Refactored a few git statemets in terms of subprocess.run

src/metadata_review_lib.py

@@ -35,16 +35,25 @@ def get_review_status(filename_path):
             workflow_steps.append(line)
     return workflow_steps[-1]
 
-def checkout_review_branch(repo_obj,branch_name):    
+def checkout_review_branch(branch_name):    
     # Create a new branch
     #branch_name = 'metadata-review-by-'+initials
     head_commit = repo_obj.head.peel()# Get the commit hash associated with HEAD
 
-    if not branch_name in repo_obj.branches:
+    checkout_branch_command = lambda branch_name : ['git','checkout', branch_name]
-        branch = repo_obj.create_branch(branch_name, head_commit)
+    output = subprocess.run(checkout_branch_command(branch_name), capture_output=True,text=True,check=True)
-    else:
+
-        branch = repo_obj.branches[branch_name]    
+    print(output.stdout)
-    repo_obj.checkout(branch)
+
+    #if not branch_name in repo_obj.branches:
+    #    branch = repo_obj.create_branch(branch_name, head_commit)
+    #else:
+    #    branch = repo_obj.branches[branch_name]    
+    #repo_obj.checkout(branch)
+    
+status_command = ['git','status']
+add_command = lambda add_list: ['git','add'] + add_list
+commit_command = lambda message: ['git','commit','-m', message]
 
 def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
 
@@ -70,34 +79,54 @@ def first_initialize_metadata_review(hdf5_file_path, reviewer_attrs):
 
     # Initialize metadata review workflow
     print("Create branch metadata-review-by-"+initials+"\n")
+
+    checkout_review_branch(branch_name)
     
+
+    current_branch_command = ['git','branch','--show-current']
+    curr_branch = subprocess.run(current_branch_command,capture_output=True,text=True,check=True)
+    if not branch_name in curr_branch.stdout:
+        print('Fail to checkout branch. ')
+        
     # Check if review file already exists and then check if it is still untracked
     review_yaml_file_path = os.path.join("review/",filename+YAML_EXT)
+
     if not os.path.exists(review_yaml_file_path):
         review_yaml_file_path = utils.make_file_copy(os.path.join(hdf5_file_path_tail,filename+YAML_EXT), 'review') 
-    #else:
-    #    raise Warning("the file " + os.path.join("review/",filename+YAML_EXT)+ " already exists. Delete this file to reinitialize the metadata review process.")
-
 
     review_yaml_file_path_tail, ext = os.path.splitext(review_yaml_file_path)
 
     with open(os.path.join(review_yaml_file_path_tail+"-review_status"+".txt"),'w') as f:
         f.write('under review')  
 
-    checkout_review_branch(repo_obj, branch_name)
+    # Stage review files and commit them to local repository
+    status = subprocess.run(status_command,capture_output=True,text=True,check=True)
+    untracked_files_for_review = []
+    for line in status.stdout.splitlines():
+        if 'review/' in line.decode('utf8'):
+            untracked_files_for_review.append(line)
 
-    status_dict = repo_obj.status()
+    result = subprocess.run(add_command(untracked_files_for_review),capture_output=True,check=True)
-    for filepath, file_status in status_dict.items():
+    message = 'Initialized metadata review.'
+    commit_output = subprocess.run(commit_command(message),capture_output=True,check=True)
+
+    print(commit_output.stdout)
+
+
+
+
+    #status_dict = repo_obj.status()
+    #for filepath, file_status in status_dict.items():
         # Identify keys associated to review files and stage them
-        if 'review/'+filename in filepath:
+    #    if 'review/'+filename in filepath:
             # Stage changes
-            repo_obj.index.add(filepath)
+    #        repo_obj.index.add(filepath)
 
-    author = config_file.author #default_signature
+    #author = config_file.author #default_signature
-    committer = config_file.committer
+    #committer = config_file.committer
-    message = "Initialized metadata review process."
+    #message = "Initialized metadata review process."
-    tree = repo_obj.index.write_tree()
+    #tree = repo_obj.index.write_tree()
-    oid = repo_obj.create_commit('HEAD', author, committer, message, tree, [repo_obj.head.peel().oid])
+    #oid = repo_obj.create_commit('HEAD', author, committer, message, tree, [repo_obj.head.peel().oid])
 
     #print("Add and commit"+"\n") 
 
@@ -119,7 +148,13 @@ def second_submit_metadata_review(review_yaml_file_path, reviewer_attrs):
     initials = reviewer_attrs['initials']
     branch_name = '-'.join([reviewer_attrs['type'],'review','by',initials])
     # TODO: replace with subprocess + git
-    checkout_review_branch(repo_obj, branch_name)
+    #checkout_review_branch(repo_obj, branch_name)
+
+    current_branch_command = ['git','branch','--show-current']
+    curr_branch = subprocess.run(current_branch_command,capture_output=True,text=True,check=True)
+
+    if not branch_name in curr_branch.stdout:
+        raise ValueError('Make sure you run initial workflow step. If you are running the workflow using the jupyter notebook. Excecute Cell associated with Step 1.')
 
 
     #if any([status in get_review_status(filename_path) for status in ['under review','submitted']]):
@@ -129,9 +164,7 @@ def second_submit_metadata_review(review_yaml_file_path, reviewer_attrs):
 
 
     ##
-    status_command = ['git','status']
+
-    add_command = lambda add_list: ['git','add'] + add_list
-    commit_command = lambda message: ['git','commit','-m', message]
     #push_command = lambda repository,refspec: ['git','push',repository,refspec]
 
     status = subprocess.run(status_command,capture_output=True,check=True)