From b013cdbe70ee4c781c5444e2f1e1042b1f3bea7b Mon Sep 17 00:00:00 2001
From: mh17 <mh17>
Date: Thu, 3 Dec 2009 15:03:08 +0000
Subject: [PATCH] added code for pipeServer
---
src/include/ZMap/zmapView.h | 6 +-
src/zmapApp/zmapApp_P.h | 7 +-
src/zmapServer/pipe/pipeServer.c | 138 ++++++++++++++++-----
src/zmapServer/pipe/pipeServer_P.h | 12 +-
src/zmapServer/zmapServerProtocolHandler.c | 4 +-
src/zmapServer/zmapServerPrototype.h | 6 +-
src/zmapView/zmapViewUtils.c | 20 ++-
7 files changed, 150 insertions(+), 43 deletions(-)
diff --git a/src/include/ZMap/zmapView.h b/src/include/ZMap/zmapView.h
index fb1349e15..32a78266d 100755
--- a/src/include/ZMap/zmapView.h
+++ b/src/include/ZMap/zmapView.h
@@ -31,7 +31,7 @@
* HISTORY:
* Last edited: Jun 12 14:36 2009 (edgrif)
* Created: Thu May 13 14:59:14 2004 (edgrif)
- * CVS info: $Id: zmapView.h,v 1.53 2009-06-12 13:58:16 edgrif Exp $
+ * CVS info: $Id: zmapView.h,v 1.54 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAPVIEW_H
@@ -162,6 +162,10 @@ typedef struct
struct {
char *path ;
} file ;
+ struct {
+ char *path ;
+ char *query ;
+ } pipe ;
} scheme_data ;
} ZMapViewSessionServerStruct, *ZMapViewSessionServer ;
diff --git a/src/zmapApp/zmapApp_P.h b/src/zmapApp/zmapApp_P.h
index 76ffef03a..1292dae6e 100755
--- a/src/zmapApp/zmapApp_P.h
+++ b/src/zmapApp/zmapApp_P.h
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Dec 19 09:12 2008 (edgrif)
* Created: Thu Jul 24 14:35:41 2003 (edgrif)
- * CVS info: $Id: zmapApp_P.h,v 1.26 2008-12-19 10:00:04 edgrif Exp $
+ * CVS info: $Id: zmapApp_P.h,v 1.27 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_APP_PRIV_H
@@ -101,6 +101,11 @@ typedef struct _ZMapAppContextStruct
char *locale;
gboolean sent_finalised ;
+
+ char *script_dir; /* where scripts are kept for the pipeServer module
+ * can be set in [ZMap] or defaults to run-time directory
+ */
+
} ZMapAppContextStruct, *ZMapAppContext ;
diff --git a/src/zmapServer/pipe/pipeServer.c b/src/zmapServer/pipe/pipeServer.c
index 552bcdb81..81307a24c 100755
--- a/src/zmapServer/pipe/pipeServer.c
+++ b/src/zmapServer/pipe/pipeServer.c
@@ -1,6 +1,6 @@
/* File: pipeServer.c
* Author: Malcolm Hinsley (mh17@sanger.ac.uk)
- * derived from pipeServer.c by Ed Griffiths (edgrif@sanger.ac.uk)
+ * derived from fileServer.c by Ed Griffiths (edgrif@sanger.ac.uk)
* Copyright (c) 2009: Genome Research Ltd.
*-------------------------------------------------------------------
* ZMap is free software; you can redistribute it and/or
@@ -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 1.3 2009-11-30 10:50:01 edgrif Exp $
+ * CVS info: $Id: pipeServer.c,v 1.4 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -51,7 +51,7 @@
#include <ZMap/zmapGFF.h>
#include <zmapServerPrototype.h>
#include <pipeServer_P.h>
-
+#include <ZMap/zmapConfigLoader.h>
/* Used to control getting features in all alignments in all blocks... */
typedef struct
@@ -70,6 +70,7 @@ static gboolean createConnection(void **server_out,
ZMapURL url, char *format,
char *version_str, int timeout) ;
+static gboolean pipe_server_spawn(PipeServer server,GError **error);
static ZMapServerResponseType openConnection(void *server) ;
static ZMapServerResponseType getInfo(void *server, ZMapServerInfo info) ;
static ZMapServerResponseType getFeatureSetNames(void *server,
@@ -142,9 +143,37 @@ static gboolean globalInit(void)
}
-/* spawn a new process to run our script ans open a pipe for read to get the output
- *
- *
+
+/* Read ZMap application defaults. */
+static gboolean getConfiguration(PipeServer server)
+{
+ gboolean result = FALSE ;
+ ZMapConfigIniContext context;
+
+ if((context = zMapConfigIniContextProvide()))
+ {
+ char *tmp_string = NULL;
+
+ /* script directory to use */
+ if(zMapConfigIniContextGetString(context, ZMAPSTANZA_APP_CONFIG, ZMAPSTANZA_APP_CONFIG,
+ ZMAPSTANZA_APP_SCRIPTS, &tmp_string))
+ {
+ server->script_dir = tmp_string;
+ result = TRUE;
+ }
+ zMapConfigIniContextDestroy(context);
+ }
+ if(!result)
+ server->script_dir = g_get_current_dir();
+ return result ;
+}
+
+
+
+/* spawn a new process to run our script and open a pipe for read to get the output
+ * global config of the default scripts directory is via '[ZMap] scripts-dir=there'
+ * to get absolute path you need 4 slashes eg for pipe://<host>/<path>
+ * where <host> is null and <path> begins with a /
* For now we will assume that "host" contains the script name and then we just ignore the other
* parameters....
