added support for initialising from a remote repository

acmc.py

@@ -26,7 +26,7 @@ def omop_delete(args):
 
 def phen_init(args):
 	"""Handle the `phen init` command."""  
-	phen.init(args.phen_dir)
+	phen.init(args.phen_dir, args.remote_url)
 
 def phen_validate(args):
 	"""Handle the `phen validate` command."""  
@@ -99,6 +99,7 @@ def main():
 	# phen init
 	phen_init_parser = phen_subparsers.add_parser("init", help="Initiatise phenotype directory")
 	phen_init_parser.add_argument("-d", "--phen-dir", type=str, default=str(phen.DEFAULT_PHEN_PATH.resolve()), help="Phenotype directory")
+	phen_init_parser.add_argument("-r", "--remote_url", help="URL to remote git repository")	
 	phen_init_parser.set_defaults(func=phen_init)
 
 	# phen validate
@@ -109,7 +110,7 @@ def main():
 	# phen map
 	phen_map_parser = phen_subparsers.add_parser("map", help="Process phen mapping")
 	phen_map_parser.add_argument("-d", "--phen-dir", type=str, default=str(phen.DEFAULT_PHEN_PATH.resolve()), help="Phenotype directory")
-	phen_map_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
+	phen_map_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2_code, read3_code, icd10_code, snomed_code, opcs4_code)")
 	# phen map flags
 	phen_map_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Translate code types")
 	phen_map_parser.add_argument("-v", "--verify", action="store_true", default=False, help="Verify codes")

phen.py

@@ -8,6 +8,7 @@ import sys
 import shutil
 import git
 import re
+import requests
 from pathlib import Path
 
 import trud
@@ -29,7 +30,8 @@ from omop import setup
 
 pd.set_option("mode.chained_assignment", None)
 
-DEFAULT_PHEN_PATH = Path('build') / 'phen'
+PHEN_DIR = 'phen'
+DEFAULT_PHEN_PATH = Path('build') / PHEN_DIR
 CODES_DIR = 'codes'
 OUTPUT_DIR = 'output'
 CONFIG_FILE = 'config.json'
@@ -47,7 +49,7 @@ class PhenValidationException(Exception):
 		super().__init__(message)
 		self.validation_errors = validation_errors
 
-def init(phen_dir):
+def init(phen_dir, remote_url):
 	"""Initial phenotype directory as git repo with standard structure"""	
 	print(f"Initialising Phenotype in directory: {phen_dir}")
 	phen_path = Path(phen_dir)
@@ -55,7 +57,7 @@ def init(phen_dir):
 	# check if directory already exists and ask user if they want to recreate it
 	configure = False
 	if phen_path.exists() and phen_path.is_dir():  # Check if it exists and is a directory
-		user_input = input(f"The phen directory '{phen_path}' already exists. Do you want to reinitialise, deleting all current configuration? (yes/no): ").strip().lower()
+		user_input = input(f"The phen directory '{phen_path}' already exists. Do you want to reinitialise? (yes/no): ").strip().lower()
 		if user_input in ['yes', 'y']:
 			shutil.rmtree(phen_path)  
 			configure = True;
@@ -66,9 +68,27 @@ def init(phen_dir):
 
 	# configure the phen directories 
 	if configure:
-		# create root phen directory
+		repo = None
+		# remote then clone the repo
+		if remote_url != None:
+			try:
+				repo = git.cmd.Git()
+				repo.clone(remote_url, phen_path)	
+				repo = git.Repo(phen_path)
+			except Exception:
+				raise Exception(f"Error: remote_url for the repo {remote_url} ")
+		else:
+			# local then create the directories and init
 			phen_path.mkdir(parents=True, exist_ok=True) 
 			print(f"Phen directory '{phen_path}' has been created.")
+			repo = git.Repo.init(phen_path)
+			#repo.create_tag(initial_version, message=f"Release {initial_version}")		
+			
+
+		# check if the phen path has already been configured which would be the case for remote clones
+		config_path = phen_path / CONFIG_FILE
+		if not config_path.exists():
+			print("Creating configuration files")	
 			# create codes directory
 			codes_path = phen_path / CODES_DIR
 			codes_path.mkdir(exist_ok=True)
@@ -101,15 +121,14 @@ def init(phen_dir):
 				json.dump(config, f, indent=4) 
 				
 			# initialise phen directory as a git repo includ .gitkeep to keep the codes dir
-		repo = git.Repo.init(phen_path)
 			repo.git.add(codes_path)
 			repo.git.add(output_path)				
 			repo.git.add(all=True)
 			msg = "Initialized phen git repo."				
 			repo.index.commit(msg)
-		repo.create_tag(initial_version, message=f"Release {initial_version}")		
 			print(msg)
-		
+		else:
+			print(f"Phenotype configuration files already exist")
 		print(f"Phenotype initialised")
 	else:
 		print(f"Phenotype not initiatised")
@@ -520,6 +539,15 @@ def publish(phen_dir):
 	repo.create_tag(version, message=f"Release {version}")
 	print(f"Created tag: {version}")
 
+	# push to origin if a remote repo
+	try:
+		origin = repo.remotes.origin
+		print(f"Remote 'origin' exists: {origin.url}")
+		origin.push(tags=True)
+		print("Changes pushed to 'origin'.")
+	except AttributeError:
+		print("No remote named 'origin' found, local repo.")
+
 def copy(phen_dir, target_dir, version=None):
 	"""Copys a phen repo at a specific tagged version into a target directory"""