diff --git a/acmc.py b/acmc.py
index 22aed7441057f3cd9649aaa6e9b35715345ce9f6..6ecf0358c7d5d5c427ffa022057c17b1aec434af 100644
--- a/acmc.py
+++ b/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")
diff --git a/phen.py b/phen.py
index 9fa324f2ef1ea39d6f5459d2297e84aebb204742..216a73aa7941c53f71cc1a259d199cfd7cb95288 100644
--- a/phen.py
+++ b/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'
@@ -47,15 +49,15 @@ 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)
-
+
# 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;
@@ -66,50 +68,67 @@ def init(phen_dir):
# configure the phen directories
if configure:
- # create root phen directory
- phen_path.mkdir(parents=True, exist_ok=True)
- print(f"Phen directory '{phen_path}' has been created.")
- # create codes directory
- codes_path = phen_path / CODES_DIR
- codes_path.mkdir(exist_ok=True)
- keep_path = codes_path / '.gitkeep'
- keep_path.touch(exist_ok=True)
- # create maps directory
- output_path = phen_path / OUTPUT_DIR
- output_path.mkdir(exist_ok=True)
- keep_path = output_path / '.gitkeep'
- keep_path.touch(exist_ok=True)
- # create empty config file
- initial_version = "v1.0.1"
- config = {
- "concept_sets": {
- "version": initial_version,
- "omop": {
- "vocabulary_id": "",
- "vocabulary_name": "",
- "vocabulary_reference": ""
+ 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)
+ keep_path = codes_path / '.gitkeep'
+ keep_path.touch(exist_ok=True)
+ # create maps directory
+ output_path = phen_path / OUTPUT_DIR
+ output_path.mkdir(exist_ok=True)
+ keep_path = output_path / '.gitkeep'
+ keep_path.touch(exist_ok=True)
+ # create empty config file
+ initial_version = "v1.0.1"
+ config = {
+ "concept_sets": {
+ "version": initial_version,
+ "omop": {
+ "vocabulary_id": "",
+ "vocabulary_name": "",
+ "vocabulary_reference": ""
+ },
+ "concept_set": [
+ ]
},
- "concept_set": [
+ "codes": [
]
- },
- "codes": [
- ]
- }
- config_path = phen_path / CONFIG_FILE
- # Write the JSON data to a file
- with open(config_path, "w", encoding="utf-8") as f:
- 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)
-
+ }
+ config_path = phen_path / CONFIG_FILE
+ # Write the JSON data to a file
+ with open(config_path, "w", encoding="utf-8") as f:
+ json.dump(config, f, indent=4)
+
+ # initialise phen directory as a git repo includ .gitkeep to keep the codes dir
+ repo.git.add(codes_path)
+ repo.git.add(output_path)
+ repo.git.add(all=True)
+ msg = "Initialized phen git repo."
+ repo.index.commit(msg)
+ 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"""