NULL;
+BIO *fbio=NULL;  // file descriptor bio
+BIO *sbio=NULL;  // ssl bio
 SSL_CTX *ctx;
 SSL *ssl;
 
 openSslInit();
 
 ctx = SSL_CTX_new(SSLv23_client_method());
 
 fd_set readfds;
 fd_set writefds;
 int err;
 struct timeval tv;
 
 
 /* TODO checking certificates 
 
 char *certFile = NULL;
 char *certPath = NULL;
 if (certFile || certPath)
     {
     SSL_CTX_load_verify_locations(ctx,certFile,certPath);
 #if (OPENSSL_VERSION_NUMBER < 0x0090600fL)
     SSL_CTX_set_verify_depth(ctx,1);
 #endif
     }
 
 // verify paths and mode.
 
 */
 
 
 
 // Don't want any retries since we are non-blocking bio now
 // This is available on newer versions of openssl
 //SSL_set_mode(ssl, SSL_MODE_AUTO_RETRY);
 
 // Support for Http Proxy
 struct netParsedUrl pxy;
 if (proxyUrl)
     {
     netParseUrl(proxyUrl, &pxy);
     if (!sameString(pxy.protocol, "http"))
 	{
 	char s[256];	
 	safef(s, sizeof s, "Unknown proxy protocol %s in %s. Should be http.", pxy.protocol, proxyUrl);
 	xerr(s);
 	goto cleanup;
 	}
     connectHost = pxy.host;
     connectPort = atoi(pxy.port);
     }
 else
     {
     connectHost = params->hostName;
     connectPort = params->port;
     }
 fd = netConnect(connectHost,connectPort);
 if (fd == -1)
     {
     xerr("netConnect() failed");
     goto cleanup;
     }
 
 if (proxyUrl)
     {
     char *logProxy = getenv("log_proxy");
     if (sameOk(logProxy,"on"))
 	verbose(1, "CONNECT %s:%d HTTP/1.0 via %s:%d\n", params->hostName, params->port, connectHost,connectPort);
     struct dyString *dy = newDyString(512);
     dyStringPrintf(dy, "CONNECT %s:%d HTTP/1.0\r\n", params->hostName, params->port);
     setAuthorization(pxy, "Proxy-Authorization", dy);
     dyStringAppend(dy, "\r\n");
     mustWriteFd(fd, dy->string, dy->stringSize);
     dyStringFree(&dy);
     // verify response
     char *newUrl = NULL;
     boolean success = netSkipHttpHeaderLinesWithRedirect(fd, proxyUrl, &newUrl);
     if (!success) 
 	{
 	xerr("proxy server response failed");
 	goto cleanup;
 	}
     if (newUrl) /* no redirects */
 	{
 	xerr("proxy server response should not be a redirect");
 	goto cleanup;
 	}
     }
 
 
-sbio=BIO_new_socket(fd,BIO_NOCLOSE);
-if (sbio == NULL)
+fbio=BIO_new_socket(fd,BIO_NOCLOSE);  
+// BIO_NOCLOSE because we handle closing fd ourselves.
+if (fbio == NULL)
     {
     xerr("BIO_new_socket() failed");
     goto cleanup;
     }
-ssbio = BIO_new_ssl(ctx, 1);
-if (ssbio == NULL) 
+sbio = BIO_new_ssl(ctx, 1);
+if (sbio == NULL) 
     {
     xerr("BIO_new_ssl() failed");
     goto cleanup;
     }
-sbio = BIO_push(ssbio, sbio);
+sbio = BIO_push(sbio, fbio);
 BIO_get_ssl(sbio, &ssl);
 if(!ssl) 
     {
     xerr("Can't locate SSL pointer");
     goto cleanup;
     }
 
 
 /* 
 Server Name Indication (SNI)
 Required to complete tls ssl negotiation for systems which house multiple domains. (SNI)
 This is common when serving HTTPS requests with a wildcard certificate (*.domain.tld).
 This line will allow the ssl connection to send the hostname at tls negotiation time.
 It tells the remote server which hostname the client is connecting to.
 The hostname must not be an IP address.
 */ 
 if (!internetIsDottedQuad(params->hostName))
     SSL_set_tlsext_host_name(ssl,params->hostName);
 
