SLURM: Give full path to indexamajig, and set up path

3 files changed, 107 insertions, 4 deletions

diff --git a/src/gui_backend_slurm.c b/src/gui_backend_slurm.c
index c5cc130c..4db8d7d6 100644
--- a/src/gui_backend_slurm.c
+++ b/src/gui_backend_slurm.c
@@ -73,14 +73,42 @@ static void cancel_task(void *job_priv)
 }
 
 
-static char **create_env(uint32_t *psize)
+static char **create_env(uint32_t *psize, char *path_add)
 {
 	char **env;
+	const char *base_path = "PATH=/bin:/usr/bin";
+	char *crystfel_path;
+	size_t path_len;
 
 	env = malloc(10*sizeof(char *));
 	if ( env == NULL ) return NULL;
 
-	env[0] = strdup("PATH=/path/to/indexamajig");
+	crystfel_path = get_crystfel_path_str();
+
+	path_len = 4 + strlen(base_path);
+
+	if ( path_add != NULL ) {
+		path_len += strlen(path_add);
+	}
+
+	if ( crystfel_path != NULL ) {
+		path_len += strlen(crystfel_path);
+	}
+
+	env[0] = malloc(path_len);
+	if ( env[0] == NULL ) return NULL;
+
+	strcpy(env[0], base_path);
+	if ( crystfel_path != NULL ) {
+		strcat(env[0], ":");
+		strcat(env[0], crystfel_path);
+		g_free(crystfel_path);
+	}
+	if ( path_add != NULL ) {
+		strcat(env[0], ":");
+		strcat(env[0], path_add);
+	}
+
 	*psize = 1;
 
 	return env;
@@ -173,7 +201,8 @@ static void *run_indexing(const char *job_title,
 	job_desc_msg.std_out = strdup("job.out");
 	job_desc_msg.work_dir = g_file_get_path(workdir_file);
 	job_desc_msg.script = script;
-	job_desc_msg.environment = create_env(&job_desc_msg.env_size);
+	job_desc_msg.environment = create_env(&job_desc_msg.env_size,
+	                                      opts->path_add);
 
 	g_object_unref(workdir_file);
 
diff --git a/src/gui_index.c b/src/gui_index.c
index f989b538..a5655a8c 100644
--- a/src/gui_index.c
+++ b/src/gui_index.c
@@ -554,6 +554,69 @@ static void add_arg_int(char **args, int pos, const char *label,
 }
 
 
+GFile *get_crystfel_path_gfile()
+{
+	GFile *self;
+	GFileInfo *self_info;
+	const char *self_target;
+	GFile *tar;
+	GFile *parent_dir;
+	GError *error = NULL;
+
+	self = g_file_new_for_path("/proc/self/exe");
+	self_info = g_file_query_info(self, "standard",
+	                              G_FILE_QUERY_INFO_NONE,
+	                              NULL, &error);
+	if ( self_info == NULL ) return NULL;
+
+	self_target = g_file_info_get_symlink_target(self_info);
+	if ( self_target == NULL ) return NULL;
+
+	tar = g_file_new_for_path(self_target);
+	if ( tar == NULL ) return NULL;
+
+	parent_dir = g_file_get_parent(tar);
+	if ( parent_dir == NULL ) return NULL;
+
+	g_object_unref(self);
+	g_object_unref(self_info);
+	g_object_unref(tar);
+
+	return parent_dir;
+}
+
+
+char *get_crystfel_path_str()
+{
+	char *path;
+	GFile *crystfel_path = get_crystfel_path_gfile();
+	if ( crystfel_path == NULL ) return NULL;
+	path = g_file_get_path(crystfel_path);
+	g_object_unref(crystfel_path);
+	return path;
+}
+
+
+static char *get_indexamajig_exe()
+{
+	GFile *crystfel_path;
+	char *indexamajig_path;
+	GFile *indexamajig;
+
+	crystfel_path = get_crystfel_path_gfile();
+	if ( crystfel_path == NULL ) return NULL;
+
+	indexamajig = g_file_get_child(crystfel_path, "indexamajig");
+	if ( indexamajig == NULL ) return NULL;
+
+	indexamajig_path = g_file_get_path(indexamajig);
+	g_object_unref(indexamajig);
+	g_object_unref(crystfel_path);
+
+	return indexamajig_path;
+}
+
+
 char **indexamajig_command_line(const char *geom_filename,
                                 const char *n_thread_str,
                                 struct peak_params *peak_search_params,
@@ -561,13 +624,22 @@ char **indexamajig_command_line(const char *geom_filename,
 {
 	char **args;
 	char tols[2048];
+	char *indexamajig_path;
 	int n_args = 0;
 
 	args = malloc(64*sizeof(char *));
 	if ( args == NULL ) return NULL;
 
+	indexamajig_path = get_indexamajig_exe();
+	if ( indexamajig_path == NULL ) {
+		ERROR("Couldn't determine indexamajig path. "
+		      "This is OK provided the executable path is set "
+		      "correctly.\n");
+		indexamajig_path = strdup("indexamajig");
+	}
+
 	/* The basics */
-	add_arg(args, n_args++, "indexamajig");
+	add_arg(args, n_args++, indexamajig_path);
 	add_arg(args, n_args++, "-i");
 	add_arg(args, n_args++, "files.lst");
 	add_arg(args, n_args++, "-g");
diff --git a/src/gui_index.h b/src/gui_index.h
index 89b6a7e3..f0454271 100644
--- a/src/gui_index.h
+++ b/src/gui_index.h
@@ -46,4 +46,6 @@ extern char **indexamajig_command_line(const char *geom_filename,
                                        struct peak_params *peak_search_params,
                                        struct index_params *indexing_params);
 
+extern char *get_crystfel_path_str(void);
+
 #endif