From ad350c468698a3d89eb92aefe59d08a02e6625a0 Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Fri, 4 Dec 2009 16:01:39 +0000
Subject: [PATCH] script args implemented and STDERR reported to user
---
src/zmapServer/pipe/pipeServer.c | 111 ++++++++++++++++++++++++-----
src/zmapServer/pipe/pipeServer_P.h | 12 ++--
2 files changed, 103 insertions(+), 20 deletions(-)
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index 81307a24c..71c0aed90 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -34,7 +34,7 @@
* HISTORY:
* Last edited: Nov 30 09:18 2009 (edgrif)
* Created: 2009-11-26 12:02:40 (mh17)
- * CVS info: $Id: pipeServer.c,v 1.4 2009-12-03 15:03:08 mh17 Exp $
+ * CVS info: $Id: pipeServer.c,v 1.5 2009-12-04 16:01:39 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -212,6 +212,8 @@ static gboolean createConnection(void **server_out,
}
server->query = url->query;
+ server->zmap_start = 0;
+ server->zmap_end = 0; // default to all of it
return result ;
}
@@ -222,39 +224,92 @@ static gboolean createConnection(void **server_out,
/*
* fork and exec the script and read teh output via a pipe
* no data sent to STDIN and STDERR ignored
- * in case of errors or hangups eevntually we will time out and an error popped up.
- * downside is limited to not having the data, whcih is what happens anyway
+ * in case of errors or hangups eventually we will time out and an error popped up.
+ * downside is limited to not having the data, which is what happens anyway
*/
static gboolean pipe_server_spawn(PipeServer server,GError **error)
{
gboolean result = FALSE;
- gchar **argv;
+ gchar **argv, **q_args, *z_start,*z_end;
gint pipe_fd;
- GError *pipe_error = NULL;;
-
- argv = (gchar **) g_malloc (sizeof(gchar *) * (PIPE_MAX_ARGS + 4));
- /* initially we have one arg which is the query string
- * but implement flexible arg handling anyway
- */
+ GError *pipe_error = NULL;
+ int i;
+ gint err_fd;
+ q_args = g_strsplit(server->query,"&",0);
+ argv = (gchar **) g_malloc (sizeof(gchar *) * (PIPE_MAX_ARGS + g_strv_length(q_args)));
argv[0] = server->script_path; // scripts can get exec'd, as long as they start w/ #!
- argv[1] = server->query; // may be NULL
- argv[2]= NULL;
+ for(i = 1;q_args[i-1];i++)
+ argv[i] = q_args[i-1];
+
+ // now add on zmap args such as start and end
+ if(server->zmap_start || server->zmap_end)
+ {
+ argv[i++] = z_start = g_strdup_printf("%s=%d",PIPE_ARG_ZMAP_START,server->zmap_start);
+ argv[i++] = z_end = g_strdup_printf("%s=%d",PIPE_ARG_ZMAP_END,server->zmap_end);
+ }
+
+ argv[i]= NULL;
- result = g_spawn_async_with_pipes(server->script_dir,argv,NULL,G_SPAWN_STDERR_TO_DEV_NULL,
- NULL,NULL,&server->child_pid,NULL,&pipe_fd,NULL,&pipe_error);
+ result = g_spawn_async_with_pipes(server->script_dir,argv,NULL,G_SPAWN_CHILD_INHERITS_STDIN, // can't not give a flag!
+ NULL,NULL,&server->child_pid,NULL,&pipe_fd,&err_fd,&pipe_error);
if(result)
{
server->gff_pipe = g_io_channel_unix_new(pipe_fd);
+ server->gff_error = g_io_channel_unix_new(err_fd);
+ }
+
+ g_free(argv); // strings allocated and freed seperately
+ g_strfreev(q_args);
+ if(server->zmap_start || server->zmap_end)
+ {
+ g_free(z_start);
+ g_free(z_end);
}
- g_free(argv);
if(error)
*error = pipe_error;
return(result);
}
+/*
+ * read stderr from the external source and if non empty display and log some messages
+ * use non-blocking i/o so we don't hang ???
