aplos-nca-saas-sdk 0.0.16__tar.gz → 0.0.17__tar.gz

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aplos_nca_saas_sdk
-Version: 0.0.16
+Version: 0.0.17
 Summary: Aplos NCA SaaS SDK
 Project-URL: Homepage, https://aplosanalytics.com/
 Project-URL: Documentation, https://docs.aplosanalytics.com/

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/pyproject.toml

@@ -26,7 +26,7 @@ keywords = [
     "Clinical Trials"
 ]
 
-version = "0.0.16"
+version = "0.0.17"
 authors = [
   { name="Eric Wilson", email="eric.wilson@aplosanalytics.com" }
 ]

aplos_nca_saas_sdk-0.0.17/requirements.dev.txt

@@ -0,0 +1 @@
+mypy

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/configs/login_config.py

@@ -17,13 +17,13 @@ class LoginConfig(ConfigBase):
     def __init__(
         self,
         username: Optional[str] = None,
-        passord: Optional[str] = None,
+        password: Optional[str] = None,
         host: Optional[str] = None,
         roles: Optional[List[str]] = None,
     ):
         super().__init__()
         self.__username: Optional[str] = username
-        self.__password: Optional[str] = passord
+        self.__password: Optional[str] = password
         self.__host: Optional[str] = host
         self.__roles: List[str] = roles if roles is not None else []
 
@@ -110,7 +110,7 @@ class LoginConfigs(ConfigBase):
 
     @staticmethod
     def try_load_login(login_config: Dict[str, Any]) -> LoginConfig | None:
-        """Attempts to intialize a Login from a configuration object"""
+        """Attempts to initialize a Login from a configuration object"""
         login: LoginConfig | None = None
         if login_config is not None:
             username = login_config.get("username", None)

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/configs/nca_execution_config.py

@@ -34,6 +34,9 @@ class NCAExecutionConfig(ConfigBase):
         meta_data: str | dict | None = None,
         output_dir: str | None = None,
         unzip_after_download: bool = False,
+        data_processing: str | dict | None = None,
+        post_processing: str | dict | None = None,
+        full_payload: str | dict | None = None,
     ):
         super().__init__()
 
@@ -52,6 +55,9 @@ class NCAExecutionConfig(ConfigBase):
         self.__meta_data = meta_data
         self.__output_dir = output_dir
         self.__unzip_after_download = unzip_after_download
+        self.__data_processing = data_processing
+        self.__post_processing = post_processing
+        self.__full_payload = full_payload
 
     @property
     def login(self) -> LoginConfig:
@@ -83,6 +89,20 @@ class NCAExecutionConfig(ConfigBase):
         """Indicates if the download should be unzipped"""
         return self.__unzip_after_download
 
+    @property
+    def data_processing(self) -> str | Dict[str, Any] | None:
+        """Pre Processing"""
+        return self.__data_processing
+    
+    @property
+    def post_processing(self) -> str | Dict[str, Any] | None:
+        """Post Processing"""
+        return self.__post_processing
+    
+    @property
+    def full_payload(self) -> str | Dict[str, Any] | None:
+        """Full Payload"""
+        return self.__full_payload
 
 class NCAExecutionConfigs(ConfigBase):
     """
@@ -106,21 +126,27 @@ class NCAExecutionConfigs(ConfigBase):
         input_file_path: str,
         config_data: dict,
         meta_data: str | dict | None = None,
+        data_processing: str | dict | None = None,
+        post_processing: str | dict | None = None,
         output_dir: str | None = None,
         unzip_after_download: bool = False,
         enabled: bool = True,
+        full_payload: str | dict | None = None,
     ):
         """Add an NCA Execution Config"""
-        nca_excution_config = NCAExecutionConfig(
+        nca_execution_config = NCAExecutionConfig(
             login,
             input_file_path,
             config_data,
             meta_data,
             output_dir,
             unzip_after_download,
+            data_processing,
+            post_processing,
+            full_payload,
         )
-        nca_excution_config.enabled = enabled
-        self.__nca_executions.append(nca_excution_config)
+        nca_execution_config.enabled = enabled
+        self.__nca_executions.append(nca_execution_config)
 
     def load(self, test_config: Dict[str, Any]):
         """Loads the NCA Execution configs from a list of dictionaries"""
@@ -150,41 +176,55 @@ class NCAExecutionConfigs(ConfigBase):
             if not login:
                 raise RuntimeError("Failed to load the login configuration")
 
+
+            full_payload = self.__load_dictionary_data_or_file(key="payload", analysis=analysis, optional=True)
+            config_data = self.__load_dictionary_data_or_file(key="config", analysis=analysis, optional=True)
+
+            if not config_data and not full_payload:
+                raise RuntimeError("Failed to load the config data")
+
+            meta_data = self.__load_dictionary_data_or_file(key="meta", analysis=analysis, optional=True)
+            data_cleaning = self.__load_dictionary_data_or_file(key="data_cleaning", analysis=analysis, optional=True)
+            post_processing = self.__load_dictionary_data_or_file(key="post_processing", analysis=analysis, optional=True) 
+
             self.add(
                 login=login,
                 input_file_path=analysis["file"],
-                config_data=self.__load_config_data(analysis=analysis),
-                meta_data=self.__load_meta_data(analysis=analysis),
+                config_data=config_data,
+                meta_data=meta_data,
                 output_dir=output_dir,
                 unzip_after_download=True,
                 enabled=enabled,
+                full_payload=full_payload,
+                data_processing=data_cleaning,
+                post_processing=post_processing
             )
 
