From 8c0343d45f72b3ec93eb93a4101a7632aa90ab6a Mon Sep 17 00:00:00 2001
From: edgrif <edgrif>
Date: Fri, 25 Jan 2008 15:49:40 +0000
Subject: [PATCH] add option to allow blixem processes to be left running after
view dies.
---
src/zmapView/zmapView.c | 33 +++++++++++++++----------
src/zmapView/zmapViewCallBlixem.c | 40 ++++++++++++++++++++++++++-----
src/zmapView/zmapView_P.h | 13 +++++-----
3 files changed, 62 insertions(+), 24 deletions(-)
diff --git a/src/zmapView/zmapView.c b/src/zmapView/zmapView.c
index 236b82c27..5dda50062 100755
--- a/src/zmapView/zmapView.c
+++ b/src/zmapView/zmapView.c
@@ -25,9 +25,9 @@
* Description:
* Exported functions: See ZMap/zmapView.h
* HISTORY:
- * Last edited: Nov 19 13:48 2007 (rds)
+ * Last edited: Jan 25 15:37 2008 (edgrif)
* Created: Thu May 13 15:28:26 2004 (edgrif)
- * CVS info: $Id: zmapView.c,v 1.126 2007-11-22 12:48:34 rds Exp $
+ * CVS info: $Id: zmapView.c,v 1.127 2008-01-25 15:49:40 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -1395,6 +1395,9 @@ static ZMapView createZMapView(GtkWidget *xremote_widget, char *view_name, GList
zmap_view->revcomped_features = FALSE ;
+ zmap_view->kill_blixems = TRUE ;
+
+
return zmap_view ;
}
@@ -1445,17 +1448,22 @@ static void killAllSpawned(ZMapView zmap_view)
GPid pid;
GList *processes = zmap_view->spawned_processes;
- while(processes)
+ if (zmap_view->kill_blixems)
{
- pid = GPOINTER_TO_INT(processes->data);
- g_spawn_close_pid(pid);
- kill(pid, 9);
- processes = processes->next;
+ while (processes)
+ {
+ pid = GPOINTER_TO_INT(processes->data);
+ g_spawn_close_pid(pid);
+ kill(pid, 9);
+ processes = processes->next;
+ }
}
- if(zmap_view->spawned_processes)
- g_list_free(zmap_view->spawned_processes);
- zmap_view->spawned_processes = NULL ;
+ if (zmap_view->spawned_processes)
+ {
+ g_list_free(zmap_view->spawned_processes);
+ zmap_view->spawned_processes = NULL ;
+ }
return ;
}
@@ -1633,7 +1641,8 @@ static gboolean checkStateConnections(ZMapView zmap_view)
/* Got the sequences so launch blixem. */
if ((status = zmapViewCallBlixem(zmap_view,
get_sequence->orig_feature, get_sequence->sequences,
- &blixem_pid)))
+ &blixem_pid,
+ &(zmap_view->kill_blixems))))
zmap_view->spawned_processes = g_list_append(zmap_view->spawned_processes,
GINT_TO_POINTER(blixem_pid)) ;
@@ -2335,7 +2344,7 @@ static void commandCB(ZMapWindow window, void *caller_data, void *window_data)
{
GPid blixem_pid ;
- if ((status = zmapViewCallBlixem(view, align_cmd->feature, NULL, &blixem_pid)))
+ if ((status = zmapViewCallBlixem(view, align_cmd->feature, NULL, &blixem_pid, &(view->kill_blixems))))
view->spawned_processes = g_list_append(view->spawned_processes, GINT_TO_POINTER(blixem_pid)) ;
}
diff --git a/src/zmapView/zmapViewCallBlixem.c b/src/zmapView/zmapViewCallBlixem.c
index 9742a0669..0996c827f 100755
--- a/src/zmapView/zmapViewCallBlixem.c
+++ b/src/zmapView/zmapViewCallBlixem.c
@@ -29,9 +29,9 @@
* Exported functions: see zmapView_P.h
*
* HISTORY:
- * Last edited: Nov 12 13:48 2007 (rds)
+ * Last edited: Jan 25 15:34 2008 (edgrif)