*
@@ -162,18 +191,19 @@ static gboolean createConnection(void **server_out,
server = (PipeServer)g_new0(PipeServerStruct, 1) ;
*server_out = (void *)server ;
+ getConfiguration(server); // get scripts directory
/* We could check both format and version here if we wanted to..... */
/* This code is a hack to get round the fact that the url code we use in zmapView.c to parse
- * urls from our config firle will chop the leading "/" off the path....which causes the
+ * urls from our config file will chop the leading "/" off the path....which causes the
* zMapGetPath() call below to construct an incorrect path.... */
{
char *tmp_path = url->path ;
if (*(url->path) != '/')
- tmp_path = g_strdup_printf("/%s", url->path) ;
+ tmp_path = g_strdup_printf("%s/%s", server->script_dir,url->path) ;
server->script_path = zMapGetPath(tmp_path) ;
@@ -181,11 +211,50 @@ static gboolean createConnection(void **server_out,
g_free(tmp_path) ;
}
+ server->query = url->query;
return result ;
}
+
+
+/*
+ * 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
+ */
+static gboolean pipe_server_spawn(PipeServer server,GError **error)
+{
+ gboolean result = FALSE;
+ gchar **argv;
+ 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
+ */
+
+ 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;
+
+ 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);
+ if(result)
+ {
+ server->gff_pipe = g_io_channel_unix_new(pipe_fd);
+ }
+
+ g_free(argv);
+ if(error)
+ *error = pipe_error;
+ return(result);
+}
+
+
static ZMapServerResponseType openConnection(void *server_in)
{
ZMapServerResponseType result = ZMAP_SERVERRESPONSE_REQFAIL ;
@@ -200,19 +269,17 @@ static ZMapServerResponseType openConnection(void *server_in)
{
GError *gff_pipe_err = NULL ;
- if ((server->gff_pipe = g_io_channel_new_file(server->script_path, "r", &gff_pipe_err)))
- {
- result = ZMAP_SERVERRESPONSE_OK ;
- }
- else
- {
- setLastErrorMsg(server, &gff_pipe_err) ;
-
- result = ZMAP_SERVERRESPONSE_REQFAIL ;
- }
+ if(pipe_server_spawn(server,&gff_pipe_err))
+ {
+ result = ZMAP_SERVERRESPONSE_OK ;
+ }
+ else
+ {
+ setLastErrorMsg(server, &gff_pipe_err) ;
+ result = ZMAP_SERVERRESPONSE_REQFAIL ;
+ }
}
-
return result ;
}
@@ -230,7 +297,7 @@ static ZMapServerResponseType getInfo(void *server_in, ZMapServerInfo info)
else
{
result = ZMAP_SERVERRESPONSE_REQFAIL ;
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,server->query,
"Could not get server info because: %s", server->last_err_msg) ;
}
@@ -256,7 +323,7 @@ static ZMapServerResponseType getFeatureSetNames(void *server_in,
zMapAssert(server) ;
setErrMsg(server, g_strdup("Feature Sets cannot be read from GFF stream.")) ;
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
@@ -279,7 +346,7 @@ static ZMapServerResponseType getStyles(void *server_in, GData **styles_out)
zMapAssert(server) ;
setErrMsg(server, g_strdup("Reading styles from a GFF stream is not supported.")) ;
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path, server->query,
"%s", server->last_err_msg) ;
result = ZMAP_SERVERRESPONSE_UNSUPPORTED ;
@@ -358,7 +425,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
- get_features.result = ZMAP_SERVERRESPONSE_OK ;
+ get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ; // to catch empty file
get_features.server = (PipeServer)server_in ;
get_features.parser = zMapGFFCreateParser() ;
@@ -376,6 +443,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
&gff_pipe_err)) == G_IO_STATUS_NORMAL)
{
gboolean done_header = FALSE ;
+ get_features.result = ZMAP_SERVERRESPONSE_OK; // now we have data default is 'OK'
*(get_features.gff_line->str + terminator_pos) = '\0' ; /* Remove terminating newline. */
@@ -399,7 +467,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
setErrMsg(server,
g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
}
else
@@ -417,7 +485,7 @@ static ZMapServerResponseType getFeatures(void *server_in, GData *styles, ZMapFe
