GUI: Run all jobs with same CWD as GUI itself

This requires changing all the paths to relative ones.

Previously, the jobs ran with their CWDs set to the corresponding
"result" folder.  The trouble is, this breaks everything that uses a
relative location: image filenames, mask/satmap files referenced by the
geometry, etc.

Note that this change also means that the temporary folders
("indexamajig.XXX") are now produced in the top-level working directory.
Eventually, a GUI option should be added to allow these folders to be
put somewhere better (i.e. somewhere fast).

Closes: https://gitlab.desy.de/thomas.white/crystfel/-/issues/44

1 files changed, 89 insertions, 70 deletions

diff --git a/src/gui_backend_local.c b/src/gui_backend_local.c
index d78fc037..ba56bd7c 100644
--- a/src/gui_backend_local.c
+++ b/src/gui_backend_local.c
@@ -116,11 +116,7 @@ static int write_file_list(GFile *workdir,
 	if ( fh == NULL ) return 1;
 
 	for ( i=0; i<n_frames; i++ ) {
-		if ( filenames[i][0] != '/' ) {
-			fprintf(fh, "../%s", filenames[i]);
-		} else {
-			fprintf(fh, "%s", filenames[i]);
-		}
+		fprintf(fh, "%s", filenames[i]);
 		if ( events[i] != NULL ) {
 			fprintf(fh, " %s\n", events[i]);
 		} else {
@@ -177,7 +173,7 @@ static struct local_job *start_local_job(char **args,
 	r = g_spawn_async_with_pipes(NULL, args, NULL,
 	                             G_SPAWN_SEARCH_PATH
 	                           | G_SPAWN_DO_NOT_REAP_CHILD,
-	                             setup_subprocess, workdir_str,
+	                             setup_subprocess, NULL,
 	                             &job->pid,
 	                             NULL, NULL, &ch_stderr,
 	                             &error);
@@ -387,29 +383,37 @@ static void *run_ambi(const char *job_title,
 	struct local_job *job;
 	struct local_merging_opts *opts = opts_priv;
 	GFile *workdir;
-	GFile *sc_gfile;
-	gchar *sc_filename;
-	GFile *stream_gfile;
-	char *stream_str;
+	gchar *sc_rel_filename;
+	gchar *stream_rel_filename;
+	gchar *stderr_rel_filename;
+	gchar *stdout_rel_filename;
+	gchar *fg_rel_filename;
+	gchar *intermediate_rel_filename;
+	gchar *harvest_rel_filename;
 
 	workdir = make_job_folder(job_title, job_notes);
 	if ( workdir == NULL ) return NULL;
 
-	stream_gfile = g_file_get_child(workdir, "ambi.stream");
-	stream_str = g_file_get_path(stream_gfile);
-	g_object_unref(stream_gfile);
+	stream_rel_filename = relative_to_cwd(workdir, "ambi.stream");
+	stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+	stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+	sc_rel_filename = relative_to_cwd(workdir, "run_ambigator.sh");
+	fg_rel_filename = relative_to_cwd(workdir, "fg.dat");
+	intermediate_rel_filename = relative_to_cwd(workdir, "ambigator-input.stream");
+	harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
 
 	snprintf(n_thread_str, 64, "%i", opts->n_threads);
-	sc_gfile = g_file_get_child(workdir, "run_ambigator.sh");
-	sc_filename = g_file_get_path(sc_gfile);
-	g_object_unref(sc_gfile);
-	if ( sc_filename == NULL ) return NULL;
-	if ( !write_ambigator_script(sc_filename, input, n_thread_str,
-	                             &proj->ambi_params, stream_str) )
+
+	if ( !write_ambigator_script(sc_rel_filename, input, n_thread_str,
+	                             &proj->ambi_params, stream_rel_filename,
+	                             stdout_rel_filename, stderr_rel_filename,
+	                             fg_rel_filename,
+	                             intermediate_rel_filename,
+	                             harvest_rel_filename) )
 	{
 		char *args[3];
 		args[0] = "sh";
-		args[1] = sc_filename;
+		args[1] = sc_rel_filename;
 		args[2] = NULL;
 		job = start_local_job(args, job_title, workdir,
 		                      proj, GUI_JOB_AMBIGATOR);
@@ -419,10 +423,18 @@ static void *run_ambi(const char *job_title,
 	}
 