 BIO_set_nbio(sbio, 1);     /* non-blocking mode */
 
 while (1) 
     {
     if (BIO_do_handshake(sbio) == 1) 
 	{
 	break;  /* Connected */
 	}
     if (! BIO_should_retry(sbio)) 
 	{
 	xerr("BIO_do_handshake() failed");
 	char s[256];	
 	safef(s, sizeof s, "SSL error: %s", ERR_reason_error_string(ERR_get_error()));
 	xerr(s);
 	goto cleanup;
 	}
 
     fd = BIO_get_fd(sbio, NULL);
     if (fd == -1) 
 	{
 	xerr("unable to get BIO descriptor");
 	goto cleanup;
 	}
     FD_ZERO(&readfds);
     FD_ZERO(&writefds);
     if (BIO_should_read(sbio)) 
 	{
 	FD_SET(fd, &readfds);
 	}
     else if (BIO_should_write(sbio)) 
 	{
 	FD_SET(fd, &writefds);
 	}
     else 
 	{  /* BIO_should_io_special() */
 	FD_SET(fd, &readfds);
 	FD_SET(fd, &writefds);
 	}
     tv.tv_sec = (long) (DEFAULTCONNECTTIMEOUTMSEC/1000);  // timeout default 10 seconds
     tv.tv_usec = (long) (((DEFAULTCONNECTTIMEOUTMSEC/1000)-tv.tv_sec)*1000000);
 
     err = select(fd + 1, &readfds, &writefds, NULL, &tv);
     if (err < 0) 
 	{
 	xerr("select() error");
 	goto cleanup;
 	}
 
     if (err == 0) 
 	{
 	char s[256];	
 	safef(s, sizeof s, "connection timeout to %s", params->hostName);
 	xerr(s);
 	goto cleanup;
 	}
     }
 
 
 /* TODO checking certificates 
 
 if (certFile || certPath)
     if (!check_cert(ssl, host))
 	return -1;
 
 */
 
 /* we need to wait on both the user's socket and the BIO SSL socket 
  * to see if we need to ferry data from one to the other */
 
 
 char sbuf[32768];  // socket buffer sv[1] to user
 char bbuf[32768];  // bio buffer
 int srd = 0;
 int swt = 0;
 int brd = 0;
 int bwt = 0;
 while (1) 
     {
 
     // Do NOT move this outside the while loop. 
     /* Get underlying file descriptor, needed for select call */
     fd = BIO_get_fd(sbio, NULL);
     if (fd == -1) 
 	{
 	xerr("BIO doesn't seem to be initialized in https, unable to get descriptor.");
 	goto cleanup;
 	}
 
 
     FD_ZERO(&readfds);
     FD_ZERO(&writefds);
 
     if (brd == 0)
 	FD_SET(fd, &readfds);
     if (swt < srd)
 	FD_SET(fd, &writefds);
     if (srd == 0)
 	FD_SET(params->sv[1], &readfds);
 
     tv.tv_sec = (long) (DEFAULTCONNECTTIMEOUTMSEC/1000);  // timeout default 10 seconds
     tv.tv_usec = (long) (((DEFAULTCONNECTTIMEOUTMSEC/1000)-tv.tv_sec)*1000000);
 
     err = select(max(fd,params->sv[1]) + 1, &readfds, &writefds, NULL, &tv);
 
     /* Evaluate select() return code */
     if (err < 0) 
 	{
 	xerr("error during select()");
 	goto cleanup;
 	}
     else if (err == 0) 
 	{
 	/* Timed out - just quit */
 	xerr("https timeout expired");
 	goto cleanup;
 	}
 
     else 
 	{
 	if (FD_ISSET(params->sv[1], &readfds))
 	    {
 	    swt = 0;
 	    srd = read(params->sv[1], sbuf, 32768);
 	    if (srd == -1)
 		{
 		if (errno != 104) // udcCache often closes causing "Connection reset by peer"
 		    xerrno("error reading user pipe for https socket");
 		goto cleanup;
 		}
 	    if (srd == 0) 
 		break;  // user closed socket, we are done
 	    }
 
