GList * add_header(GList *headers, HTTP_HEADER *h) { headers = strip_header(headers, h->key); headers = g_list_append(headers, h); return headers; }
FILE * hopen( const char *url, const char *mode ) { FILE *fd = NULL; if (!url) return NULL; act("opening stream: '%s'", url); if (strstr(url, HTTP_PREFIX)) { fd = http_open(url); if (fd) { strip_header(fd); /*if server replies with err message and closes*/ if (feof(fd)) {fclose(fd); fd=NULL;} } return fd; } else { return fopen(url, mode); } }
/* Calculate L_b and P_b for the 2MM QY measurement method. DATA can be a scan * of a directly or indirectly excited sample in the integrating sphere. LMIN, * LMAX describe the bounds on the summation of the excitation peak. PMIN and * PMAX bound the photoluminescence peak summation. Must be called after get_L_a. */ double TwoMMQY(FILE* data, int lmin, int lmax, int pmin, int pmax) { double x[MAX_NUM_POINTS]; double y[MAX_NUM_POINTS]; char line[LINE_SIZE]; char* p; int index = 0; double baseline = 0.0; if (!strip_header(data)) { return 0.0; } while(fgets(line, sizeof(line), data)) { strtok(line, "\n"); if (index >= num_points) break; double xval = strtod(line, &p); double yval = atof(p); x[index] = xval; y[index] = yval; if ((index < NAP/2) || (index >= num_points - NAP/2)) { baseline += yval; } index++; } baseline = baseline / NAP; printf("BASELINE %f\n",baseline); for (int j = 0; j < num_points; j++) { y[j] -= baseline; if (is_corr) y[j] *= corr[j]; if ((j + offset_data > lmin) && (j + offset_data < lmax)) { L_b += y[j]; L_b_err += pow(corr[j], 2) * (y[j] + baseline + baseline) + pow(y[j], 2) * pow(.04148 * corr[j], 2); } else if ((j + offset_data >= pmin) && (j + offset_data <= pmax)) { P_b += y[j]; P_b_err += pow(corr[j], 2) * (y[j] + baseline + baseline) + pow(y[j], 2) * pow(.04148 * corr[j], 2); } L_b_err = sqrt(L_b_err); P_b_err = sqrt(P_b_err); } TGraph* g = new TGraph(300, x, y); g->Draw("SAME"); return P_b / (L_a - L_b); }
/* Determine the value for L_a, which is the number of counts in the * excitation peak without the sample in the solvent. Data comes from * file DATA, points are summed from MIN to MAX. */ void get_L_a(FILE* data, int min, int max) { double x[MAX_NUM_POINTS]; double y[MAX_NUM_POINTS]; char line[LINE_SIZE]; char* p; int index = 0; double baseline = 0.0; offset_ref = strip_header(data); if (!offset_ref) { return; } while(fgets(line, sizeof(line), data)) { strtok(line, "\n"); if (index >= num_points) break; double xval = strtod(line, &p); double yval = atof(p); x[index] = xval; y[index] = yval; if ((index < (3 * NAP) / 2)||(index >= num_points - (3 * NAP ) / 2)) { //if (index >= num_points - 45) { baseline += yval; } index++; } baseline = baseline / (3 * NAP); //baseline /= 45; for (int j = 0; j < num_points; j++) { y[j] -= baseline; if (is_corr) y[j] *= corr[j + offset_ref - offset_data]; if ((j + offset_ref) > min && (j + offset_ref) < max) { L_a += y[j]; L_a_err += pow(corr[j], 2) * (y[j] + baseline + baseline) + pow(y[j], 2) * pow(.04148 * corr[j], 2); } } L_a_err = sqrt(L_a_err); TGraph* g = new TGraph(80, x, y); //g->Draw(); }
/* Determine the value for L_a, which is the number of counts in the * excitation peak without the sample in the solvent. Data comes from * file DATA, points are summed around excitation wavelength EX. */ void get_L_a(FILE* data, int ex) { double x[MAX_NUM_POINTS]; double y[MAX_NUM_POINTS]; char line[LINE_SIZE]; char* p; int index = 0; double baseline = 0.0; offset_ref = strip_header(data); if (!offset_ref) { return; } while(fgets(line, sizeof(line), data)) { strtok(line, "\n"); if (index >= num_points) break; double xval = strtod(line, &p); double yval = atof(p); x[index] = xval; y[index] = yval; if (((index < NAP) || (index >= num_points - NAP)) && (ex > 330)) { baseline += yval; } else if ((index >= num_points - (2 * NAP)) && (ex <= 330)) { baseline += yval; } index++; } baseline = baseline / (2 * NAP); for (int j = 0; j < num_points; j++) { y[j] -= baseline; if (is_corr) y[j] *= corr[j + offset_ref - offset_data]; if (((j + offset_ref) >= (ex - 8)) && ((j + offset_ref) <= (ex + 4))) { L_a += y[j]; L_a_err += pow(corr[j], 2) * (y[j] + baseline + baseline) + pow(y[j], 2) * pow(.04148 * corr[j], 2); } } L_a_err = sqrt(L_a_err); }