-    def __load_meta_data(self, analysis: Dict[str, Any]) -> Dict[str, Any]:
-        data: Dict[str, Any] = {}
-        data = analysis.get("meta", {}).get("data", {})
-
-        return data
 
-    def __load_config_data(self, analysis: Dict[str, Any]) -> Dict[str, Any]:
-        config_data: Dict[str, Any] = {}
-        config_data = analysis.get("config", {}).get("data")
+    def __load_dictionary_data_or_file(self, key: str, analysis: Dict[str, Any], optional: bool = False ) -> Dict[str, Any] | None:
+        data: Dict[str, Any] = {}
+        data = analysis.get(key, {}).get("data", {})
 
-        if config_data:
-            return config_data
+        if data:
+            return data
 
-        config_file_path: str = analysis.get("config", {}).get("file")
+        file_path: str = analysis.get(key, {}).get("file")
 
         logger.info(
             {
-                "message": "Initializing config_data from file",
-                "config_data": config_file_path,
+                "message": f"Initializing {key} from file",
+                "key": key,
+                "file_path": file_path,
             }
         )
-        config_path = FileUtility.load_filepath(config_file_path)
-        if os.path.exists(config_path) is False:
-            raise RuntimeError(f"Config file not found: {config_path}")
-        with open(config_path, "r", encoding="utf-8") as f:
-            config_data = json.load(f)
+        path = FileUtility.load_filepath(file_path)
+        if os.path.exists(path) is False:
+            if optional:
+                return None
+            raise RuntimeError(f"Data for {key} not found: {path}")
+        with open(path, "r", encoding="utf-8") as f:
+            data = json.load(f)
+
+        return data
 
-        return config_data
+    

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/example_main.py

@@ -18,8 +18,8 @@ from aplos_nca_saas_sdk.integration_testing.integration_test_configurations impo
 def main():
     """This is an example on how you can run the unit tests"""
 
-    # Optionally use our convient Environment Services loader
-    # which can help during intial testings.
+    # Optionally use our convenient Environment Services loader
+    # which can help during initial testings.
     evs: EnvironmentServices = EnvironmentServices()
     # see if we have a local .env, .env.uat, etc configured to look up
     env_file = os.getenv("ENV_FILE")

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/readme.md

@@ -12,7 +12,7 @@ The integration tests will require the following:
 ### Users
 You will need valid user accounts with the appropriate permissions for the endpoints they are executing.
 
-If you are testing permission bounderies then you should set up multiple users with different permissions.
+If you are testing permission boundaries then you should set up multiple users with different permissions.
 
 
 ### Subscriptions
@@ -44,8 +44,8 @@ from aplos_nca_saas_sdk.integration_testing.integration_test_configurations impo
 def main():
     """This is an example on how you can run the unit tests"""
 
-    # Optionally use our convient Environment Services loader
-    # which can help during intial testings.
+    # Optionally use our convenient Environment Services loader
+    # which can help during initial testings.
     evs: EnvironmentServices = EnvironmentServices()
     # See if we have a local .env, .env.uat, etc configured to look up
     # for local configuration settings
@@ -83,7 +83,7 @@ def main():
 ### Configs
 Tests are run based on configurations.  The following is an example of supported configurations:
 
-- Appliction Configuration Settings
+- Application Configuration Settings
 - Logins & Access
 - Executing an Analysis
 - Running a Validation

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/tests/file_upload_test.py

@@ -5,11 +5,13 @@ Property of Aplos Analytics, Utah, USA
 """
 
 import time
-from datetime import datetime, timedelta
-from typing import Any, Dict, List
+from typing import Any, Dict
 
-import requests
 from aws_lambda_powertools import Logger
+
+from aplos_nca_saas_sdk.integration_testing.configs.file_upload_config import (
+    FileUploadConfig,
+)
 from aplos_nca_saas_sdk.integration_testing.configs.login_config import LoginConfig
 from aplos_nca_saas_sdk.integration_testing.integration_test_base import (
     IntegrationTestBase,
@@ -17,13 +19,9 @@ from aplos_nca_saas_sdk.integration_testing.integration_test_base import (
 from aplos_nca_saas_sdk.integration_testing.integration_test_response import (
     IntegrationTestResponse,
 )
-from aplos_nca_saas_sdk.nca_resources.nca_file_upload import NCAFileUpload
-from aplos_nca_saas_sdk.nca_resources.nca_file_download import NCAFileDownload
 from aplos_nca_saas_sdk.nca_resources.nca_authenticator import NCAAuthenticator
-from aplos_nca_saas_sdk.utilities.http_utility import HttpUtilities
-from aplos_nca_saas_sdk.integration_testing.configs.file_upload_config import (
-    FileUploadConfig,
-)
+from aplos_nca_saas_sdk.nca_resources.nca_file_download import NCAFileDownload
+from aplos_nca_saas_sdk.nca_resources.nca_file_upload import NCAFileUpload
 
 logger = Logger()
 
