diff --git a/pipelines/metadata_revision.py b/pipelines/metadata_revision.py index 09a5e5f..5311cb5 100644 --- a/pipelines/metadata_revision.py +++ b/pipelines/metadata_revision.py @@ -7,7 +7,7 @@ import subprocess import h5py import yaml import utils.g5505_utils as utils -import src.hdf5_vis as hdf5_vis +import src.hdf5_ops as hdf5_ops import src.hdf5_lib as hdf5_lib import src.git_ops as git_ops @@ -53,7 +53,7 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs, restart = F # Verify if yaml snapshot of input h5 file exists if not os.path.exists(os.path.join(hdf5_file_path_tail,filename+YAML_EXT)): - raise ValueError("metadata review cannot be initialized. The associated .yaml file under review was not found. Run take_yml_snapshot_of_hdf5_file(filename_path) ") + raise ValueError("metadata review cannot be initialized. The associated .yaml file under review was not found. Run to_yaml(filename_path) ") # Initialize metadata review workflow # print("Create branch metadata-review-by-"+initials+"\n") @@ -217,7 +217,7 @@ def update_hdf5_file_with_review(input_hdf5_file, yaml_review_file): yaml_dict = load_yaml(yaml_review_file) update_hdf5_attributes(input_hdf5_file, yaml_dict) # Regenerate yaml snapshot of updated HDF5 file - output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(input_hdf5_file) + output_yml_filename_path = hdf5_ops.to_yaml(input_hdf5_file) print(f'{output_yml_filename_path} was successfully regenerated from the updated version of{input_hdf5_file}') def third_update_hdf5_file_with_review(input_hdf5_file, yaml_review_file, reviewer_attrs={}, hdf5_upload=False): @@ -278,7 +278,7 @@ def last_submit_metadata_review(reviewer_attrs): #import config_file -#import hdf5_vis +#import hdf5_ops class MetadataHarvester: def __init__(self, parent_files=None): @@ -367,7 +367,7 @@ def main(): output_filename_path = "output_files/unified_file_smog_chamber_2024-03-19_UTC-OFST_+0100_NG.h5" output_yml_filename_path = "output_files/unified_file_smog_chamber_2024-03-19_UTC-OFST_+0100_NG.yalm" output_yml_filename_path_tail, filename = os.path.split(output_yml_filename_path) - #output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(output_filename_path) + #output_yml_filename_path = hdf5_ops.to_yaml(output_filename_path) #first_initialize_metadata_review(output_filename_path,initials='NG') #second_submit_metadata_review() diff --git a/src/hdf5_ops.py b/src/hdf5_ops.py index 883fc07..5f08c29 100644 --- a/src/hdf5_ops.py +++ b/src/hdf5_ops.py @@ -352,7 +352,7 @@ def print_metadata(name, obj, folder_depth, yaml_dict): #elif len(obj.name.split('/')) == 3: # print(yaml.dump()) -def take_yml_snapshot_of_hdf5_file(input_filename_path,folder_depth: int = 4): +def to_yaml(input_filename_path,folder_depth: int = 4): yaml_dict = {}