Moved remaining git operations in metadata_review_lib.py to git_ops.py and refactored accoringly

src/git_ops.py

@@ -33,4 +33,11 @@ def add_files_to_git(files_to_add_list):
 def commit_changes(message):
     commit_command = ['git', 'commit', '-m', message]
     commit_output = subprocess.run(commit_command, capture_output=True, check=True)
-    print(commit_output.stdout)
+    print(commit_output.stdout)
+
+def get_status():
+    return subprocess.run(['git','status'],capture_output=True,text=True,check=True)
+
+def show_current_branch():
+    current_branch_command = ['git','branch','--show-current']    
+    subprocess.run(current_branch_command,capture_output=True,text=True,check=True)

src/metadata_review_lib.py

@@ -10,14 +10,7 @@ import src.g5505_utils as utils
 import src.hdf5_vis as hdf5_vis
 import src.hdf5_lib as hdf5_lib
 import src.git_ops as git_ops
-# TODO: incorporate lines 14-18 in git_ops module and refactor code where needed
-current_branch_command = ['git','branch','--show-current']    
-status_command = ['git','status']
-add_command = lambda add_list: ['git','add'] + add_list
-rm_command = lambda add_list: ['git','add'] + add_list
-commit_command = lambda message: ['git','commit','-m', message]
 
-#import input_files.config_file as config_file
 
 import numpy as np
 
@@ -97,8 +90,8 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs, restart = F
     #checkout_review_branch(branch_name)
     
     # Check you are working at the right branch   
-    current_branch_command = ['git','branch','--show-current']
-    curr_branch = subprocess.run(current_branch_command,capture_output=True,text=True,check=True)
+    
+    curr_branch = git_ops.show_current_branch()
     if not branch_name in curr_branch.stdout:
         raise ValueError("Branch "+branch_name+" was not found. \nPlease open a Git Bash Terminal, and follow the below instructions: \n1. Change directory to your project's directory. \n2. Excecute the command: git checkout "+branch_name)
         
@@ -120,7 +113,7 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs, restart = F
             f.write('under review')  
 
     # Stage untracked review files and commit them to local repository
-    status = subprocess.run(status_command,capture_output=True,text=True,check=True)
+    status = git_ops.get_status()
     untracked_files = []
     for line in status.stdout.splitlines():
         #tmp = line.decode("utf-8")
@@ -135,9 +128,9 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs, restart = F
             untracked_files.append(line.strip())
 
     if untracked_files:
-        result = subprocess.run(add_command(untracked_files),capture_output=True,check=True)
+        result = subprocess.run(git_ops.add_files_to_git(untracked_files),capture_output=True,check=True)
         message = 'Initialized metadata review.'
-        commit_output = subprocess.run(commit_command(message),capture_output=True,check=True)
+        commit_output = subprocess.run(git_ops.commit_changes(message),capture_output=True,check=True)
 
         for line in commit_output.stdout.splitlines():
             print(line.decode('utf-8'))
@@ -184,12 +177,12 @@ def second_save_metadata_review(review_yaml_file_path, reviewer_attrs):
     #checkout_review_branch(repo_obj, branch_name)
 
     # Check you are working at the right branch    
-    curr_branch = subprocess.run(current_branch_command,capture_output=True,text=True,check=True)
+    curr_branch = git_ops.show_current_branch()
     if not branch_name in curr_branch.stdout:
         raise ValueError('Please checkout ' + branch_name + ' via Git Bash before submitting metadata review files. ')
 
     # Collect modified review files
-    status = subprocess.run(status_command,capture_output=True,check=True)
+    status = git_ops.get_status()
     modified_files = []
     os.path.basename(review_yaml_file_path)
     for line in status.stdout.splitlines():
@@ -208,9 +201,9 @@ def second_save_metadata_review(review_yaml_file_path, reviewer_attrs):
 
         modified_files.append(review_status_file_path)
 
-        result = subprocess.run(add_command(modified_files),capture_output=True,check=True)
+        result = subprocess.run(git_ops.add_files_to_git(modified_files),capture_output=True,check=True)
         message = 'Submitted metadata review.'
-        commit_output = subprocess.run(commit_command(message),capture_output=True,check=True)
+        commit_output = subprocess.run(git_ops.commit_changes(message),capture_output=True,check=True)
 
         for line in commit_output.stdout.splitlines():
             print(line.decode('utf-8'))
@@ -283,7 +276,7 @@ def last_submit_metadata_review(reviewer_attrs):
     branch_name = '_'.join(['review',initials])
 
     push_command = lambda repository,refspec: ['git','push',repository,refspec]
-    current_branch_command = ['git','branch','--show-current']
+    
     list_branches_command = ['git','branch','--list']
 
     branches = subprocess.run(list_branches_command,capture_output=True,text=True,check=True)
@@ -292,7 +285,7 @@ def last_submit_metadata_review(reviewer_attrs):
         print('Make sure to run data owner review workflow from the beginning without missing any steps.')
         return
 
-    curr_branch = subprocess.run(current_branch_command,capture_output=True,text=True,check=True)
+    curr_branch = git_ops.show_current_branch()
     if not branch_name in curr_branch.stdout:
         print('Complete metadata review could not be completed.\n')
         print('Make sure a data-owner workflow has already been started on branch '+branch_name+'\n')