* Created: Thu Jun 28 18:10:08 2007 (edgrif)
- * CVS info: $Id: zmapViewCallBlixem.c,v 1.5 2007-11-12 13:49:18 rds Exp $
+ * CVS info: $Id: zmapViewCallBlixem.c,v 1.6 2008-01-25 15:49:40 edgrif Exp $
*-------------------------------------------------------------------
*/
@@ -70,6 +70,8 @@ enum
typedef struct BlixemDataStruct
{
/* user preferences for blixem */
+ gboolean kill_on_exit ; /* TRUE => remove this blixem on
+ program exit (default). */
gchar *netid; /* eg pubseq */
int port; /* eg 22100 */
gchar *script; /* script to call blixem standalone */
@@ -128,6 +130,9 @@ typedef struct
{
/* User configurable */
gboolean init ; /* TRUE when struct has been initialised. */
+
+ gboolean kill_on_exit ; /* TRUE => remove this blixem on
+ program exit (default). */
gchar *netid ; /* eg pubseq */
int port ; /* eg 22100 */
gchar *script ; /* script to call blixem standalone */
@@ -283,7 +288,8 @@ gboolean zmapViewBlixemLocalSequences(ZMapView view, ZMapFeature feature, GList
* The function returns TRUE if blixem was successfully launched and also returns the pid of the blixem
* process so that the blixems can be cleared up when the view exits.
* */
-gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_sequences, GPid *child_pid)
+gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_sequences,
+ GPid *child_pid, gboolean *kill_on_exit)
{
gboolean status = TRUE ;
char *argv[BLX_ARGV_ARGC + 1] = {NULL} ;
@@ -332,8 +338,11 @@ gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_seq
else
zMapLogMessage("Blixem process spawned successfully. PID = '%d'", spawned_pid);
- if(status && child_pid)
- *child_pid = spawned_pid;
+ if (status && child_pid)
+ *child_pid = spawned_pid ;
+
+ if (kill_on_exit)
+ *kill_on_exit = blixem_data.kill_on_exit ;
}
freeBlixemData(&blixem_data) ;
@@ -450,6 +459,7 @@ static void setPrefs(BlixemConfigData curr_prefs, blixemData blixem_data)
blixem_data->scope = curr_prefs->scope ;
blixem_data->homolmax = curr_prefs->homolmax ;
blixem_data->keep_tmpfiles = curr_prefs->keep_tmpfiles ;
+ blixem_data->kill_on_exit = curr_prefs->kill_on_exit ;
if (blixem_data->dna_sets)
{
@@ -487,10 +497,17 @@ static gboolean getUserPrefs(BlixemConfigData prefs)
{"scope" , ZMAPCONFIG_INT , {NULL}},
{"homol_max" , ZMAPCONFIG_INT , {NULL}},
{"keep_tempfiles", ZMAPCONFIG_BOOL, {NULL}},
+ {"kill_on_exit", ZMAPCONFIG_BOOL, {NULL}},
{"dna_featuresets", ZMAPCONFIG_STRING, {NULL}},
{"protein_featuresets", ZMAPCONFIG_STRING, {NULL}},
{"transcript_featuresets", ZMAPCONFIG_STRING, {NULL}},
{NULL, -1, {NULL}}} ;
+
+
+ /* Set defaults... */
+ zMapConfigGetStructBool(elements, "kill_on_exit") = TRUE ;
+
+
if ((config = zMapConfigCreate()))
{
char *dnaset_string, *proteinset_string, *transcriptset_string ;
@@ -524,6 +541,8 @@ static gboolean getUserPrefs(BlixemConfigData prefs)
prefs->transcript_sets = zMapFeatureString2QuarkList(transcriptset_string) ;
prefs->keep_tmpfiles = zMapConfigGetElementBool(next, "keep_tempfiles") ;
+
+ prefs->kill_on_exit = zMapConfigGetElementBool(next, "kill_on_exit") ;
zMapConfigDeleteStanzaSet(list) ; /* Not needed anymore. */
