no copying if no push

reportservice/automatic_run.py

@@ -73,7 +73,7 @@ if __name__ == "__main__":
     args = vars(arg_parser.parse_args())
     conf_file = args["config_file"]
     with open(conf_file, "r") as f:
-        cfg = yaml.load(f.read())
+        cfg = yaml.load(f.read(), Loader=yaml.FullLoader)
 
     logfile = args["log_file"]
     fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'

reportservice/manual_run.py

@@ -35,11 +35,11 @@ def manual_run(request, cfg):
 arg_parser = argparse.ArgumentParser(description='Manual Launch')
 arg_parser.add_argument('--instrument', default=['all'], nargs='+',
                         help='select the requested instruments. '
-                             'Default=None. "all" can be used for selecting'
+                             'Default=\"all\", which can be used for selecting'
                              ' all instruments')
 arg_parser.add_argument('--gitpush', dest='Push to git', action='store_true',
                         help='required for pushing the generated figures '
-                             'to the DC git repository')
+                             'to the DC git repository. Default=bool(False)')
 arg_parser.set_defaults(gitpush=False)
 arg_parser.add_argument('--config-file', type=str, 
                         default='./report_conf.yaml',
@@ -56,7 +56,7 @@ if __name__ == "__main__":
     args = vars(arg_parser.parse_args())
     conf_file = args["config_file"]
     with open(conf_file, "r") as f:
-        cfg = yaml.load(f.read())
+        cfg = yaml.load(f.read(), Loader=yaml.FullLoader)
 
     logfile = args["log_file"]
     fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'

reportservice/report_service.py

@@ -156,7 +156,7 @@ async def server_runner(conf_file):
     be accessed through ReadTheDocs.
     """
     with open(conf_file, "r") as f:
-        config = yaml.load(f.read())
+        config = yaml.load(f.read(), Loader=yaml.FullLoader)
 
     # perform git-dir checks and pull the project for updates.
     init_config_repo(config['GLOBAL']['git'])
@@ -263,57 +263,60 @@ async def server_runner(conf_file):
                     logging.error('Jobs have timed-out!')
                     logging.error('{}/temp has not been deleted.'.format(
                                   os.path.dirname(os.path.abspath(__file__))))
+                # Avoid copying files if no git-push is planned
+                # to avoid causing local git repository errors.
+                if git_push:
+                    # Copy all plots
+                    for det_name, det_conf in instrument.items():
 
-                # Copy all plots
-                for det_name, det_conf in instrument.items():
-                    
-                    out_folder = det_conf['out-folder'].format(
-                                          instrument=instr_name,
-                                          detector=det_name)
+                        out_folder = det_conf['out-folder'].format(
+                                              instrument=instr_name,
+                                              detector=det_name)
 
-                    figures = glob.glob("{}/*png".format(out_folder))
+                        figures = glob.glob("{}/*png".format(out_folder))
 
-                    det_new_files = {}
+                        det_new_files = {}
 
-                    for f in figures:
-                        const = f.split('/')[-1].split('_')[0]
-                        fpath = '{}/{}/{}/{}'.format(fig_local, instr_name,
-                                                     det_name, const)
+                        for f in figures:
+                            const = f.split('/')[-1].split('_')[0]
+                            fpath = '{}/{}/{}/{}'.format(fig_local, instr_name,
+                                                         det_name, const)
 
-                        os.makedirs(fpath, exist_ok=True)
-                        det_new_files[f] = fpath
+                            os.makedirs(fpath, exist_ok=True)
+                            det_new_files[f] = fpath
 
-                        # Set concurrency limitation.
-                        # 50 have been chosen by trial 
-                        # Note: This is not the max limitation.
-                        sem = asyncio.Semaphore(50)
-                        all_new_files.append(
-                            '{}/{}'.format(fpath, f.split('/')[-1]))
+                            # Set concurrency limitation.
+                            # 50 have been chosen by trial
+                            # Note: This is not the max limitation.
+                            sem = asyncio.Semaphore(50)
+                            all_new_files.append(
+                                '{}/{}'.format(fpath, f.split('/')[-1]))
 
-                    await asyncio.gather(*[copy_files(k, v, sem)
-                                        for k, v in det_new_files.items()])
+                        await asyncio.gather(*[copy_files(k, v, sem)
+                                            for k, v in det_new_files.items()])
 
-                    logging.info('{} figures of {} are copied into {}'.format(
-                                           len(figures), det_name, fig_local))
+                        logging.info('{} figures of {} are copied into {}'.format(
+                                               len(figures), det_name, fig_local))
 
-            # Remove sensitive information from the config file.
-            del cfg['GLOBAL']
-            # Write the requested cfg.yaml before pushing all figures.
-            with open('{}/report_conf.yaml'.format(
-                                          fig_local), 'w') as outfile:
-                yaml.dump(cfg, outfile, default_flow_style=False)
+            if git_push:
+                # Remove sensitive information from the config file.
+                del cfg['GLOBAL']
+                # Write the requested cfg.yaml before pushing all figures.
+                with open('{}/report_conf.yaml'.format(
+                                              fig_local), 'w') as outfile:
+                    yaml.dump(cfg, outfile, default_flow_style=False)
 
-            all_new_files.append('{}/report_conf.yaml'.format(fig_local))
+                all_new_files.append('{}/report_conf.yaml'.format(fig_local))
 
-            if git_push:
                 asyncio.ensure_future(push_figures(local_repo, all_new_files))
 
-            # TODO:delete out-folder
-            #try:
-                # asyncio.ensure_future(del_folder(out_folder))
-            #except:
-                #logging.error(str(e))
-            logging.info('All done')
+                # TODO:delete out-folder
+                #try:
+                    # asyncio.ensure_future(del_folder(out_folder))
+                #except:
+                    #logging.error(str(e))
+
+            logging.info('Generating requested plots is finished!')
 
             return