+ * gets called by setErrMsg() - if the server fails we read STDERR and possibly report why
+ * if no failures we ignore STDERR
+ * the last message is the one that gets popped up to the user
+ * We log all messages except the last as that generally appears twice in the log anyway
+ */
+gchar *pipe_server_get_stderr(PipeServer server)
+{
+ GIOStatus status ;
+ gsize terminator_pos = 0;
+ GError *gff_pipe_err = NULL;
+ gchar * msg = NULL;
+ GString *line;
+
+ line = g_string_sized_new(2000) ; /* Probably not many lines will be > 2k chars. */
+
+ while (1)
+ {
+ status = g_io_channel_read_line_string(server->gff_error, line,
+ &terminator_pos,&gff_pipe_err);
+ if(status != G_IO_STATUS_NORMAL)
+ break;
+
+ if(msg)
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,server->query,"%s", msg) ;
+
+ *(line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
+ msg = g_strdup(line->str);
+ }
+
+ g_string_free(line,TRUE);
+ return(msg);
+}
+
+
static ZMapServerResponseType openConnection(void *server_in)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -746,10 +801,24 @@ static ZMapServerResponseType closeConnection(void *server_in)
{
/* this seems to be required to destroy the GIOChannel.... */
g_io_channel_unref(server->gff_pipe) ;
-
server->gff_pipe = NULL ;
}
+ if (server->gff_error && g_io_channel_shutdown(server->gff_error, FALSE, &gff_pipe_err) != G_IO_STATUS_NORMAL)
+ {
+ zMapLogCritical("Could not close error pipe \"%s\"", server->script_path) ;
+
+ setLastErrorMsg(server, &gff_pipe_err) ;
+
+ result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ }
+ else
+ {
+ /* this seems to be required to destroy the GIOChannel.... */
+ g_io_channel_unref(server->gff_error) ;
+ server->gff_error = NULL ;
+ }
+
return result ;
}
@@ -972,8 +1041,18 @@ static gboolean getServerInfo(PipeServer server, ZMapServerInfo info)
/* It's possible for us to have reported an error and then another error to come along. */
+/* mgh: if we get an error such as pipe broken then let's look at stderr and if there's a message there report it */
static void setErrMsg(PipeServer server, char *new_msg)
{
+ gchar *errmsg;
+
+ errmsg = pipe_server_get_stderr(server);
+ if(errmsg)
+ {
+ g_free(new_msg);
+ new_msg = errmsg; // explain the cause of the error not the symptom
+ }
+
if (server->last_err_msg)
g_free(server->last_err_msg) ;
diff --git a/src/zmapServer/pipe/pipeServer_P.h b/src/zmapServer/pipe/pipeServer_P.h
index 9360665f6..60f5c2ae2 100755
--- a/src/zmapServer/pipe/pipeServer_P.h
+++ b/src/zmapServer/pipe/pipeServer_P.h
@@ -28,7 +28,7 @@
*
* HISTORY:
* Created: Thu Nov 26 10:30:21 2009 (mh17)
- * CVS info: $Id: pipeServer_P.h,v 1.2 2009-12-03 15:03:08 mh17 Exp $
+ * CVS info: $Id: pipeServer_P.h,v 1.3 2009-12-04 16:01:39 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef PIPE_SERVER_P_H
@@ -37,20 +37,24 @@
#define PIPE_PROTOCOL_STR "GFF Pipe" /* For error messages. */
-#define PIPE_MAX_ARGS 2 // extra args we add on to the query
+#define PIPE_MAX_ARGS 4 // extra args we add on to the query, including the program and terminating NULL
#define PIPE_ARG_ZMAP_START "zmap_start"
#define PIPE_ARG_ZMAP_END "zmap_end"
+
/* Holds all the state we need to create and access the script output. */
typedef struct _PipeServerStruct
{
gchar *script_dir; // default location for relative paths
- gchar *script_path ; // where our configured script is, includign script-dir
+ gchar *script_path ; // where our configured script is, includign script-dir
gchar *query; // from query string
- GIOChannel *gff_pipe ;// the pipe we read the script's output from
+ GIOChannel *gff_pipe ; // the pipe we read the script's output from
+ GIOChannel *gff_error ; // the pipe we read the script's error output from
GPid child_pid;
+ gint zmap_start,zmap_end; // display coordinates of interesting region
+ gint wait; // delay before gettign data, mainly for testing
char *styles_file ;
--
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