}
@@ -619,7 +638,7 @@ static gboolean makeTmpfiles(blixemData blixem_data)
char *path;
char *login;
- if ((login = g_get_user_name()))
+ if ((login = (char *)g_get_user_name()))
{
path = g_strdup_printf("/tmp/%s_ZMAP_BLIXEM/", login);
}
@@ -1592,6 +1611,10 @@ static ZMapGuiNotebookChapter makeChapter(ZMapGuiNotebook note_book_parent)
ZMAPGUI_NOTEBOOK_TAGVALUE_CHECKBOX,
"bool", blixem_config_curr_G.keep_tmpfiles) ;
+ tagvalue = zMapGUINotebookCreateTagValue(paragraph, "Kill Blixem on Exit",
+ ZMAPGUI_NOTEBOOK_TAGVALUE_CHECKBOX,
+ "bool", blixem_config_curr_G.kill_on_exit) ;
+
return chapter ;
}
@@ -1665,6 +1688,11 @@ static void readChapter(ZMapGuiNotebookChapter chapter)
blixem_config_curr_G.keep_tmpfiles = bool_value ;
}
+ if (zMapGUINotebookGetTagValue(page, "Kill Blixem on Exit", "bool", &bool_value))
+ {
+ blixem_config_curr_G.kill_on_exit = bool_value ;
+ }
+
}
diff --git a/src/zmapView/zmapView_P.h b/src/zmapView/zmapView_P.h
index d5c115950..068bb95e8 100755
--- a/src/zmapView/zmapView_P.h
+++ b/src/zmapView/zmapView_P.h
@@ -24,9 +24,9 @@
*
* Description:
* HISTORY:
- * Last edited: Jul 30 12:23 2007 (rds)
+ * Last edited: Jan 25 15:36 2008 (edgrif)
* Created: Thu May 13 15:06:21 2004 (edgrif)
- * CVS info: $Id: zmapView_P.h,v 1.31 2007-07-30 11:23:40 rds Exp $
+ * CVS info: $Id: zmapView_P.h,v 1.32 2008-01-25 15:49:40 edgrif Exp $
*-------------------------------------------------------------------
*/
#ifndef ZMAP_VIEW_P_H
@@ -144,6 +144,9 @@ typedef struct _ZMapViewStruct
GList *navigator_set_names;
+ /* view spawns blixem processes when requested, kill_blixems flag controls whether they are
+ * killed when view dies (default is TRUE). */
+ gboolean kill_blixems ;
GList *spawned_processes;
GHashTable *cwh_hash;
@@ -155,19 +158,17 @@ void zmapViewBusy(ZMapView zmap_view, gboolean busy) ;
gboolean zmapAnyConnBusy(GList *connection_list) ;
char *zmapViewGetStatusAsStr(ZMapViewState state) ;
gboolean zmapViewBlixemLocalSequences(ZMapView view, ZMapFeature feature, GList **local_sequences_out) ;
-gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_sequences, GPid *child_pid) ;
-
+gboolean zmapViewCallBlixem(ZMapView view, ZMapFeature feature, GList *local_sequences,
+ GPid *child_pid, gboolean *kill_on_exit) ;
ZMapFeatureContext zmapViewMergeInContext(ZMapView view, ZMapFeatureContext context);
gboolean zmapViewDrawDiffContext(ZMapView view, ZMapFeatureContext *diff_context);
void zmapViewEraseFromContext(ZMapView replace_me, ZMapFeatureContext context_inout);
-
void zmapViewSetupXRemote(ZMapView view, GtkWidget *widget);
gboolean zmapViewRemoteSendCommand(ZMapView view,
char *action, GArray *xml_events,
ZMapXMLObjTagFunctions start_handlers,
ZMapXMLObjTagFunctions end_handlers,
gpointer *handler_data);
-
/* Context Window Hash (CWH) for the correct timing of the call to zMapFeatureContextDestroy */
GHashTable *zmapViewCWHHashCreate(void);
void zmapViewCWHSetList(GHashTable *hash, ZMapFeatureContext context, GList *list);
--
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