[WIP] Config refactoring

cli/medperf/account_management/account_management.py

@@ -1,15 +1,15 @@
 from .token_storage import TokenStore
-from medperf.config_management import read_config, write_config
-from medperf import config
+from medperf.config_management import config
+from medperf import settings
 from medperf.exceptions import MedperfException
 
 
 def read_user_account():
-    config_p = read_config()
-    if config.credentials_keyword not in config_p.active_profile:
+    config_p = config.read_config()
+    if settings.credentials_keyword not in config_p.active_profile:
         return
 
-    account_info = config_p.active_profile[config.credentials_keyword]
+    account_info = config_p.active_profile[settings.credentials_keyword]
     return account_info
 
 
@@ -23,15 +23,15 @@ def set_credentials(
 ):
     email = id_token_payload["email"]
     TokenStore().set_tokens(email, access_token, refresh_token)
-    config_p = read_config()
+    config_p = config.read_config()
 
     if login_event:
         # Set the time the user logged in, so that we can track the lifetime of
         # the refresh token
         logged_in_at = token_issued_at
     else:
         # This means this is a refresh event. Preserve the logged_in_at timestamp.
-        logged_in_at = config_p.active_profile[config.credentials_keyword][
+        logged_in_at = config_p.active_profile[settings.credentials_keyword][
             "logged_in_at"
         ]
 
@@ -42,8 +42,8 @@ def set_credentials(
         "logged_in_at": logged_in_at,
     }
 
-    config_p.active_profile[config.credentials_keyword] = account_info
-    write_config(config_p)
+    config_p.active_profile[settings.credentials_keyword] = account_info
+    config_p.write_config()
 
 
 def read_credentials():
@@ -61,35 +61,35 @@ def read_credentials():
 
 
 def delete_credentials():
-    config_p = read_config()
-    if config.credentials_keyword not in config_p.active_profile:
+    config_p = config.read_config()
+    if settings.credentials_keyword not in config_p.active_profile:
         raise MedperfException("You are not logged in")
 
-    email = config_p.active_profile[config.credentials_keyword]["email"]
+    email = config_p.active_profile[settings.credentials_keyword]["email"]
     TokenStore().delete_tokens(email)
 
-    config_p.active_profile.pop(config.credentials_keyword)
-    write_config(config_p)
+    config_p.active_profile.pop(settings.credentials_keyword)
+    config_p.write_config()
 
 
 def set_medperf_user_data():
     """Get and cache user data from the MedPerf server"""
-    config_p = read_config()
+    config_p = config.read_config()
     medperf_user = config.comms.get_current_user()
 
-    config_p.active_profile[config.credentials_keyword]["medperf_user"] = medperf_user
-    write_config(config_p)
+    config_p.active_profile[settings.credentials_keyword]["medperf_user"] = medperf_user
+    config_p.write_config()
 
     return medperf_user
 
 
 def get_medperf_user_data():
     """Return cached medperf user data. Get from the server if not found"""
-    config_p = read_config()
-    if config.credentials_keyword not in config_p.active_profile:
+    config_p = config.read_config()
+    if settings.credentials_keyword not in config_p.active_profile:
         raise MedperfException("You are not logged in")
 
-    medperf_user = config_p.active_profile[config.credentials_keyword].get(
+    medperf_user = config_p.active_profile[settings.credentials_keyword].get(
         "medperf_user", None
     )
     if medperf_user is None:

cli/medperf/account_management/token_storage/filesystem.py

@@ -2,12 +2,12 @@
 import base64
 import logging
 from medperf.utils import remove_path
-from medperf import config
+from medperf import settings
 
 
 class FilesystemTokenStore:
     def __init__(self):
-        self.creds_folder = config.creds_folder
+        self.creds_folder = settings.creds_folder
         os.makedirs(self.creds_folder, mode=0o700, exist_ok=True)
 
     def __get_paths(self, account_id):
@@ -19,9 +19,9 @@ def __get_paths(self, account_id):
         account_folder = os.path.join(self.creds_folder, account_id_encoded)
         os.makedirs(account_folder, mode=0o700, exist_ok=True)
 
-        access_token_file = os.path.join(account_folder, config.access_token_storage_id)
+        access_token_file = os.path.join(account_folder, settings.access_token_storage_id)
         refresh_token_file = os.path.join(
-            account_folder, config.refresh_token_storage_id
+            account_folder, settings.refresh_token_storage_id
         )
 
         return access_token_file, refresh_token_file

cli/medperf/account_management/token_storage/keyring_.py

@@ -2,7 +2,7 @@
 users who connect to remote machines through passwordless SSH faced some issues."""
 
