Modified some mongo dict defaults

docker/docker-compose.yml

@@ -14,6 +14,8 @@ services:
             - driver: nvidia
               count: 1
               capabilities: [gpu]
+    volumes:
+      - ..:/workdir:cached
     depends_on:
       - mongodb
     networks:

src/storable/decorator.py

@@ -1,3 +1,4 @@
+import os
 from pymongo import MongoClient
 from typing import Any, Dict, Tuple, List
 from functools import wraps
@@ -202,7 +203,7 @@ def print_db(self):
                 print(f'{key}: {value}')
         print("===== End Printing =====")
 
-    def db_exists(self, _db_name, host='localhost', port=27017):
+    def db_exists(self, _db_name, host=os.getenv("MONGODB_HOST"), port=None):
         _db_name = MongoDict._sanitize_db_name(_db_name)
         client = MongoClient(host, port)
         try:
@@ -212,7 +213,7 @@ def db_exists(self, _db_name, host='localhost', port=27017):
         finally:
             client.close()
 
-    def delete_db(self, _db_name, host='localhost', port=27017):
+    def delete_db(self, _db_name, host=os.getenv("MONGODB_HOST"), port=None):
         # Delete the specified database
         _db_name = MongoDict._sanitize_db_name(_db_name)
         client = MongoClient(host, port)

tests/conftest.py

@@ -8,6 +8,7 @@
 import datasets
 import ray
 import os
+from pathlib import Path
 from tests.tsettings import *
 from typing import Dict
 from utils.IO import *
@@ -25,9 +26,15 @@ def pytest_configure(config) -> None:
     os.environ["DEBUG"] = "0"
 
     if SEMITEMP_DIR.is_dir() and not config.getoption("--no-cleanup"):
-        shutil.rmtree(str(SEMITEMP_DIR))
+        for item in SEMITEMP_DIR.iterdir():
+            if item.name != '.gitignore':
+                if item.is_file():
+                    item.unlink()
+                elif item.is_dir():
+                    shutil.rmtree(str(item))
 
     for task_name in TASK_NAMES:
+        print(Path.cwd())
         tests_io(f"Loading preproceesing data for task {task_name}...", end="\r")
         datasets.load_data(chunksize=75835,
                            source_path=TEST_DATA_DEMO,
@@ -152,4 +159,9 @@ def discretizer_listfiles() -> None:
 def pytest_unconfigure(config) -> None:
     os.environ["DEBUG"] = "0"
     if SEMITEMP_DIR.is_dir() and not config.getoption("--no-cleanup"):
-        shutil.rmtree(str(SEMITEMP_DIR))
+        for item in SEMITEMP_DIR.iterdir():
+            if item.name != '.gitignore':
+                if item.is_file():
+                    item.unlink()
+                elif item.is_dir():
+                    shutil.rmtree(str(item))

tests/test_datasets/test_trackers/test_mongo_dict.py

@@ -260,7 +260,7 @@ def test_db_name_handling():
     tests_io("Starting test_db_sanitization_and_collection_handling", level=0)
 
     # Test with a long path
-    db_path = Path(TEMP_DIR, "workspaces/pymimic3/tests/data/semitemp/processed/DECOMP_progress")
+    db_path = Path(TEMP_DIR, "workdir/tests/data/semitemp/processed/DECOMP_progress")
     db = MongoDict(db_path)
     assert db._db_name == 'db_paces_pymimic3_tests_data_semitemp_processed_DECOMP_progress'