/* Calculate L_c and P_c for the 3MM QY measurement method. Must be called * after TwoMMQY has been called on in data. DATA must specify a scan of * an indirectly excited sample. EX, PMIN and PMAX are the same as * in TwoMMQY. */ double ThreeMMQY(FILE* data, int ex, int pmin, int pmax) { double A = 0.0; double y[MAX_NUM_POINTS]; char line[LINE_SIZE]; char* p; int index = 0; double baseline = 0.0; if (!strip_header(data)) { return 0.0; } while(fgets(line, sizeof(line), data)) { strtok(line, "\n"); if (index >= num_points) break; double xval = strtod(line, &p); double yval = atof(p); y[index] = yval; if ((index < NAP/2) || (index >= num_points - NAP/2)) { baseline += yval; } index++; } baseline = baseline / NAP; for (int j = 0; j < num_points; j++) { y[j] -= baseline; if (is_corr) y[j] *= corr[j]; if ((j + offset_data >= (EX - 8)) && (j + offset_data <= (EX + 4))) { L_c += y[j]; } else if ((j + offset_data >= pmin) && (j + offset_data <= pmax)) { P_c += y[j]; } } A = 1 - (L_b / L_c); return (P_b - ((1 - A) * P_c)) / (A * L_a); }
php_stream *php_stream_url_wrap_http_ex(php_stream_wrapper *wrapper, const char *path, const char *mode, int options, char **opened_path, php_stream_context *context, int redirect_max, int flags STREAMS_DC TSRMLS_DC) /* {{{ */ { php_stream *stream = NULL; php_url *resource = NULL; int use_ssl; int use_proxy = 0; char *scratch = NULL; char *tmp = NULL; char *ua_str = NULL; zval **ua_zval = NULL, **tmpzval = NULL, *ssl_proxy_peer_name = NULL; int scratch_len = 0; int body = 0; char location[HTTP_HEADER_BLOCK_SIZE]; zval *response_header = NULL; int reqok = 0; char *http_header_line = NULL; char tmp_line[128]; size_t chunk_size = 0, file_size = 0; int eol_detect = 0; char *transport_string, *errstr = NULL; int transport_len, have_header = 0, request_fulluri = 0, ignore_errors = 0; char *protocol_version = NULL; int protocol_version_len = 3; /* Default: "1.0" */ struct timeval timeout; char *user_headers = NULL; int header_init = ((flags & HTTP_WRAPPER_HEADER_INIT) != 0); int redirected = ((flags & HTTP_WRAPPER_REDIRECTED) != 0); int follow_location = 1; php_stream_filter *transfer_encoding = NULL; int response_code; tmp_line[0] = '\0'; if (redirect_max < 1) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Redirection limit reached, aborting"); return NULL; } resource = php_url_parse(path); if (resource == NULL) { return NULL; } if (strncasecmp(resource->scheme, "http", sizeof("http")) && strncasecmp(resource->scheme, "https", sizeof("https"))) { if (!context || php_stream_context_get_option(context, wrapper->wops->label, "proxy", &tmpzval) == FAILURE || Z_TYPE_PP(tmpzval) != IS_STRING || Z_STRLEN_PP(tmpzval) <= 0) { php_url_free(resource); return php_stream_open_wrapper_ex(path, mode, REPORT_ERRORS, NULL, context); } /* Called from a non-http wrapper with http proxying requested (i.e. ftp) */ request_fulluri = 1; use_ssl = 0; use_proxy = 1; transport_len = Z_STRLEN_PP(tmpzval); transport_string = estrndup(Z_STRVAL_PP(tmpzval), Z_STRLEN_PP(tmpzval)); } else { /* Normal http request (possibly with proxy) */ if (strpbrk(mode, "awx+")) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "HTTP wrapper does not support writeable connections"); php_url_free(resource); return NULL; } use_ssl = resource->scheme && (strlen(resource->scheme) > 4) && resource->scheme[4] == 's'; /* choose default ports */ if (use_ssl && resource->port == 0) resource->port = 443; else if (resource->port == 0) resource->port = 80; if (context && php_stream_context_get_option(context, wrapper->wops->label, "proxy", &tmpzval) == SUCCESS && Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval) > 0) { use_proxy = 1; transport_len = Z_STRLEN_PP(tmpzval); transport_string = estrndup(Z_STRVAL_PP(tmpzval), Z_STRLEN_PP(tmpzval)); } else { transport_len = spprintf(&transport_string, 0, "%s://%s:%d", use_ssl ? "ssl" : "tcp", resource->host, resource->port); } } if (context && php_stream_context_get_option(context, wrapper->wops->label, "timeout", &tmpzval) == SUCCESS) { SEPARATE_ZVAL(tmpzval); convert_to_double_ex(tmpzval); timeout.tv_sec = (time_t) Z_DVAL_PP(tmpzval); timeout.tv_usec = (size_t) ((Z_DVAL_PP(tmpzval) - timeout.tv_sec) * 1000000); } else { timeout.tv_sec = FG(default_socket_timeout); timeout.tv_usec = 0; } stream = php_stream_xport_create(transport_string, transport_len, options, STREAM_XPORT_CLIENT | STREAM_XPORT_CONNECT, NULL, &timeout, context, &errstr, NULL); if (stream) { php_stream_set_option(stream, PHP_STREAM_OPTION_READ_TIMEOUT, 0, &timeout); } if (errstr) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "%s", errstr); efree(errstr); errstr = NULL; } efree(transport_string); if (stream && use_proxy && use_ssl) { smart_str header = {0}; /* Set peer_name or name verification will try to use the proxy server name */ if (!context || php_stream_context_get_option(context, "ssl", "peer_name", &tmpzval) == FAILURE) { MAKE_STD_ZVAL(ssl_proxy_peer_name); ZVAL_STRING(ssl_proxy_peer_name, resource->host, 1); php_stream_context_set_option(stream->context, "ssl", "peer_name", ssl_proxy_peer_name); } smart_str_appendl(&header, "CONNECT ", sizeof("CONNECT ")-1); smart_str_appends(&header, resource->host); smart_str_appendc(&header, ':'); smart_str_append_unsigned(&header, resource->port); smart_str_appendl(&header, " HTTP/1.0\r\n", sizeof(" HTTP/1.0\r\n")-1); /* check if we have Proxy-Authorization header */ if (context && php_stream_context_get_option(context, "http", "header", &tmpzval) == SUCCESS) { char *s, *p; if (Z_TYPE_PP(tmpzval) == IS_ARRAY) { HashPosition pos; zval **tmpheader = NULL; for (zend_hash_internal_pointer_reset_ex(Z_ARRVAL_PP(tmpzval), &pos); SUCCESS == zend_hash_get_current_data_ex(Z_ARRVAL_PP(tmpzval), (void *)&tmpheader, &pos); zend_hash_move_forward_ex(Z_ARRVAL_PP(tmpzval), &pos)) { if (Z_TYPE_PP(tmpheader) == IS_STRING) { s = Z_STRVAL_PP(tmpheader); do { while (*s == ' ' || *s == '\t') s++; p = s; while (*p != 0 && *p != ':' && *p != '\r' && *p !='\n') p++; if (*p == ':') { p++; if (p - s == sizeof("Proxy-Authorization:") - 1 && zend_binary_strcasecmp(s, sizeof("Proxy-Authorization:") - 1, "Proxy-Authorization:", sizeof("Proxy-Authorization:") - 1) == 0) { while (*p != 0 && *p != '\r' && *p !='\n') p++; smart_str_appendl(&header, s, p - s); smart_str_appendl(&header, "\r\n", sizeof("\r\n")-1); goto finish; } else { while (*p != 0 && *p != '\r' && *p !='\n') p++; } } s = p; while (*s == '\r' || *s == '\n') s++; } while (*s != 0); } } } else if (Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval)) { s = Z_STRVAL_PP(tmpzval); do { while (*s == ' ' || *s == '\t') s++; p = s; while (*p != 0 && *p != ':' && *p != '\r' && *p !='\n') p++; if (*p == ':') { p++; if (p - s == sizeof("Proxy-Authorization:") - 1 && zend_binary_strcasecmp(s, sizeof("Proxy-Authorization:") - 1, "Proxy-Authorization:", sizeof("Proxy-Authorization:") - 1) == 0) { while (*p != 0 && *p != '\r' && *p !='\n') p++; smart_str_appendl(&header, s, p - s); smart_str_appendl(&header, "\r\n", sizeof("\r\n")-1); goto finish; } else { while (*p != 0 && *p != '\r' && *p !='\n') p++; } } s = p; while (*s == '\r' || *s == '\n') s++; } while (*s != 0); } } finish: smart_str_appendl(&header, "\r\n", sizeof("\r\n")-1); if (php_stream_write(stream, header.c, header.len) != header.len) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Cannot connect to HTTPS server through proxy"); php_stream_close(stream); stream = NULL; } smart_str_free(&header); if (stream) { char header_line[HTTP_HEADER_BLOCK_SIZE]; /* get response header */ while (php_stream_gets(stream, header_line, HTTP_HEADER_BLOCK_SIZE-1) != NULL) { if (header_line[0] == '\n' || header_line[0] == '\r' || header_line[0] == '\0') { break; } } } /* enable SSL transport layer */ if (stream) { if (php_stream_xport_crypto_setup(stream, STREAM_CRYPTO_METHOD_ANY_CLIENT, NULL TSRMLS_CC) < 0 || php_stream_xport_crypto_enable(stream, 1 TSRMLS_CC) < 0) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Cannot