Add option to prevent param log and fix issue where token encryption isn't available (#55)

* add option to skip logging of param

* add fallback to plaintext token cache

* import on use

* change email

Author: nathanthorpe

README.md

@@ -109,10 +109,10 @@ See the following set of Jupyter notebooks that contain examples on the followin
 
 ### Supported environment variables
 
-| Name        | Description                   | Default        |
-|-------------|-------------------------------|----------------|
-| PW_HOME     | Local configuration directory | ~/.cirro      |
-| PW_BASE_URL | Base URL of the data portal   | data-portal.io |
+| Name        | Description                   | Default         |
+|-------------|-------------------------------|-----------------|
+| PW_HOME     | Local configuration directory | ~/.cirro        |
+| PW_BASE_URL | Base URL of the data portal   | data-portal.io  |
 
 ### Configuration
 

cirro/api/auth/oauth_client.py

@@ -11,8 +11,7 @@
 import jwt
 import requests
 from botocore.exceptions import ClientError
-from msal_extensions import FilePersistence, FilePersistenceWithDataProtection, \
-    KeychainPersistence, LibsecretPersistence
+from msal_extensions import FilePersistence
 from requests.auth import AuthBase
 
 from cirro.api.auth.base import AuthInfo, RequestAuthWrapper
@@ -26,16 +25,19 @@
 def _build_token_persistence(location, fallback_to_plaintext=False):
     try:
         if sys.platform.startswith('win'):
+            from msal_extensions import FilePersistenceWithDataProtection
             return FilePersistenceWithDataProtection(location)
         if sys.platform.startswith('darwin'):
+            from msal_extensions import KeychainPersistence
             return KeychainPersistence(location, service_name='cirro-client')
         if sys.platform.startswith('linux'):
+            from msal_extensions import LibsecretPersistence
             return LibsecretPersistence(location)
         raise RuntimeError(f"Unsupported platform: {sys.platform}")
     except Exception:
         if not fallback_to_plaintext:
             raise
-        logger.warning("Encryption unavailable. Opting in to plain text.")
+        logger.debug("Encryption unavailable. Opting in to plain text.")
         return FilePersistence(location)
 
 
@@ -87,7 +89,7 @@ def __init__(self, client_id: str, region: str, auth_endpoint: str, enable_cache
         self._persistence = None
 
         if enable_cache:
-            self._persistence = _build_token_persistence(str(TOKEN_PATH), fallback_to_plaintext=False)
+            self._persistence = _build_token_persistence(str(TOKEN_PATH), fallback_to_plaintext=True)
             self._token_info = self._load_token_info()
 
         if not self._token_info:

cirro/helpers/preprocess_dataset.py

@@ -89,16 +89,18 @@ def _write_json(self, dat, local_path: str, indent=4):
         with Path(local_path).open(mode="wt") as handle:
             return json.dump(dat, handle, indent=indent)
 
-    def add_param(self, name: str, value, overwrite=False):
+    def add_param(self, name: str, value, overwrite=False, log=True):
         """Add a parameter to the dataset."""
 
         assert overwrite or name not in self.params, \
             f"Cannot add parameter {name}, already exists (and overwrite=False)"
 
-        self.logger.info(f"Adding parameter {name} = {value}")
+        if log:
+            self.logger.info(f"Adding parameter {name} = {value}")
         self.params[name] = value
 
-        self.logger.info("Saving parameters")
+        if log:
+            self.logger.info("Saving parameters")
         self._write_json(self.params, "nextflow.json")
 
     def remove_param(self, name: str, force=False):
@@ -126,11 +128,11 @@ def update_compute(self, from_str, to_str, fp="nextflow-override.config"):
             handle.write(compute)
 
     def wide_samplesheet(
-        self,
-        index=["sampleIndex", "sample", "lane"],
-        columns="read",
-        values="file",
-        column_prefix="fastq_"
+            self,
+            index=["sampleIndex", "sample", "lane"],
+            columns="read",
+            values="file",
+            column_prefix="fastq_"
     ):
         """Format a wide samplesheet with each read-pair on a row."""
 

setup.py

@@ -32,10 +32,10 @@
 
 setup(
     name='cirro',
-    version='0.6.1',
+    version='0.6.2',
     author='Fred Hutch',
     license='MIT',
-    author_email='hutchdatacore@fredhutch.org',
+    author_email='cirro@fredhutch.org',
     description='CLI tool for interacting with the Cirro platform',
     packages=find_packages(include=['cirro*']),
     install_requires=install_requires,