 	if ( job != NULL ) {
-		add_indexing_result(proj, job_title, &stream_str, 1);
+		add_indexing_result(proj, job_title, &stream_rel_filename, 1);
 	}
 
 	g_object_unref(workdir);
+	free(sc_rel_filename);
+	free(stream_rel_filename);
+	free(stdout_rel_filename);
+	free(stderr_rel_filename);
+	free(fg_rel_filename);
+	free(intermediate_rel_filename);
+	free(harvest_rel_filename);
+
 	return job;
 }
 
@@ -437,25 +449,32 @@ static void *run_merging(const char *job_title,
 	struct local_job *job;
 	struct local_merging_opts *opts = opts_priv;
 	GFile *workdir;
-	GFile *sc_gfile;
-	gchar *sc_filename;
+	gchar *sc_rel_filename;
+	gchar *output_rel_filename;
+	gchar *stderr_rel_filename;
+	gchar *stdout_rel_filename;
+	gchar *harvest_rel_filename;
 
 	workdir = make_job_folder(job_title, job_notes);
 	if ( workdir == NULL ) return NULL;
 
+	sc_rel_filename = relative_to_cwd(workdir, "run_merge.sh");
+	output_rel_filename = relative_to_cwd(workdir, "crystfel.hkl");
+	stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+	stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+	harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+
 	snprintf(n_thread_str, 63, "%i", opts->n_threads);
-	sc_gfile = g_file_get_child(workdir, "run_merge.sh");
-	sc_filename = g_file_get_path(sc_gfile);
-	g_object_unref(sc_gfile);
-	if ( sc_filename == NULL ) return NULL;
 
-	if ( !write_merge_script(sc_filename, input, n_thread_str,
-	                         &proj->merging_params, "crystfel.hkl") )
+	if ( !write_merge_script(sc_rel_filename, input, n_thread_str,
+	                         &proj->merging_params, output_rel_filename,
+	                         stdout_rel_filename, stderr_rel_filename,
+	                         harvest_rel_filename) )
 	{
 		char *args[3];
 		enum gui_job_type type;
 		args[0] = "sh";
-		args[1] = sc_filename;
+		args[1] = sc_rel_filename;
 		args[2] = NULL;
 		if ( strcmp(proj->merging_params.model, "process_hkl") == 0 ) {
 			if ( proj->merging_params.scale ) {
@@ -470,34 +489,27 @@ static void *run_merging(const char *job_title,
 	} else {
 		job = NULL;
 	}
-	g_free(sc_filename);
 
 	if ( job != NULL ) {
 
-		GFile *hkl_gfile;
-		char *hkl;
 		char *hkl1;
 		char *hkl2;
 
-		hkl_gfile = g_file_get_child(workdir, "crystfel.hkl");
-		hkl = g_file_get_path(hkl_gfile);
-		g_object_unref(hkl_gfile);
-
-		hkl_gfile = g_file_get_child(workdir, "crystfel.hkl1");
-		hkl1 = g_file_get_path(hkl_gfile);
-		g_object_unref(hkl_gfile);
-
-		hkl_gfile = g_file_get_child(workdir, "crystfel.hkl2");
-		hkl2 = g_file_get_path(hkl_gfile);
-		g_object_unref(hkl_gfile);
+		hkl1 = relative_to_cwd(workdir, "crystfel.hkl1");
+		hkl2 = relative_to_cwd(workdir, "crystfel.hkl2");
 