 import keyring
-from medperf import config
+from medperf import settings
 
 
 class KeyringTokenStore:
@@ -11,33 +11,33 @@ def __init__(self):
 
     def set_tokens(self, account_id, access_token, refresh_token):
         keyring.set_password(
-            config.access_token_storage_id,
+            settings.access_token_storage_id,
             account_id,
             access_token,
         )
         keyring.set_password(
-            config.refresh_token_storage_id,
+            settings.refresh_token_storage_id,
             account_id,
             refresh_token,
         )
 
     def read_tokens(self, account_id):
         access_token = keyring.get_password(
-            config.access_token_storage_id,
+            settings.access_token_storage_id,
             account_id,
         )
         refresh_token = keyring.get_password(
-            config.refresh_token_storage_id,
+            settings.refresh_token_storage_id,
             account_id,
         )
         return access_token, refresh_token
 
     def delete_tokens(self, account_id):
         keyring.delete_password(
-            config.access_token_storage_id,
+            settings.access_token_storage_id,
             account_id,
         )
         keyring.delete_password(
-            config.refresh_token_storage_id,
+            settings.refresh_token_storage_id,
             account_id,
         )

cli/medperf/cli.py

@@ -4,7 +4,8 @@
 import logging.handlers
 
 from medperf import __version__
-import medperf.config as config
+from medperf import settings
+from medperf.config_management import config
 from medperf.decorators import clean_except, add_inline_parameters
 import medperf.commands.result.result as result
 from medperf.commands.result.create import BenchmarkExecution
@@ -92,10 +93,10 @@ def main(
     # Set inline parameters
     inline_args = ctx.params
     for param in inline_args:
-        setattr(config, param, inline_args[param])
+        setattr(settings, param, inline_args[param])
 
     # Update logging level according to the passed inline params
-    loglevel = config.loglevel.upper()
+    loglevel = settings.loglevel.upper()
     logging.getLogger().setLevel(loglevel)
     logging.getLogger("requests").setLevel(loglevel)
 

cli/medperf/commands/association/approval.py

@@ -1,4 +1,4 @@
-from medperf import config
+from medperf.config_management import config
 from medperf.exceptions import InvalidArgumentError
 
 

cli/medperf/commands/association/association.py

@@ -1,7 +1,7 @@
 import typer
 from typing import Optional
 
-import medperf.config as config
+from medperf.config_management import config
 from medperf.decorators import clean_except
 from medperf.commands.association.list import ListAssociations
 from medperf.commands.association.approval import Approval

cli/medperf/commands/association/list.py

@@ -1,6 +1,6 @@
 from tabulate import tabulate
 
-from medperf import config
+from medperf.config_management import config
 
 
 class ListAssociations:

cli/medperf/commands/association/priority.py

@@ -1,4 +1,4 @@
-from medperf import config
+from medperf.config_management import config
 from medperf.exceptions import InvalidArgumentError
 from medperf.entities.benchmark import Benchmark
 

cli/medperf/commands/auth/auth.py

@@ -3,7 +3,7 @@
 from medperf.commands.auth.logout import Logout
 from medperf.commands.auth.status import Status
 from medperf.decorators import clean_except
-import medperf.config as config
+from medperf.config_management import config
 import typer
 
 app = typer.Typer()

cli/medperf/commands/auth/login.py

@@ -1,4 +1,4 @@
-import medperf.config as config
+from medperf.config_management import config
 from medperf.account_management import read_user_account
 from medperf.exceptions import InvalidArgumentError, MedperfException
 from email_validator import validate_email, EmailNotValidError

cli/medperf/commands/auth/logout.py

@@ -1,4 +1,4 @@
-import medperf.config as config
+from medperf.config_management import config
 
 
 class Logout:

cli/medperf/commands/auth/status.py

@@ -1,4 +1,4 @@
-import medperf.config as config
+from medperf.config_management import config
 from medperf.account_management import read_user_account
 
 

cli/medperf/commands/auth/synapse_login.py

@@ -1,6 +1,6 @@
 import synapseclient
 from synapseclient.core.exceptions import SynapseAuthenticationError
-from medperf import config
+from medperf.config_management import config
 from medperf.exceptions import CommunicationAuthenticationError
 