connect to HTTPS server through proxy"); php_stream_close(stream); stream = NULL; } } } if (stream == NULL) goto out; /* avoid buffering issues while reading header */ if (options & STREAM_WILL_CAST) chunk_size = php_stream_set_chunk_size(stream, 1); /* avoid problems with auto-detecting when reading the headers -> the headers * are always in canonical \r\n format */ eol_detect = stream->flags & (PHP_STREAM_FLAG_DETECT_EOL | PHP_STREAM_FLAG_EOL_MAC); stream->flags &= ~(PHP_STREAM_FLAG_DETECT_EOL | PHP_STREAM_FLAG_EOL_MAC); php_stream_context_set(stream, context TSRMLS_CC); php_stream_notify_info(context, PHP_STREAM_NOTIFY_CONNECT, NULL, 0); if (header_init && context && php_stream_context_get_option(context, "http", "max_redirects", &tmpzval) == SUCCESS) { SEPARATE_ZVAL(tmpzval); convert_to_long_ex(tmpzval); redirect_max = Z_LVAL_PP(tmpzval); } if (context && php_stream_context_get_option(context, "http", "method", &tmpzval) == SUCCESS) { if (Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval) > 0) { /* As per the RFC, automatically redirected requests MUST NOT use other methods than * GET and HEAD unless it can be confirmed by the user */ if (!redirected || (Z_STRLEN_PP(tmpzval) == 3 && memcmp("GET", Z_STRVAL_PP(tmpzval), 3) == 0) || (Z_STRLEN_PP(tmpzval) == 4 && memcmp("HEAD",Z_STRVAL_PP(tmpzval), 4) == 0) ) { scratch_len = strlen(path) + 29 + Z_STRLEN_PP(tmpzval); scratch = emalloc(scratch_len); strlcpy(scratch, Z_STRVAL_PP(tmpzval), Z_STRLEN_PP(tmpzval) + 1); strncat(scratch, " ", 1); } } } if (context && php_stream_context_get_option(context, "http", "protocol_version", &tmpzval) == SUCCESS) { SEPARATE_ZVAL(tmpzval); convert_to_double_ex(tmpzval); protocol_version_len = spprintf(&protocol_version, 0, "%.1F", Z_DVAL_PP(tmpzval)); } if (!scratch) { scratch_len = strlen(path) + 29 + protocol_version_len; scratch = emalloc(scratch_len); strncpy(scratch, "GET ", scratch_len); } /* Should we send the entire path in the request line, default to no. */ if (!request_fulluri && context && php_stream_context_get_option(context, "http", "request_fulluri", &tmpzval) == SUCCESS) { zval ztmp = **tmpzval; zval_copy_ctor(&ztmp); convert_to_boolean(&ztmp); request_fulluri = Z_BVAL(ztmp) ? 1 : 0; zval_dtor(&ztmp); } if (request_fulluri) { /* Ask for everything */ strcat(scratch, path); } else { /* Send the traditional /path/to/file?query_string */ /* file */ if (resource->path && *resource->path) { strlcat(scratch, resource->path, scratch_len); } else { strlcat(scratch, "/", scratch_len); } /* query string */ if (resource->query) { strlcat(scratch, "?", scratch_len); strlcat(scratch, resource->query, scratch_len); } } /* protocol version we are speaking */ if (protocol_version) { strlcat(scratch, " HTTP/", scratch_len); strlcat(scratch, protocol_version, scratch_len); strlcat(scratch, "\r\n", scratch_len); } else { strlcat(scratch, " HTTP/1.0\r\n", scratch_len); } /* send it */ php_stream_write(stream, scratch, strlen(scratch)); if (context && php_stream_context_get_option(context, "http", "header", &tmpzval) == SUCCESS) { tmp = NULL; if (Z_TYPE_PP(tmpzval) == IS_ARRAY) { HashPosition pos; zval **tmpheader = NULL; smart_str tmpstr = {0}; for (zend_hash_internal_pointer_reset_ex(Z_ARRVAL_PP(tmpzval), &pos); SUCCESS == zend_hash_get_current_data_ex(Z_ARRVAL_PP(tmpzval), (void *)&tmpheader, &pos); zend_hash_move_forward_ex(Z_ARRVAL_PP(tmpzval), &pos) ) { if (Z_TYPE_PP(tmpheader) == IS_STRING) { smart_str_appendl(&tmpstr, Z_STRVAL_PP(tmpheader), Z_STRLEN_PP(tmpheader)); smart_str_appendl(&tmpstr, "\r\n", sizeof("\r\n") - 1); } } smart_str_0(&tmpstr); /* Remove newlines and spaces from start and end. there's at least one extra \r\n at the end that needs to go. */ if (tmpstr.c) { tmp = php_trim(tmpstr.c, strlen(tmpstr.c), NULL, 0, NULL, 3 TSRMLS_CC); smart_str_free(&tmpstr); } } if (Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval)) { /* Remove newlines and spaces from start and end php_trim will estrndup() */ tmp = php_trim(Z_STRVAL_PP(tmpzval), Z_STRLEN_PP(tmpzval), NULL, 0, NULL, 3 TSRMLS_CC); } if (tmp && strlen(tmp) > 0) { char *s; user_headers = estrdup(tmp); /* Make lowercase for easy comparison against 'standard' headers */ php_strtolower(tmp, strlen(tmp)); if (!header_init) { /* strip POST headers on redirect */ strip_header(user_headers, tmp, "content-length:"); strip_header(user_headers, tmp, "content-type:"); } if ((s = strstr(tmp, "user-agent:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_USER_AGENT; } if ((s = strstr(tmp, "host:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_HOST; } if ((s = strstr(tmp, "from:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_FROM; } if ((s = strstr(tmp, "authorization:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_AUTH; } if ((s = strstr(tmp, "content-length:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_CONTENT_LENGTH; } if ((s = strstr(tmp, "content-type:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_TYPE; } if ((s = strstr(tmp, "connection:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { have_header |= HTTP_HEADER_CONNECTION; } /* remove Proxy-Authorization header */ if (use_proxy && use_ssl && (s = strstr(tmp, "proxy-authorization:")) && (s == tmp || *(s-1) == '\r' || *(s-1) == '\n' || *(s-1) == '\t' || *(s-1) == ' ')) { char *p = s + sizeof("proxy-authorization:") - 1; while (s > tmp && (*(s-1) == ' ' || *(s-1) == '\t')) s--; while (*p != 0 && *p != '\r' && *p != '\n') p++; while (*p == '\r' || *p == '\n') p++; if (*p == 0) { if (s == tmp) { efree(user_headers); user_headers = NULL; } else { while (s > tmp && (*(s-1) == '\r' || *(s-1) == '\n')) s--; user_headers[s - tmp] = 0; } } else { memmove(user_headers + (s - tmp), user_headers + (p - tmp), strlen(p) + 1); } } } if (tmp) { efree(tmp); } } /* auth header if it was specified */ if (((have_header & HTTP_HEADER_AUTH) == 0) && resource->user) { /* decode the strings first */ php_url_decode(resource->user, strlen(resource->user)); /* scratch is large enough, since it was made large enough for the whole URL */ strcpy(scratch, resource->user); strcat(scratch, ":"); /* Note: password is optional! */ if (resource->pass) { php_url_decode(resource->pass, strlen(resource->pass)); strcat(scratch, resource->pass); } tmp = (char*)php_base64_encode((unsigned char*)scratch, strlen(scratch), NULL); if (snprintf(scratch, scratch_len, "Authorization: Basic %s\r\n", tmp) > 0) { php_stream_write(stream, scratch, strlen(scratch)); php_stream_notify_info(context, PHP_STREAM_NOTIFY_AUTH_REQUIRED, NULL, 0); } efree(tmp); tmp = NULL; } /* if the user has configured who they are, send a From: line */ if (((have_header & HTTP_HEADER_FROM) == 0) && FG(from_address)) { if (snprintf(scratch, scratch_len, "From: %s\r\n", FG(from_address)) > 0) php_stream_write(stream, scratch, strlen(scratch)); } /* Send Host: header so name-based virtual hosts work */ if ((have_header & HTTP_HEADER_HOST) == 0) { if ((use_ssl && resource->port != 443 && resource->port != 0) || (!use_ssl && resource->port != 80 && resource->port != 0)) { if (snprintf(scratch, scratch_len, "Host: %s:%i\r\n", resource->host, resource->port) > 0) php_stream_write(stream, scratch, strlen(scratch)); } else { if (snprintf(scratch, scratch_len, "Host: %s\r\n", resource->host) > 0) { php_stream_write(stream, scratch, strlen(scratch)); } } } /* Send a Connection: close header when using HTTP 1.1 or later to avoid * hanging when the server interprets the RFC literally and establishes a * keep-alive connection, unless the user specifically requests something * else by specifying a Connection header in the context options. */ if (protocol_version && ((have_header & HTTP_HEADER_CONNECTION) == 0) && (strncmp(protocol_version, "1.0", MIN(protocol_version_len, 3)) > 0)) { php_stream_write_string(stream, "Connection: close\r\n"); } if (context && php_stream_context_get_option(context, "http", "user_agent", &ua_zval) == SUCCESS && Z_TYPE_PP(ua_zval) == IS_STRING) { ua_str = Z_STRVAL_PP(ua_zval); } else if (FG(user_agent)) { ua_str = FG(user_agent); } if (((have_header & HTTP_HEADER_USER_AGENT) == 0) && ua_str) { #define _UA_HEADER "User-Agent: %s\r\n" char *ua; size_t ua_len; ua_len = sizeof(_UA_HEADER) + strlen(ua_str); /* ensure the header is only sent if user_agent is not blank */ if (ua_len > sizeof(_UA_HEADER)) { ua = emalloc(ua_len + 1); if ((ua_len = slprintf(ua, ua_len, _UA_HEADER, ua_str)) > 0) { ua[ua_len] = 0; php_stream_write(stream, ua, ua_len); } else { php_error_docref(NULL TSRMLS_CC, E_WARNING, "Cannot construct User-agent header"); } if (ua) { efree(ua); } } } if (user_headers) { /* A bit weird, but some servers require that Content-Length be sent prior to Content-Type for POST * see bug #44603 for details. Since Content-Type maybe part of user's headers we need to do this check first. */ if ( header_init && context && !(have_header & HTTP_HEADER_CONTENT_LENGTH) && php_stream_context_get_option(context, "http", "content", &tmpzval) == SUCCESS && Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval) > 0 ) { scratch_len = slprintf(scratch, scratch_len, "Content-Length: %d\r\n", Z_STRLEN_PP(tmpzval)); php_stream_write(stream, scratch, scratch_len); have_header |= HTTP_HEADER_CONTENT_LENGTH; } php_stream_write(stream, user_headers, strlen(user_headers)); php_stream_write(stream, "\r\n", sizeof("\r\n")-1); efree(user_headers); } /* Request content, such as for POST requests */ if (header_init && context && php_stream_context_get_option(context, "http", "content", &tmpzval) == SUCCESS && Z_TYPE_PP(tmpzval) == IS_STRING && Z_STRLEN_PP(tmpzval) > 0) { if (!(have_header & HTTP_HEADER_CONTENT_LENGTH)) { scratch_len = slprintf(scratch, scratch_len, "Content-Length: %d\r\n", Z_STRLEN_PP(tmpzval)); php_stream_write(stream, scratch, scratch_len); } if (!(have_header & HTTP_HEADER_TYPE)) { php_stream_write(stream, "Content-Type: application/x-www-form-urlencoded\r\n", sizeof("Content-Type: application/x-www-form-urlencoded\r\n") - 1); php_error_docref(NULL TSRMLS_CC, E_NOTICE, "Content-type not specified assuming application/x-www-form-urlencoded"); } php_stream_write(stream, "\r\n", sizeof("\r\n")-1); php_stream_write(stream, Z_STRVAL_PP(tmpzval), Z_STRLEN_PP(tmpzval)); } else { php_stream_write(stream, "\r\n", sizeof("\r\n")-1); } location[0] = '\0'; if (!EG(active_symbol_table)) { zend_rebuild_symbol_table(TSRMLS_C); } if (header_init) { zval *ztmp; MAKE_STD_ZVAL(ztmp); array_init(ztmp); ZEND_SET_SYMBOL(EG(active_symbol_table), "http_response_header", ztmp); } { zval **rh; zend_hash_find(EG(active_symbol_table), "http_response_header", sizeof("http_response_header"), (void **) &rh); response_header = *rh; } if (!php_stream_eof(stream)) { size_t tmp_line_len; /* get response header */ if (php_stream_get_line(stream, tmp_line, sizeof(tmp_line) - 1, &tmp_line_len) != NULL) { zval *http_response; if (tmp_line_len > 9) { response_code = atoi(tmp_line + 9); } else { response_code = 0; } if (context && SUCCESS==php_stream_context_get_option(context, "http", "ignore_errors", &tmpzval)) { ignore_errors = zend_is_true(*tmpzval TSRMLS_CC); } /* when we request only the header, don't fail even on error codes */ if ((options & STREAM_ONLY_GET_HEADERS) || ignore_errors) { reqok = 1; } /* all status codes in the 2xx range are defined by the specification as successful; * all status codes in the 3xx range are for redirection, and so also should never * fail */ if (response_code >= 200 && response_code < 400) { reqok = 1; } else { switch(response_code) { case 403: php_stream_notify_error(context, PHP_STREAM_NOTIFY_AUTH_RESULT, tmp_line, response_code); break; default: /* safety net in the event tmp_line == NULL */ if (!tmp_line_len) { tmp_line[0] = '\0'; } php_stream_notify_error(context, PHP_STREAM_NOTIFY_FAILURE, tmp_line, response_code); } } if (tmp_line[tmp_line_len - 1] == '\n') { --tmp_line_len; if (tmp_line[tmp_line_len - 1] == '\r') { --tmp_line_len; } } MAKE_STD_ZVAL(http_response); ZVAL_STRINGL(http_response, tmp_line, tmp_line_len, 1); zend_hash_next_index_insert(Z_ARRVAL_P(response_header), &http_response, sizeof(zval *), NULL); } } else { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "HTTP request failed, unexpected end of