fix run method

.gitignore

@@ -7,3 +7,5 @@
 *.pyc
 /src/sh/*.sh
 *.swp
+/emp-env
+

config/conf.json

@@ -10,7 +10,7 @@
   "hg_th" : "0.05",
   "permuted_datasets_folder" : "../../data/emp_test/permuted_datasets",
   "permuted_solutions_folder" : "../../data/emp_test/permuted_solutions",
-  "true_solutions_folder" : "../../emp_test/true_solutions",
+  "true_solutions_folder" : "../../data/emp_test/true_solutions",
   "report_folder" : "../../data/emp_test/report",
   "n_start" : "0",
   "n_end" : "1010",

src/emp/generate_permuted_solutions.py

@@ -69,6 +69,8 @@ def main():
             params=[ [empirical_dist_iteration, [dataset_file, x, algo, network_file, go_folder, permuted_datasets_folder, permuted_solutions_folder, additional_args]] for x in np.arange(int(n_start), int(n_end)) if override_permutations or not permutation_solution_exists(dataset_name, algo, x, permuted_solutions_folder)]
             print("about to start generation of {} permuted solutions".format(len(params)))
             p.map(func_star, params)
+            # for a in params:
+            #     a[0](*a[1])
             break_loop=True
 
         except (Exception, MemoryError, OSError) as e:

src/runners/abstract_runner.py

@@ -71,3 +71,4 @@ def main(self, dataset_file_name, network_file_name, go_folder, output_folder, *
         print(f'about to run algo with the following parameters: {os.path.abspath(dataset_file_name)}, {os.path.abspath(network_file_name)}, {os.path.abspath(output_folder)}, {kwargs}')
 
         modules, all_bg_genes = self.run(os.path.abspath(dataset_file_name), os.path.abspath(network_file_name), os.path.abspath(output_folder), **kwargs)
+        self.build_all_reports(self.ALGO_NAME, modules, all_bg_genes, os.path.abspath(go_folder), os.path.abspath(os.path.join(output_folder, "report")))

src/utils/network.py

@@ -197,13 +197,12 @@ def build_all_reports(algo_name, modules, all_bg_genes, go_folder, output_folder
     modules_summary = manager.list()
 
     params=[]
-    # p=multiprocessing.Pool(3)
+    p=multiprocessing.Pool(3)
     for i, module in enumerate(modules):
-        # params.append([module_report, [algo_name, i, module, all_bg_genes[i], score_file_name, network_file_name, dataset_name, all_hg_reports,
-        #      modules_summary]])
-        module_report(algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary)
+        params.append([module_report, [algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary]])
+        # module_report(algo_name, i, module, all_bg_genes[i], go_folder, output_folder, modules_summary)
 
-    # p.map(func_star, params)
+    p.map(func_star, params)
 
     modules_summary=list(modules_summary)
     all_hg_reports=list(all_hg_reports)