Replaced git commands in terms of subprocess.run
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@ -166,10 +166,11 @@ def second_save_metadata_review(review_yaml_file_path, reviewer_attrs):
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# Collect modified review files
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# Collect modified review files
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status = subprocess.run(status_command,capture_output=True,check=True)
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status = subprocess.run(status_command,capture_output=True,check=True)
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modified_files = []
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modified_files = []
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os.path.basename(review_yaml_file_path)
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for line in status.stdout.splitlines():
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for line in status.stdout.splitlines():
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# conver line from bytes to str
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# conver line from bytes to str
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tmp = line.decode("utf-8")
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tmp = line.decode("utf-8")
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if 'modified' in tmp and review_yaml_file_path in tmp:
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if 'modified' in tmp and 'review/' in tmp and os.path.basename(review_yaml_file_path) in tmp:
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modified_files.append(tmp.split()[1])
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modified_files.append(tmp.split()[1])
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# Stage modified files and commit them to local repository
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# Stage modified files and commit them to local repository
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@ -245,7 +246,18 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, review
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if isinstance(attr_value,dict):
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if isinstance(attr_value,dict):
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# Retreive possibly new attribute's name and value
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# Retreive possibly new attribute's name and value
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new_attr_name = attr_value.get('rename_as',attr_name) # if 'rename_as' is a key in attr_value returns the value, otherwise it return the existing value
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new_attr_name = attr_value.get('rename_as',attr_name) # if 'rename_as' is a key in attr_value returns the value, otherwise it return the existing value
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new_attr_value = attr_value.get('value',hdf5_obj.attrs[attr_name])
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dtype = []
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values_list = []
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max_length = 100
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for key in attr_value.keys():
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if (not key=='rename_as'):
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dtype.append((key,f'S{max_length}'))
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values_list.append(attr_value.get(key,hdf5_obj.attrs[attr_name]))
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if len(values_list)>2:
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new_attr_value = np.array([tuple(values_list)],dtype=dtype)
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else:
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new_attr_value = attr_value.get('value',hdf5_obj.attrs[attr_name])
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hdf5_obj.attrs[new_attr_name] = new_attr_value
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hdf5_obj.attrs[new_attr_name] = new_attr_value
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