Generalized workflow functions to consider reviewer attributes such as initials and type e.g., data-owner and metadata-reviewer.
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@ -35,9 +35,9 @@ def get_review_status(filename_path):
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workflow_steps.append(line)
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return workflow_steps[-1]
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def checkout_review_branch(repo_obj,initials):
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def checkout_review_branch(repo_obj,branch_name):
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# Create a new branch
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branch_name = 'metadata-review-by-'+initials
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#branch_name = 'metadata-review-by-'+initials
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head_commit = repo_obj.head.peel()# Get the commit hash associated with HEAD
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if not branch_name in repo_obj.branches:
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@ -46,45 +46,45 @@ def checkout_review_branch(repo_obj,initials):
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branch = repo_obj.branches[branch_name]
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repo_obj.checkout(branch)
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def first_initialize_metadata_review(filename_path,initials):
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def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
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"""
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Initialize metadata review by creating review folder with a copy of yaml representation of
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Initialize review branch with review folder with a copy of yaml representation of
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hdf5 file under review and by creating a txt file with the state of the review process, e.g., under review.
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"""
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filename_path_tail, filename_path_head = os.path.split(filename_path)
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filename, ext = os.path.splitext(filename_path_head)
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initials = reviewer_attrs['initials']
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branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
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hdf5_file_path_tail, filename_path_head = os.path.split(hdf5_file_path)
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filename, ext = os.path.splitext(filename_path_head)
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# Check file_path points to h5 file
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if not 'h5' in ext:
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raise ValueError("filename_path needs to point to a suitable h5 file.")
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raise ValueError("filename_path needs to point to an h5 file.")
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# Verify if yaml snapshot of input h5 file exists
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if not os.path.exists(os.path.join(filename_path_tail,filename+YAML_EXT)):
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if not os.path.exists(os.path.join(hdf5_file_path_tail,filename+YAML_EXT)):
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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) ")
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# Initialize metadata review workflow
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print("Create branch metadata-review-by-"+initials+"\n")
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# Check if review file already exists and then check if it is still untracked
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if not os.path.exists(os.path.join("review/",filename+YAML_EXT)):
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review_filename_path = utils.make_file_copy(os.path.join(filename_path_tail,filename+YAML_EXT), 'review')
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else:
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review_filename_path = os.path.join("review/",filename+YAML_EXT)
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review_yaml_file_path = os.path.join("review/",filename+YAML_EXT)
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if not os.path.exists(review_yaml_file_path):
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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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#else:
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# raise Warning("the file " + os.path.join("review/",filename+YAML_EXT)+ " already exists. Delete this file to reinitialize the metadata review process.")
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review_filename_tail, ext = os.path.splitext(review_filename_path)
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review_yaml_file_path_tail, ext = os.path.splitext(review_yaml_file_path)
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with open(os.path.join(review_filename_tail+"-review_status"+".txt"),'w') as f:
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with open(os.path.join(review_yaml_file_path_tail+"-review_status"+".txt"),'w') as f:
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f.write('under review')
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checkout_review_branch(repo_obj,initials)
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checkout_review_branch(repo_obj, branch_name)
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status_dict = repo_obj.status()
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for filepath, file_status in status_dict.items():
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@ -101,9 +101,11 @@ def first_initialize_metadata_review(filename_path,initials):
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#print("Add and commit"+"\n")
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return review_yaml_file_path
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def second_submit_metadata_review(filename_path, initials):
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def second_submit_metadata_review(filename_path, reviewer_attrs):
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"""
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Once you're done reviewing the yaml representation of hdf5 file in review folder.
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Change the review status to complete and save (add and commit) modified .yalm and .txt files in the project by
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@ -114,6 +116,8 @@ def second_submit_metadata_review(filename_path, initials):
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# 2. change review status in txt to complete
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# 3. git add review/ and git commit -m "Submitted metadata review"
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initials = reviewer_attrs['initials']
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branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
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if any([status in get_review_status(filename_path) for status in ['under review','submitted']]):
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filename_path_tail, filename_path_head = os.path.split(filename_path)
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@ -122,16 +126,8 @@ def second_submit_metadata_review(filename_path, initials):
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with open(os.path.join("review/",filename+"-review_status"+TXT_EXT),'a') as f:
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f.write('\nsubmitted')
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# Create a new branch
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branch_name = 'metadata-review-by-'+initials
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head_commit = repo_obj.head.peel()# Get the commit hash associated with HEAD
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if not branch_name in repo_obj.branches:
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branch = repo_obj.create_branch(branch_name, head_commit)
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else:
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branch = repo_obj.branches[branch_name]
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repo_obj.checkout(branch)
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# TODO: replace with subprocess + git
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checkout_review_branch(repo_obj, branch_name)
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status_dict = repo_obj.status()
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for filepath, file_status in status_dict.items():
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@ -148,13 +144,16 @@ def second_submit_metadata_review(filename_path, initials):
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def third_complete_metadata_review(initials):
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def third_complete_metadata_review(reviewer_attrs):
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initials = reviewer_attrs['initials']
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push_command = lambda repository,refspec: ['git','push',repository,refspec]
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list_branches_command = ['git','branch','--list']
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repository = 'origin'
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branch_name = 'metadata-review-by-'+initials # refspec
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branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
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branches = subprocess.run(list_branches_command,capture_output=True,text=True,check=True)
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if not branch_name in branches.stdout:
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@ -177,8 +176,9 @@ def third_complete_metadata_review(initials):
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return result.returncode
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def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
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def third_update_hdf5_file_with_review(input_hdf5_file, yalm_review_file, reviewer_attrs = {}):
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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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# groups that changed :). the below approach is suboptimal
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@ -202,7 +202,7 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
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print('additions',count_additions, 'deletions', count_delections)
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with open(yaml_file,'r') as stream:
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with open(yalm_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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@ -282,10 +282,12 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
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# print(exc)
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def fourth_complete_metadata_review(initials):
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def fourth_complete_metadata_review(reviewer_attrs):
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initials =reviewer_attrs['initials']
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repository = 'origin'
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branch_name = 'data-owner-review-by-'+initials
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branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
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current_branch_command = ['git','branch','--show-current']
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list_branches_command = ['git','branch','--list']
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