Implemented git add and commit for second metadata review step, and create it function to checkout branches.

src/metadata_review_lib.py

@@ -8,6 +8,7 @@ import yaml
 import shutil
 import src.g5505_utils as utils
 import src.hdf5_vis as hdf5_vis
+import input_files.config_file as config_file
 
 import numpy as np
 
@@ -30,6 +31,16 @@ def get_review_status(filename_path):
             workflow_steps.append(line)
     return workflow_steps[-1]
 
+def checkout_review_branch(repo_obj,initials):    
+    # 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:
+        branch = repo_obj.create_branch(branch_name, head_commit)
+    else:
+        branch = repo_obj.branches[branch_name]    
+    repo_obj.checkout(branch)
 
 def first_initialize_metadata_review(filename_path,initials):
 
@@ -54,39 +65,41 @@ def first_initialize_metadata_review(filename_path,initials):
 
     # Initialize metadata review workflow
     print("Create branch metadata-review-by-"+initials+"\n")
-
+    
+    # Check if review file already exists and then check if it is still untracked
     if not os.path.exists(os.path.join("review/",filename+YAML_EXT)):
         review_filename_path = utils.make_file_copy(os.path.join(filename_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_filename_path = os.path.join("review/",filename+YAML_EXT)
+    #else:
+    #    raise Warning("the file " + os.path.join("review/",filename+YAML_EXT)+ " already exists. Delete this file to reinitialize the metadata review process.")
+
 
     review_filename_tail, ext = os.path.splitext(review_filename_path)
 
     with open(os.path.join(review_filename_tail+"-review_status"+".txt"),'w') as f:
         f.write('under review')  
 
-
-    # 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:
-        new_branch = repo_obj.create_branch(branch_name, head_commit)
-    repo_obj.checkout(new_branch)
+    checkout_review_branch(repo_obj,initials)
 
     status_dict = repo_obj.status()
-    for key in status_dict:
+    for filepath, file_status in status_dict.items():
         # Identify keys associated to review files and stage them
-        if 'review/'+filename in key:
+        if 'review/'+filename in filepath:
             # Stage changes
-            repo_obj.index.add(key)
-    repo_obj.create_commit(message="Initialized metadata review process.")
+            repo_obj.index.add(filepath)
+
+    author = config_file.author #default_signature
+    committer = config_file.committer
+    message = "Initialized metadata review process."
+    tree = repo_obj.index.write_tree()
+    oid = repo_obj.create_commit('HEAD', author, committer, message, tree, [repo_obj.head.peel().oid])
 
     #print("Add and commit"+"\n") 
 
     
         
-def second_submit_metadata_review(filename_path):
+def second_submit_metadata_review(filename_path, initials):
     """
     Once you're done reviewing the yaml representation of hdf5 file in review folder. 
     Change the review status to complete and save (add and commit) modified .yalm and .txt files in the project by
@@ -103,8 +116,36 @@ def second_submit_metadata_review(filename_path):
         filename, ext = os.path.splitext(filename_path_head)
         # TODO:    
         with open(os.path.join("review/",filename+"-review_status"+TXT_EXT),'a') as f:
-            f.write('\nsubmitted')        
-    #return True
+            f.write('\nsubmitted')
+
+    # 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:
+        branch = repo_obj.create_branch(branch_name, head_commit)
+    else:
+        branch = repo_obj.branches[branch_name]
+
+    repo_obj.checkout(branch)
+
+    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) and (file_status == pygit.GIT_STATUS_WT_MODIFIED):
+            # Stage changes
+            repo_obj.index.add(filepath)
+
+    author = config_file.author #default_signature
+    committer = config_file.committer
+    message = "Submitted metadata review."
+    tree = repo_obj.index.write_tree()
+    oid = repo_obj.create_commit('HEAD', author, committer, message, tree, [repo_obj.head.peel().oid])
+
+            
+def third_complete_metadata_review():
+
+    return
 
 def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):