socket!"); goto out; } /* read past HTTP headers */ http_header_line = emalloc(HTTP_HEADER_BLOCK_SIZE); while (!body && !php_stream_eof(stream)) { size_t http_header_line_length; if (php_stream_get_line(stream, http_header_line, HTTP_HEADER_BLOCK_SIZE, &http_header_line_length) && *http_header_line != '\n' && *http_header_line != '\r') { char *e = http_header_line + http_header_line_length - 1; if (*e != '\n') { do { /* partial header */ if (php_stream_get_line(stream, http_header_line, HTTP_HEADER_BLOCK_SIZE, &http_header_line_length) == NULL) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Failed to read HTTP headers"); goto out; } e = http_header_line + http_header_line_length - 1; } while (*e != '\n'); continue; } while (*e == '\n' || *e == '\r') { e--; } http_header_line_length = e - http_header_line + 1; http_header_line[http_header_line_length] = '\0'; if (!strncasecmp(http_header_line, "Location: ", 10)) { if (context && php_stream_context_get_option(context, "http", "follow_location", &tmpzval) == SUCCESS) { SEPARATE_ZVAL(tmpzval); convert_to_long_ex(tmpzval); follow_location = Z_LVAL_PP(tmpzval); } else if (!(response_code >= 300 && response_code < 304 || 307 == response_code || 308 == response_code)) { /* we shouldn't redirect automatically if follow_location isn't set and response_code not in (300, 301, 302, 303 and 307) see http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html#sec10.3.1 RFC 7238 defines 308: http://tools.ietf.org/html/rfc7238 */ follow_location = 0; } strlcpy(location, http_header_line + 10, sizeof(location)); } else if (!strncasecmp(http_header_line, "Content-Type: ", 14)) { php_stream_notify_info(context, PHP_STREAM_NOTIFY_MIME_TYPE_IS, http_header_line + 14, 0); } else if (!strncasecmp(http_header_line, "Content-Length: ", 16)) { file_size = atoi(http_header_line + 16); php_stream_notify_file_size(context, file_size, http_header_line, 0); } else if (!strncasecmp(http_header_line, "Transfer-Encoding: chunked", sizeof("Transfer-Encoding: chunked"))) { /* create filter to decode response body */ if (!(options & STREAM_ONLY_GET_HEADERS)) { long decode = 1; if (context && php_stream_context_get_option(context, "http", "auto_decode", &tmpzval) == SUCCESS) { SEPARATE_ZVAL(tmpzval); convert_to_boolean(*tmpzval); decode = Z_LVAL_PP(tmpzval); } if (decode) { transfer_encoding = php_stream_filter_create("dechunk", NULL, php_stream_is_persistent(stream) TSRMLS_CC); if (transfer_encoding) { /* don't store transfer-encodeing header */ continue; } } } } if (http_header_line[0] == '\0') { body = 1; } else { zval *http_header; MAKE_STD_ZVAL(http_header); ZVAL_STRINGL(http_header, http_header_line, http_header_line_length, 1); zend_hash_next_index_insert(Z_ARRVAL_P(response_header), &http_header, sizeof(zval *), NULL); } } else { break; } } if (!reqok || (location[0] != '\0' && follow_location)) { if (!follow_location || (((options & STREAM_ONLY_GET_HEADERS) || ignore_errors) && redirect_max <= 1)) { goto out; } if (location[0] != '\0') php_stream_notify_info(context, PHP_STREAM_NOTIFY_REDIRECTED, location, 0); php_stream_close(stream); stream = NULL; if (location[0] != '\0') { char new_path[HTTP_HEADER_BLOCK_SIZE]; char loc_path[HTTP_HEADER_BLOCK_SIZE]; *new_path='\0'; if (strlen(location)<8 || (strncasecmp(location, "http://", sizeof("http://")-1) && strncasecmp(location, "https://", sizeof("https://")-1) && strncasecmp(location, "ftp://", sizeof("ftp://")-1) && strncasecmp(location, "ftps://", sizeof("ftps://")-1))) { if (*location != '/') { if (*(location+1) != '\0' && resource->path) { char *s = strrchr(resource->path, '/'); if (!s) { s = resource->path; if (!s[0]) { efree(s); s = resource->path = estrdup("/"); } else { *s = '/'; } } s[1] = '\0'; if (resource->path && *(resource->path) == '/' && *(resource->path + 1) == '\0') { snprintf(loc_path, sizeof(loc_path) - 1, "%s%s", resource->path, location); } else { snprintf(loc_path, sizeof(loc_path) - 1, "%s/%s", resource->path, location); } } else { snprintf(loc_path, sizeof(loc_path) - 1, "/%s", location); } } else { strlcpy(loc_path, location, sizeof(loc_path)); } if ((use_ssl && resource->port != 443) || (!use_ssl && resource->port != 80)) { snprintf(new_path, sizeof(new_path) - 1, "%s://%s:%d%s", resource->scheme, resource->host, resource->port, loc_path); } else { snprintf(new_path, sizeof(new_path) - 1, "%s://%s%s", resource->scheme, resource->host, loc_path); } } else { strlcpy(new_path, location, sizeof(new_path)); } php_url_free(resource); /* check for invalid redirection URLs */ if ((resource = php_url_parse(new_path)) == NULL) { php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Invalid redirect URL! %s", new_path); goto out; } #define CHECK_FOR_CNTRL_CHARS(val) { \ if (val) { \ unsigned char *s, *e; \ int l; \ l = php_url_decode(val, strlen(val)); \ s = (unsigned char*)val; e = s + l; \ while (s < e) { \ if (iscntrl(*s)) { \ php_stream_wrapper_log_error(wrapper, options TSRMLS_CC, "Invalid redirect URL! %s", new_path); \ goto out; \ } \ s++; \ } \ } \ } /* check for control characters in login, password & path */ if (strncasecmp(new_path, "http://", sizeof("http://") - 1) || strncasecmp(new_path, "https://", sizeof("https://") - 1)) { CHECK_FOR_CNTRL_CHARS(resource->user) CHECK_FOR_CNTRL_CHARS(resource->pass) CHECK_FOR_CNTRL_CHARS(resource->path) } stream = php_stream_url_wrap_http_ex(wrapper, new_path, mode, options, opened_path, context, --redirect_max, HTTP_WRAPPER_REDIRECTED STREAMS_CC TSRMLS_CC); } else {
static void reheader_bcf(args_t *args, int is_compressed) { htsFile *fp = hts_open(args->fname, "r"); if ( !fp ) error("Failed to open: %s\n", args->fname); bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname); kstring_t htxt = {0,0,0}; int hlen; htxt.s = bcf_hdr_fmt_text(hdr, 1, &hlen); htxt.l = hlen; int i, nsamples = 0; char **samples = NULL; if ( args->samples_fname ) samples = hts_readlines(args->samples_fname, &nsamples); if ( args->header_fname ) { free(htxt.s); htxt.s = NULL; htxt.l = htxt.m = 0; read_header_file(args->header_fname, &htxt); } if ( samples ) { set_samples(samples, nsamples, &htxt); for (i=0; i<nsamples; i++) free(samples[i]); free(samples); } bcf_hdr_t *hdr_out = bcf_hdr_init("r"); bcf_hdr_parse(hdr_out, htxt.s); if ( args->header_fname ) hdr_out = strip_header(hdr, hdr_out); // write the header and the body htsFile *fp_out = hts_open("-",is_compressed ? "wb" : "wbu"); bcf_hdr_write(fp_out, hdr_out); bcf1_t *rec = bcf_init(); while ( bcf_read(fp, hdr, rec)==0 ) { // sanity checking, this slows things down. Make it optional? bcf_unpack(rec, BCF_UN_ALL); if ( rec->rid >= hdr_out->n[BCF_DT_CTG] || strcmp(bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid),bcf_hdr_int2id(hdr_out,BCF_DT_CTG,rec->rid)) ) error("The CHROM is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_CTG,rec->rid)); for (i=0; i<rec->d.n_flt; i++) { int id = rec->d.flt[i]; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FLT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FILTER ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->d.n_flt ) error("The FILTER is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.flt[i])); for (i=0; i<rec->n_info; i++) { int id = rec->d.info[i].key; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_INFO,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken INFO ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_info ) error("The INFO tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.info[i].key)); for (i=0; i<rec->n_fmt; i++) { int id = rec->d.fmt[i].id; if ( id >= hdr_out->n[BCF_DT_ID] ) break; if ( !hdr_out->id[BCF_DT_ID][id].key ) break; if ( !bcf_hdr_idinfo_exists(hdr_out,BCF_HL_FMT,id) ) break; if ( strcmp(hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key) ) error("FIXME: Broken FORMAT ids: %s vs %s\n", hdr->id[BCF_DT_ID][id].key,hdr_out->id[BCF_DT_ID][id].key); } if ( i!=rec->n_fmt ) error("The FORMAT tag is not defined: \"%s\"\n", bcf_hdr_int2id(hdr,BCF_DT_ID,rec->d.fmt[i].id)); bcf_write(fp_out,hdr_out,rec); } bcf_destroy(rec); free(htxt.s); hts_close(fp_out); hts_close(fp); bcf_hdr_destroy(hdr_out); bcf_hdr_destroy(hdr); }