Included new delete attribute and restart review features.
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@ -54,9 +54,10 @@ def checkout_review_branch(branch_name):
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current_branch_command = ['git','branch','--show-current']
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status_command = ['git','status']
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add_command = lambda add_list: ['git','add'] + add_list
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rm_command = lambda add_list: ['git','add'] + add_list
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commit_command = lambda message: ['git','commit','-m', message]
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def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs, restart = False):
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"""
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First: Initialize review branch with review folder with a copy of yaml representation of
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@ -92,14 +93,19 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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# Check if review file already exists and then check if it is still untracked
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review_yaml_file_path = os.path.join("review/",filename+YAML_EXT)
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review_yaml_file_path_tail, ext = os.path.splitext(review_yaml_file_path)
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review_status_yaml_file_path = os.path.join(review_yaml_file_path_tail+"-review_status"+".txt")
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if not os.path.exists(review_yaml_file_path):
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if not os.path.exists(review_yaml_file_path) or restart:
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review_yaml_file_path = utils.make_file_copy(os.path.join(hdf5_file_path_tail,filename+YAML_EXT), 'review')
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if restart:
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print('metadata review has been reinitialized. The review files will reflect the current state of the hdf5 files metadata')
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review_yaml_file_path_tail, ext = os.path.splitext(review_yaml_file_path)
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#if not os.path.exists(os.path.join(review_yaml_file_path_tail+"-review_status"+".txt")):
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with open(os.path.join(review_yaml_file_path_tail+"-review_status"+".txt"),'w') as f:
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with open(review_status_yaml_file_path,'w') as f:
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f.write('under review')
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# Stage untracked review files and commit them to local repository
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@ -108,7 +114,13 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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for line in status.stdout.splitlines():
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#tmp = line.decode("utf-8")
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#modified_files.append(tmp.split()[1])
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if 'review/' in line and not 'modified' in line: # untracked files
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if 'review/' in line:
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if not 'modified' in line: # untracked filesand
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untracked_files.append(line.strip())
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else:
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untracked_files.append(line.strip().split()[1])
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if 'output_files/'+filename+YAML_EXT in line and not 'modified' in line:
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untracked_files.append(line.strip())
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if untracked_files:
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@ -118,8 +130,8 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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for line in commit_output.stdout.splitlines():
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print(line.decode('utf-8'))
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else:
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print('This action will not have any effect because metadata review process has been already initialized.')
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#else:
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# print('This action will not have any effect because metadata review process has been already initialized.')
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@ -139,7 +151,7 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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#print("Add and commit"+"\n")
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return review_yaml_file_path
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return review_yaml_file_path, review_status_yaml_file_path
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@ -204,14 +216,16 @@ def parse_attribute(attr_value):
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dtype.append((key,f'S{max_length}'))
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values_list.append(attr_value[key])
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if len(values_list)>2:
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if len(values_list)>1:
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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['value']
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elif values_list:
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new_attr_value = values_list[0]
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else:
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new_attr_value = 'missing'
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return new_attr_value
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def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, reviewer_attrs = {}, hdf5_upload : bool = False):
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def third_update_hdf5_file_with_review(input_hdf5_file, yaml_review_file, reviewer_attrs = {}, hdf5_upload : bool = False):
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"""Third"""
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# compare review file with current yalm file and then based on the changes open hdf5 file and access only
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@ -237,7 +251,7 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, review
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print('additions',count_additions, 'deletions', count_delections)
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with open(yalm_review_file,'r') as stream:
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with open(yaml_review_file,'r') as stream:
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try:
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yaml_dict = yaml.load(stream, Loader=yaml.FullLoader)
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except yaml.YAMLError as exc:
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@ -277,9 +291,11 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, review
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# yaml indicates a renaming of the attribute.
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if not (new_attr_name == attr_name):
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hdf5_obj.attrs.__delitem__(attr_name)
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#else:
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# hdf5_obj.attrs[attr_name] = attr_value
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else: # attribute inclusion
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elif not attr_value.get('delete',False): # if true inclusion, else don't take any action
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#hdf5_obj.attrs.__delitem__(attr_name): # attribute inclusion
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#if isinstance(attr_value,dict):
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# Retreive 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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@ -287,9 +303,11 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, review
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hdf5_obj.attrs[attr_name] = parse_attribute(attr_value)
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#else:
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# hdf5_obj.attrs[attr_name] = attr_value
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print(input_hdf5_file + ' was successfully updated\n')
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# Recreate/or update yaml representation of updated input_hdf5_file.
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output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(input_hdf5_file)
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# Recreate/or update yaml representation of updated input_hdf5_file.
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output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(input_hdf5_file)
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print(output_yml_filename_path + ' was successfully regenerated from the updated version of ', input_hdf5_file)
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status_command = ['git','status']
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@ -317,17 +335,10 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, review
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#status = subprocess.run(status_command,capture_output=True,check=True)
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message = 'Updated hdf5 file with yaml review file.'
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commit_output = subprocess.run(commit_command(message),capture_output=True,check=True)
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print(commit_output.stdout)
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else:
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print("There were no found h5 and yaml files, needing to be saved. This action will not have effect on the review process' commit history.")
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#with open('review/review_status.txt','r+') as f:
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# f.write('hdf5 file updated w/ metadata review')
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#try:
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# yaml_dict = yaml.load(stream, Loader=yaml.FullLoader)
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#except yaml.YAMLError as exc:
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# print(exc)
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def last_submit_metadata_review(reviewer_attrs):
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@ -336,7 +347,7 @@ def last_submit_metadata_review(reviewer_attrs):
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initials =reviewer_attrs['initials']
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repository = 'origin'
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branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
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branch_name = '_'.join(['review',initials])
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push_command = lambda repository,refspec: ['git','push',repository,refspec]
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current_branch_command = ['git','branch','--show-current']
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