 

cli/medperf/commands/benchmark/benchmark.py

@@ -1,7 +1,7 @@
 import typer
 from typing import Optional
 
-import medperf.config as config
+from medperf.config_management import config
 from medperf.decorators import clean_except
 from medperf.entities.benchmark import Benchmark
 from medperf.commands.list import EntityList

cli/medperf/commands/benchmark/submit.py

@@ -1,6 +1,7 @@
 import os
 
-import medperf.config as config
+from medperf import settings
+from medperf.config_management import config
 from medperf.entities.benchmark import Benchmark
 from medperf.exceptions import InvalidEntityError
 from medperf.utils import remove_path
@@ -53,7 +54,7 @@ def __init__(
         self.no_cache = no_cache
         self.skip_data_preparation_step = skip_data_preparation_step
         self.bmk.metadata["demo_dataset_already_prepared"] = skip_data_preparation_step
-        config.tmp_paths.append(self.bmk.path)
+        settings.tmp_paths.append(self.bmk.path)
 
     def get_extra_information(self):
         """Retrieves information that must be populated automatically,

cli/medperf/commands/compatibility_test/compatibility_test.py

@@ -1,7 +1,7 @@
 import typer
 from typing import Optional
 
-import medperf.config as config
+from medperf.config_management import config
 from medperf.decorators import clean_except
 from medperf.commands.view import EntityView
 from medperf.entities.report import TestReport

cli/medperf/commands/compatibility_test/utils.py

@@ -5,7 +5,8 @@
 
 from medperf.comms.entity_resources import resources
 from medperf.entities.cube import Cube
-import medperf.config as config
+from medperf import settings
+from medperf.config_management import config
 import os
 import yaml
 from pathlib import Path
@@ -26,7 +27,7 @@ def download_demo_data(dset_url, dset_hash):
 
     # It is assumed that all demo datasets contain a file
     # which specifies the input of the data preparation step
-    paths_file = os.path.join(demo_dset_path, config.demo_dset_paths_file)
+    paths_file = os.path.join(demo_dset_path, settings.demo_dset_paths_file)
     with open(paths_file, "r") as f:
         paths = yaml.safe_load(f)
 
@@ -41,14 +42,14 @@ def download_demo_data(dset_url, dset_hash):
 
 def prepare_local_cube(path):
     temp_uid = get_folders_hash([path])
-    cubes_folder = config.cubes_folder
+    cubes_folder = settings.cubes_folder
     dst = os.path.join(cubes_folder, temp_uid)
     os.symlink(path, dst)
     logging.info(f"local cube will be linked to path: {dst}")
-    config.tmp_paths.append(dst)
-    cube_metadata_file = os.path.join(path, config.cube_metadata_filename)
+    settings.tmp_paths.append(dst)
+    cube_metadata_file = os.path.join(path, settings.cube_metadata_filename)
     if not os.path.exists(cube_metadata_file):
-        mlcube_yaml_path = os.path.join(path, config.cube_filename)
+        mlcube_yaml_path = os.path.join(path, settings.cube_filename)
         mlcube_yaml_hash = get_file_hash(mlcube_yaml_path)
         temp_metadata = {
             "id": None,
@@ -63,7 +64,7 @@ def prepare_local_cube(path):
         metadata = Cube(**temp_metadata).todict()
         with open(cube_metadata_file, "w") as f:
             yaml.dump(metadata, f)
-        config.tmp_paths.append(cube_metadata_file)
+        settings.tmp_paths.append(cube_metadata_file)
 
     return temp_uid
 
@@ -90,7 +91,7 @@ def prepare_cube(cube_uid: str):
     path = path.resolve()
 
     if os.path.exists(path):
-        mlcube_yaml_path = os.path.join(path, config.cube_filename)
+        mlcube_yaml_path = os.path.join(path, settings.cube_filename)
         if os.path.exists(mlcube_yaml_path):
             logging.info("local path provided. Creating symbolic link")
             temp_uid = prepare_local_cube(path)
@@ -137,7 +138,7 @@ def create_test_dataset(
     data_creation.create_dataset_object()
     # TODO: existing dataset could make problems
     # make some changes since this is a test dataset
-    config.tmp_paths.remove(data_creation.dataset.path)
+    settings.tmp_paths.remove(data_creation.dataset.path)
     if skip_data_preparation_step:
         data_creation.make_dataset_prepared()
     dataset = data_creation.dataset

cli/medperf/commands/dataset/associate.py

@@ -1,4 +1,4 @@
-from medperf import config
+from medperf.config_management import config
 from medperf.entities.dataset import Dataset
 from medperf.entities.benchmark import Benchmark
 from medperf.utils import dict_pretty_print, approval_prompt

cli/medperf/commands/dataset/dataset.py

@@ -1,7 +1,7 @@
 import typer
 from typing import Optional
 
-import medperf.config as config
+from medperf.config_management import config
 from medperf.decorators import clean_except
 from medperf.entities.dataset import Dataset
 from medperf.commands.list import EntityList