Remove config options from prompt, fix configure issue.

README.md

@@ -16,13 +16,11 @@ or by cloning the repository and running:
 
 `python setup.py install`
 
-## Set Up
-Run a one-time configuration of your login credentials in the command line using:
+## Authentication
 
-`cirro-cli configure`
-
- This will ask you to select an authentication method. If you are a member of Fred Hutch or the University of Washington, select the default method which will give you a link to use to log through the browser. If you are not a member of those institutions, select the non-institutional authentication method and enter your Data Portal username and password into the command line when prompted.
+Upon first use, the Cirro client will ask if you would like to save your login information and give you a link to authenticate through the web browser.
 
+If you need to change your credentials after this point, and you've opted to save your login, please see the [clearing saved login](#clearing-saved-login) section.
 
 ## Command Line Usage
 
@@ -126,4 +124,9 @@ It will pause for an increasing amount of time for each retry attempt.
 [General]
 base_url = data-portal.io
 transfer_max_retries = 15
-```
+```
+
+### Clearing saved login
+
+You can clear your saved login information by removing the `~/.cirro/token.dat` file from your system or
+by running `cirro-cli configure` and selecting **No** when it asks if you'd like to save your login information.

cirro/api/auth/oauth_client.py

@@ -59,7 +59,7 @@ def _authenticate(client_id: str, auth_endpoint: str):
     auth_status = 'authorization_pending'
     while auth_status == 'authorization_pending':
         time.sleep(flow['interval'])
-        if device_expiry < datetime.now():
+        if device_expiry < datetime.now().astimezone():
             raise RuntimeError('Authentication timed out')
 
         resp = requests.post(f'{auth_endpoint}/token', params=params)

cirro/api/config.py

@@ -31,6 +31,7 @@ def save_user_config(user_config: UserConfig):
     }
     if original_user_config:
         ini_config['General']['base_url'] = original_user_config.base_url
+        ini_config['General']['transfer_max_retries'] = str(original_user_config.transfer_max_retries)
 
     ini_config[user_config.auth_method] = user_config.auth_method_config
     Constants.config_path.parent.mkdir(exist_ok=True)
@@ -72,6 +73,8 @@ def __init__(self, base_url: str = None):
                          os.environ.get('PW_BASE_URL') or
                          (self.user_config.base_url if self.user_config else None) or
                          Constants.default_base_url)
+        self.transfer_max_retries = self.user_config.transfer_max_retries\
+            if self.user_config else Constants.default_max_retries
         self._init_config()
 
     def _init_config(self):

cirro/api/services/file.py

@@ -55,7 +55,7 @@ def upload_files(self, access_context: FileAccessContext, directory: str, files:
         """
         s3_client = S3Client(partial(self.get_access_credentials, access_context), self._configuration.region)
         upload_directory(directory, files, s3_client, access_context.bucket, access_context.path_prefix,
-                         max_retries=self._configuration.user_config.transfer_max_retries)
+                         max_retries=self._configuration.transfer_max_retries)
 
     def download_files(self, access_context: FileAccessContext, directory: str, files: List[str]):
         """

cirro/cli/controller.py

@@ -1,5 +1,5 @@
 from cirro.api.clients.portal import DataPortalClient
-from cirro.api.config import UserConfig, save_user_config
+from cirro.api.config import UserConfig, save_user_config, load_user_config
 from cirro.api.models.dataset import CreateIngestDatasetInput
 from cirro.api.models.process import Executor
 from cirro.cli.interactive.auth_args import gather_auth_config
@@ -19,8 +19,7 @@
 
 def run_list_datasets(input_params: ListArguments, interactive=False):
     """List the datasets available in a particular project."""
-
-    # Instantiate the Cirro Data Portal client
+    _check_configure()
     cirro = DataPortalClient()
 
     # If the user provided the --interactive flag
@@ -47,6 +46,7 @@ def run_list_datasets(input_params: ListArguments, interactive=False):
 
 
 def run_ingest(input_params: UploadArguments, interactive=False):
+    _check_configure()
     cirro = DataPortalClient()
     projects = cirro.project.list()
     processes = cirro.process.list(process_type=Executor.INGEST)
@@ -83,6 +83,7 @@ def run_ingest(input_params: UploadArguments, interactive=False):
 
 
 def run_download(input_params: DownloadArguments, interactive=False):
+    _check_configure()
     cirro = DataPortalClient()
 
     projects = cirro.project.list()
@@ -114,7 +115,7 @@ def run_download(input_params: DownloadArguments, interactive=False):
 
 def run_configure_workflow():
     """Configure a workflow to be run in the Data Portal as a process."""
-
+    _check_configure()
     cirro = DataPortalClient()
     process_options = cirro.process.list(process_type=Executor.NEXTFLOW)
     resources_folder, repo_prefix = get_output_resources_path()
@@ -171,4 +172,15 @@ def run_configure():
     auth_method, auth_method_config = gather_auth_config()
     save_user_config(UserConfig(auth_method=auth_method,
                                 auth_method_config=auth_method_config,
-                                base_url=None))
+                                base_url=None,
+                                transfer_max_retries=None))
+
+
+def _check_configure():
+    """
+    Prompts the user to do initial configuration if needed
+    """
+    if load_user_config() is not None:
+        return
+
+    run_configure()

cirro/cli/interactive/auth_args.py

@@ -1,35 +1,11 @@
 from typing import Tuple, Dict
 
-from cirro.api.auth import ClientAuth, UsernameAndPasswordAuth, IAMAuth
-from cirro.cli.interactive.utils import ask, ask_yes_no
+from cirro.cli.interactive.utils import ask_yes_no
 
 
 def gather_auth_config() -> Tuple[str, Dict]:
-    auth_methods_map = {
-        'Default authentication (recommended)': ClientAuth,
-        'Username/password authentication (non-institutional)': UsernameAndPasswordAuth,
-        'AWS IAM Credentials': IAMAuth
+    auth_method_config = {
+        'enable_cache': ask_yes_no("Would you like to save your login? (do not use this on shared devices)")
     }
 
-    auth_method_answer = ask('select', 'Please select and authentication method',
-                             choices=auth_methods_map.keys())
-
-    auth_method = auth_methods_map[auth_method_answer]
-    auth_method_config = {}
-
-    if auth_method == UsernameAndPasswordAuth:
-        auth_method_config['username'] = ask('text', 'Please enter your username', required=True)
-        auth_method_config['password'] = ask('password', 'Please enter your password', required=True)
-
-    if auth_method == ClientAuth:
-        auth_method_config['enable_cache'] = ask_yes_no("Would you like to cache your login?")
-
-    if auth_method == IAMAuth:
-        if ask_yes_no("Would you like to manually specify AWS credentials?"):
-            auth_method_config['access_key'] = ask('text', 'Please enter your access key ID', required=True)
-            auth_method_config['secret_key'] = ask('text', 'Please enter your secret access key', required=True)
-            auth_method_config['token'] = ask('text', 'Please enter your session token (optional)')
-        else:
-            auth_method_config['load_current'] = True
-
-    return auth_method.__name__, auth_method_config
+    return 'ClientAuth', auth_method_config

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cirro"
-version = "0.6.10"
+version = "0.6.11"
 description = "CLI tool and SDK for interacting with the Cirro platform"
 authors = ["Fred Hutch <[email protected]>"]
 license = "MIT"