-		add_merge_result(proj, job_title, hkl, hkl1, hkl2);
-		g_free(hkl);
+		add_merge_result(proj, job_title, output_rel_filename,
+		                 hkl1, hkl2);
 		g_free(hkl1);
 		g_free(hkl2);
 	}
 
 	g_object_unref(workdir);
+	g_free(sc_rel_filename);
+	free(output_rel_filename);
+	free(stdout_rel_filename);
+	free(stderr_rel_filename);
+	free(harvest_rel_filename);
 	return job;
 }
 
@@ -513,9 +525,12 @@ static void *run_indexing(const char *job_title,
 	struct local_job *job;
 	char n_thread_str[64];
 	GFile *workdir;
-	GFile *sc_gfile;
-	gchar *sc_filename;
-	GFile *stderr_gfile;
+	gchar *sc_rel_filename;
+	gchar *stdout_rel_filename;
+	gchar *stderr_rel_filename;
+	gchar *files_rel_filename;
+	gchar *stream_rel_filename;
+	gchar *harvest_rel_filename;
 
 	workdir = make_job_folder(job_title, job_notes);
 	if ( workdir == NULL ) return NULL;
@@ -530,16 +545,23 @@ static void *run_indexing(const char *job_title,
 	}
 
 	snprintf(n_thread_str, 63, "%i", opts->n_processes);
-	sc_gfile = g_file_get_child(workdir, "run_indexamajig.sh");
-	sc_filename = g_file_get_path(sc_gfile);
-	g_object_unref(sc_gfile);
-	if ( sc_filename == NULL ) return NULL;
-	if ( !write_indexamajig_script(sc_filename,
+
+	sc_rel_filename = relative_to_cwd(workdir, "run_indexamajig.sh");
+	stdout_rel_filename = relative_to_cwd(workdir, "stdout.log");
+	stderr_rel_filename = relative_to_cwd(workdir, "stderr.log");
+	files_rel_filename = relative_to_cwd(workdir, "files.lst");
+	stream_rel_filename = relative_to_cwd(workdir, "crystfel.stream");
+	harvest_rel_filename = relative_to_cwd(workdir, "parameters.json");
+
+	if ( !write_indexamajig_script(sc_rel_filename,
 	                               proj->geom_filename,
 	                               n_thread_str,
-	                               "files.lst",
-	                               "crystfel.stream",
-	                               NULL, 1,
+	                               files_rel_filename,
+	                               stream_rel_filename,
+	                               stdout_rel_filename,
+	                               stderr_rel_filename,
+	                               harvest_rel_filename,
+	                               NULL,
 	                               &proj->peak_search_params,
 	                               &proj->indexing_params,
 	                               wavelength_estimate,
@@ -547,7 +569,7 @@ static void *run_indexing(const char *job_title,
 	{
 		char *args[3];
 		args[0] = "sh";
-		args[1] = sc_filename;
+		args[1] = sc_rel_filename;
 		args[2] = NULL;
 		job = start_local_job(args, job_title, workdir,
 		                      proj, GUI_JOB_INDEXING);
@@ -557,23 +579,20 @@ static void *run_indexing(const char *job_title,
 
 	if ( job != NULL ) {
 
-		char *stream_fn;
-
 		/* Indexing-specific job data */
 		job->n_frames = proj->n_frames;
+		job->stderr_filename = strdup(stderr_rel_filename);
+		add_indexing_result(proj, job_title, &stream_rel_filename, 1);
 
-		stderr_gfile = g_file_get_child(workdir, "stderr.log");
-		job->stderr_filename = g_file_get_path(stderr_gfile);
-		g_object_unref(stderr_gfile);
-
-		GFile *stream_gfile = g_file_get_child(job->workdir,
-		                                       "crystfel.stream");
-		stream_fn = g_file_get_path(stream_gfile);
-		g_object_unref(stream_gfile);
-		add_indexing_result(proj, job_title, &stream_fn, 1);
-		g_free(stream_fn);
+	} else {
 	}
 	g_object_unref(workdir);
+	free(sc_rel_filename);
+	free(files_rel_filename);
+	free(stream_rel_filename);
+	free(stdout_rel_filename);
+	free(stderr_rel_filename);
+	free(harvest_rel_filename);
 
 	return job;
 }