g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
zMapGFFGetLineNumber(get_features.parser),
get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
}
}
@@ -479,8 +547,8 @@ static void eachBlockSequence(gpointer key, gpointer data, gpointer user_data)
setErrMsg(get_features->server,
g_strdup_printf("zMapGFFGetSequence() failed, error=%s",
error->message));
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR,
- get_features->server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR,
+ get_features->server->script_path,get_features->server->query,
"%s", get_features->server->last_err_msg);
}
else
@@ -593,7 +661,7 @@ static ZMapServerResponseType getContextSequence(void *server_in, GData *styles,
setErrMsg(server,
g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(get_features.parser), get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
}
else
@@ -604,7 +672,7 @@ static ZMapServerResponseType getContextSequence(void *server_in, GData *styles,
{
get_features.result = ZMAP_SERVERRESPONSE_REQFAIL ;
setErrMsg(server, g_strdup_printf("GFFTerminated! %s", error->message)) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ; }
else
{
@@ -612,7 +680,7 @@ static ZMapServerResponseType getContextSequence(void *server_in, GData *styles,
g_strdup_printf("zMapGFFParseHeader() failed for line %d: %s",
zMapGFFGetLineNumber(get_features.parser),
get_features.gff_line->str)) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
}
}
@@ -663,6 +731,9 @@ static ZMapServerResponseType closeConnection(void *server_in)
PipeServer server = (PipeServer)server_in ;
GError *gff_pipe_err = NULL ;
+ if(server->child_pid)
+ g_spawn_close_pid(server->child_pid);
+
if (server->gff_pipe && g_io_channel_shutdown(server->gff_pipe, FALSE, &gff_pipe_err) != G_IO_STATUS_NORMAL)
{
zMapLogCritical("Could not close feature pipe \"%s\"", server->script_path) ;
@@ -784,7 +855,8 @@ static void eachBlock(gpointer key, gpointer data, gpointer user_data)
if (!sequenceRequest(get_features->server, get_features->parser,
get_features->gff_line, feature_block))
{
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR, get_features->server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, get_features->server->script_path,
+ get_features->server->query,
"Could not map %s because: %s",
g_quark_to_string(get_features->server->req_context->sequence_name),
get_features->server->last_err_msg) ;
@@ -833,7 +905,7 @@ static gboolean sequenceRequest(PipeServer server, ZMapGFFParser parser, GString
server->last_err_msg =
g_strdup_printf("zMapGFFParseLine() failed with no GError for line %d: %s",
zMapGFFGetLineNumber(parser), gff_line->str) ;
- ZMAPSERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Critical, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", server->last_err_msg) ;
result = FALSE ;
@@ -849,7 +921,7 @@ static gboolean sequenceRequest(PipeServer server, ZMapGFFParser parser, GString
}
else
{
- ZMAPSERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,
+ ZMAPPIPESERVER_LOG(Warning, PIPE_PROTOCOL_STR, server->script_path,server->query,
"%s", error->message) ;
}
}
diff --git a/src/zmapServer/pipe/pipeServer_P.h b/src/zmapServer/pipe/pipeServer_P.h
index 36075c415..9360665f6 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 1.1 2009-11-26 12:18:47 mh17 Exp $
+ * CVS info: $Id: pipeServer_P.h,v 1.2 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef PIPE_SERVER_P_H
@@ -37,14 +37,20 @@
#define PIPE_PROTOCOL_STR "GFF Pipe" /* For error messages. */
+#define PIPE_MAX_ARGS 2 // extra args we add on to the query
+#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_path ; // where our configured script is
- GIOChannel* gff_pipe ; // the pipe we read the script's output from
+ gchar *script_dir; // default location for relative paths
+ 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