 	if (FD_ISSET(fd, &writefds))
 	    {
 	    int swtx = BIO_write(sbio, sbuf+swt, srd-swt);
 	    if (swtx <= 0)
 		{
 		if (!BIO_should_write(sbio))
 		    {
 		    ERR_print_errors_fp(stderr);
 		    xerr("Error writing SSL connection");
 		    goto cleanup;
 		    }
 		}
 	    else
 		{
 		swt += swtx;
 		if (swt >= srd)
 		    {
 		    swt = 0;
 		    srd = 0;
 		    }
 		}
 	    }
 
 	if (FD_ISSET(fd, &readfds))
 	    {
 	    bwt = 0;
 	    brd = BIO_read(sbio, bbuf, 32768);
 
 	    if (brd <= 0)
 		{
 		if (BIO_should_read(sbio))
 		    {
 		    brd = 0;
 		    continue;
 		    }
 		else
 		    {
 		    if (brd == 0) break;
 		    ERR_print_errors_fp(stderr);
 		    xerr("Error reading SSL connection");
 		    goto cleanup;
 		    }
 		}
 	    // write the https data received immediately back on socket to user, and it's ok if it blocks.
 	    while(bwt < brd)
 		{
 		// NOTE: Intended as a thread-specific library-safe way not to ignore SIG_PIPE for the entire application.
 		// temporarily block sigpipe on this thread
 		sigset_t sigpipe_mask;
 		sigemptyset(&sigpipe_mask);
 		sigaddset(&sigpipe_mask, SIGPIPE);
 		sigset_t saved_mask;
 		if (pthread_sigmask(SIG_BLOCK, &sigpipe_mask, &saved_mask) == -1) {
 		    perror("pthread_sigmask");
 		    exit(1);
 		}
 		int bwtx = write(params->sv[1], bbuf+bwt, brd-bwt);
 		int saveErrno = errno;
 		if ((bwtx == -1) && (saveErrno == EPIPE))
 		    { // if there was a EPIPE, accept and consume the SIGPIPE now.
 		    int sigErr, sig;
 		    if ((sigErr = sigwait(&sigpipe_mask, &sig)) != 0) 
 			{
 			errno = sigErr;
 			perror("sigtimedwait");
 			exit(1);
 			}
 		    }
 		// restore signal mask on this thread
 		if (pthread_sigmask(SIG_SETMASK, &saved_mask, 0) == -1) 
 		    {
 		    perror("pthread_sigmask");
 		    exit(1);
 		    }
 		errno = saveErrno;
 		if (bwtx == -1)
 		    {
 		    if ((errno != 104)  // udcCache often closes causing "Connection reset by peer"
 		     && (errno !=  32)) // udcCache often closes causing "Broken pipe"
 			xerrno("error writing https data back to user pipe");
 		    goto cleanup;
 		    }
 		bwt += bwtx;
 		}
 	    brd = 0;
 	    bwt = 0;
 	    }
 	}
     }
 
 cleanup:
 
 BIO_free_all(sbio);  // will free entire chain of bios
+close(fd);     // Needed because we use BIO_NOCLOSE above. Someday might want to re-use a connection.
 close(params->sv[1]);  /* we are done with it */
 
 return NULL;
 }
 
 int netConnectHttps(char *hostName, int port, boolean noProxy)
 /* Return socket for https connection with server or -1 if error. */
 {
 
 fflush(stdin);
 fflush(stdout);
 fflush(stderr);
 
 struct netConnectHttpsParams *params;
 AllocVar(params);
 params->hostName = cloneString(hostName);
 params->port = port;
 params->noProxy = noProxy;
 
 socketpair(AF_UNIX, SOCK_STREAM, 0, params->sv);
 
 // netBlockBrokenPipes(); works, but is heavy handed 
 //  and ignores SIGPIPE on all connections for all threads in the entire application. 
 // We are trying something more subtle and library and thread-friendly instead.
 
 int rc;
 rc = pthread_create(&params->thread, NULL, netConnectHttpsThread, (void *)params);
 if (rc)
     {
     errAbort("Unexpected error %d from pthread_create(): %s",rc,strerror(rc));
     }
 
 /* parent */
 
 return params->sv[0];
 
 }