Completed first version of metadata_review_lib.py. Still need to test and correct possible bugs.

src/metadata_review_lib.py

@@ -2,6 +2,7 @@ import sys
 import os
 root_dir = os.path.abspath(os.curdir)
 sys.path.append(root_dir)
+import subprocess
 
 import h5py
 import yaml
@@ -9,11 +10,14 @@ import shutil
 import src.g5505_utils as utils
 import src.hdf5_vis as hdf5_vis
 import input_files.config_file as config_file
+import src.hidden as hidden
 
 import numpy as np
 
 import pygit2 as pygit
 
+
+
 YAML_EXT = ".yaml"
 TXT_EXT = ".txt"
 
@@ -142,16 +146,44 @@ def second_submit_metadata_review(filename_path, initials):
     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_complete_metadata_review(initials):
+
+    push_command = lambda repository,refspec: ['git','push',repository,refspec]
+    list_branches_command = ['git','branch','--list']
+
+    repository = 'origin'
+    branch_name = 'metadata-review-by-'+initials # refspec
+
+    branches = subprocess.run(list_branches_command,capture_output=True,text=True,check=True)
+    if not branch_name in branches.stdout:
+        print('There is no branch named '+branch_name+'.\n')
+        print('Make sure to run metadata reviewer workflow from the beginning without missing any steps.')
+        return
+
+    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('Complete metadata review could not be completed.\n')
+        print('Make sure a metadata-reviewer workflow has already been started on branch '+branch_name+'\n')
+        print('The step "Complete metadata review" will have no effect.')
+        return
+    
+    result = subprocess.run(push_command(repository,branch_name),capture_output=True,check=True)
+
+    print(result.stdout)
+  
+    return result.returncode
 
 def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
 
     # compare review file with current yalm file and then based on the changes open hdf5 file and access only
     # groups that changed :). the below approach is suboptimal 
 
+    # TODO: only enable update if your branch is data owner :)
+
     if not 'submitted' in get_review_status(input_hdf5_file):
         raise ValueError('Review yaml file must be submitted before trying to perform an update. Run first second_submit_metadata_review().')
 
@@ -217,6 +249,30 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
         # Recreate/or update yaml representation of updated input_hdf5_file.                   
         output_yml_filename_path = hdf5_vis.take_yml_snapshot_of_hdf5_file(input_hdf5_file)
 
+
+    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)
+
+    files_to_add_list = []
+    for line in status.stdout.splitlines():
+        # conver line from bytes to str
+        tmp = line.decode("utf-8")
+        if 'modified' in tmp:
+            if any([ext in tmp for ext in ['.h5','.yaml']] ):
+                files_to_add_list.append(tmp.split()[1])                
+    if files_to_add_list:
+        output = subprocess.run(add_command(files_to_add_list),capture_output=True,check=True)
+        # TODO:verify if files were correctly staged
+        #status = subprocess.run(status_command,capture_output=True,check=True)
+        message = 'Updated hdf5 file with yaml review file.'
+        commit_output = subprocess.run(commit_command(message),capture_output=True,check=True)
+    else:
+        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.")
+
     #with open('review/review_status.txt','r+') as f:
     #    f.write('hdf5 file updated w/ metadata review')           
 
@@ -226,11 +282,36 @@ def third_update_hdf5_file_with_review(input_hdf5_file, yaml_file):
         #    print(exc)
 
 
-def fourth_complete_metadata_review():
+def fourth_complete_metadata_review(initials):
+
+    repository = 'origin'
+    branch_name = 'data-owner-review-by-'+initials
+
+    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)
+    if not branch_name in branches.stdout:
+        print('There is no branch named '+branch_name+'.\n')
+        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)
+    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')
+        print('The step "Complete metadata review" will have no effect.')
+        return
+
+    push_command = lambda repository,refspec: ['git','push',repository,refspec]
+ 
+    # push
+    result = subprocess.run(push_command(repository,branch_name),capture_output=True,text=True,check=True)
+    print(result.stdout)
 
     # 1. git add output_files/
     # 2. delete review/
-    shutil.rmtree(os.path.join(os.path.abspath(os.curdir),"review"))
+    #shutil.rmtree(os.path.join(os.path.abspath(os.curdir),"review"))
     # 3. git rm review/
     # 4. git commit -m "Completed review process. Current state of hdf5 file and yml should be up to date."
     return True