+ GPid child_pid;
char *styles_file ;
diff --git a/src/zmapServer/zmapServerProtocolHandler.c b/src/zmapServer/zmapServerProtocolHandler.c
index 34ef84d98..787d1a264 100755
--- a/src/zmapServer/zmapServerProtocolHandler.c
+++ b/src/zmapServer/zmapServerProtocolHandler.c
@@ -27,7 +27,7 @@
* HISTORY:
* Last edited: Nov 26 08:26 2009 (edgrif)
* Created: Thu Jan 27 13:17:43 2005 (edgrif)
- * CVS info: $Id: zmapServerProtocolHandler.c,v 1.47 2009-11-30 10:52:50 edgrif Exp $
+ * CVS info: $Id: zmapServerProtocolHandler.c,v 1.48 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -314,7 +314,6 @@ ZMapThreadReturnCode zMapServerRequestHandler(void **slave_data,
ZMapServer server = NULL ;
void *global_init_data ;
-
/* Slightly opaque here, if *slave_data is NULL this implies that we are not set up yet
* so the request should be to start a connection and we should have been passed in
* a load of connection stuff.... */
@@ -501,7 +500,6 @@ ZMapThreadReturnCode zMapServerRequestHandler(void **slave_data,
break ;
}
-
/* Return server. */
*slave_data = (void *)server ;
diff --git a/src/zmapServer/zmapServerPrototype.h b/src/zmapServer/zmapServerPrototype.h
index f1c194218..9ab8e4189 100755
--- a/src/zmapServer/zmapServerPrototype.h
+++ b/src/zmapServer/zmapServerPrototype.h
@@ -30,7 +30,7 @@
* HISTORY:
* Last edited: Oct 2 08:09 2009 (edgrif)
* Created: Wed Aug 6 15:48:47 2003 (edgrif)
- * CVS info: $Id: zmapServerPrototype.h,v 1.29 2009-11-26 15:40:18 mh17 Exp $
+ * CVS info: $Id: zmapServerPrototype.h,v 1.30 2009-12-03 15:03:08 mh17 Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_SERVER_PROTOTYPEP_H
@@ -130,11 +130,15 @@ void pipeGetServerFuncs(ZMapServerFuncs pipe_funcs) ;
/* Try to give consistent messages/logging.... */
#define ZMAP_SERVER_MSGPREFIX "Server %s:%s - "
+#define ZMAP_PIPESERVER_MSGPREFIX "Server %s:%s(%s) - "
/* LOGTYPE just be one of the zMapLogXXXX types, i.e. Message, Warning, Critical or Fatal */
#define ZMAPSERVER_LOG(LOGTYPE, PROTOCOL, HOST, FORMAT, ...) \
zMapLog##LOGTYPE(ZMAP_SERVER_MSGPREFIX FORMAT, PROTOCOL, HOST, __VA_ARGS__)
+#define ZMAPPIPESERVER_LOG(LOGTYPE, PROTOCOL, HOST, ARG, FORMAT, ...) \
+zMapLog##LOGTYPE(ZMAP_PIPESERVER_MSGPREFIX FORMAT, PROTOCOL, HOST, ARG, __VA_ARGS__)
+
#define ZMAPSERVER_MAKEMESSAGE(PROTOCOL, HOST, FORMAT, ...) \
g_strdup_printf(ZMAP_SERVER_MSGPREFIX FORMAT, PROTOCOL, HOST, __VA_ARGS__)
diff --git a/src/zmapView/zmapViewUtils.c b/src/zmapView/zmapViewUtils.c
index 745ea09bb..f0051d43c 100755
--- a/src/zmapView/zmapViewUtils.c
+++ b/src/zmapView/zmapViewUtils.c
@@ -29,7 +29,7 @@
* HISTORY:
* Last edited: Oct 1 15:42 2009 (edgrif)
* Created: Mon Sep 20 10:29:15 2004 (edgrif)
- * CVS info: $Id: zmapViewUtils.c,v 1.14 2009-10-02 09:19:32 edgrif Exp $
+ * CVS info: $Id: zmapViewUtils.c,v 1.15 2009-12-03 15:06:40 mh17 Exp $
*-------------------------------------------------------------------
*/
@@ -600,6 +600,13 @@ void zmapViewSessionAddServer(ZMapViewSession session_data, ZMapURL url, char *f
server_data->scheme_data.acedb.database = g_strdup(url->path) ;
break ;
}
+ case SCHEME_PIPE:
+ {
+ server_data->scheme_data.pipe.path = g_strdup(url->path) ;
+ server_data->scheme_data.pipe.query = g_strdup(url->query) ;
+ break ;
+ }
+
case SCHEME_FILE:
{
server_data->scheme_data.file.path = g_strdup(url->path) ;
@@ -637,6 +644,11 @@ void zmapViewSessionAddServerInfo(ZMapViewSession session_data, char *database_p
break ;
}
+ case SCHEME_PIPE:
+ {
+
+ break ;
+ }
default:
{
@@ -670,6 +682,12 @@ void zmapViewSessionFreeServer(gpointer data, gpointer user_data_unused)
g_free(server_data->scheme_data.file.path) ;
break ;
}
+ case SCHEME_PIPE:
+ {
+ g_free(server_data->scheme_data.pipe.path) ;
+ g_free(server_data->scheme_data.pipe.query) ;
+ break ;
+ }
default:
{
/* no action currently. */
--
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