@@ -46,9 +44,7 @@ class FileUploadTest(IntegrationTestBase):
             try:
                 # Confirm Login
                 nca_login = self.__login(file_upload.login)
-                # if not nca_login.cognito.jwt:
-                #     test_response.error = "Failed to authenticate"
-                # else:
+
                 # Confirm Upload
                 upload_response: Dict[str, Any] = self.__upload(
                     nca_login, file_upload.file_path

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/integration_testing/tests/nca_analysis_test.py

@@ -66,6 +66,9 @@ class NCAAnalysisTest(IntegrationTestBase):
                     wait_for_results=True,
                     output_directory=nca_execution_config.output_dir,
                     unzip_after_download=False,
+                    data_processing=nca_execution_config.data_processing,
+                    post_processing=nca_execution_config.post_processing,
+                    full_payload=nca_execution_config.full_payload,
                 )
 
                 # Verify Download

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/nca_resources/nca_analysis.py

@@ -41,13 +41,16 @@ class NCAAnalysis(NCAApiBaseClass):
         config_data: dict,
         *,
         meta_data: str | dict | None = None,
+        post_processing: str | dict | None = None,
+        data_processing: str | dict | None = None,
         wait_for_results: bool = True,
         max_wait_in_seconds: int = 900,
         output_directory: str | None = None,
         unzip_after_download: bool = False,
+        full_payload: str | dict | None = None
     ) -> Dict[str, Any]:
         """
-        Executes an analsysis.
+        Executes an analysis.
             - Uploads an analysis file.
             - Adds the execution to the queue.
 
@@ -81,7 +84,7 @@ class NCAAnalysis(NCAApiBaseClass):
                 "Unexpected empty file_id when attempting to upload file."
             )
 
-        self.log("\tAdding analyis to the queue.")
+        self.log("\tAdding analysis to the queue.")
         execution_response: Dict[str, Any] = self.__add_to_queue(
             file_id=file_id,
             config_data=config_data,
@@ -130,6 +133,9 @@ class NCAAnalysis(NCAApiBaseClass):
         file_id: str,
         config_data: dict,
         meta_data: str | dict | None = None,
+        post_processing: str | dict | None = None,
+        data_processing: str | dict | None = None,
+        full_payload: str | dict | None = None
     ) -> Dict[str, Any]:
         """
         Adds the analysis to the execution queue.
@@ -151,15 +157,19 @@ class NCAAnalysis(NCAApiBaseClass):
                 "Missing config_data.  Please provide a valid config_data."
             )
         headers = self.authenticator.get_jwt_http_headers()
-        # to start a new execution we need the location of the file (s3 bucket and object key)
-        # you basic configuration
-        # optional meta data
-
-        submission = {
-            "file": {"id": file_id},
-            "configuration": config_data,
-            "meta_data": meta_data,
-        }
+        
+        submission: Dict[str, Any] = {}
+
+        if full_payload:
+            submission = full_payload
+        else:
+            submission = {
+                "file": {"id": file_id},
+                "configuration": config_data,
+                "meta_data": meta_data,
+                "post_processing": post_processing,
+                "data_processing": data_processing
+            }
 
         response: requests.Response = requests.post(
             self.endpoints.executions,
@@ -171,13 +181,13 @@ class NCAAnalysis(NCAApiBaseClass):
 
         if response.status_code == 403:
             raise PermissionError(
-                "Failed to execute.  A 403 response occured.  "
+                "Failed to execute.  A 403 response occurred.  "
                 "This could a token issue or a url path issue  "
                 "By default unknown gateway calls return 403 errors. "
             )
         elif response.status_code != 200:
             raise RuntimeError(
-                f"Unknown Error occured during executions: {response.status_code}. "
+                f"Unknown Error occurred during executions: {response.status_code}. "
                 f"Reason: {response.reason}"
             )
 

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/nca_resources/nca_file_download.py

@@ -5,16 +5,17 @@ Property of Aplos Analytics, Utah, USA
 """
 
 import time
-from typing import Any, Dict, List
 from datetime import datetime, timedelta
+from typing import Any, Dict, List
+
+import requests
 from aws_lambda_powertools import Logger
+
 from aplos_nca_saas_sdk.nca_resources._api_base import NCAApiBaseClass
 from aplos_nca_saas_sdk.nca_resources.aws_s3_presigned_upload import (
     S3PresignedUrlUpload,
 )
-
 from aplos_nca_saas_sdk.utilities.http_utility import HttpUtilities
-import requests
 
 logger = Logger(service="nca-file-download")
 
@@ -41,7 +42,8 @@ class NCAFileDownload(NCAApiBaseClass):
             ValueError: _description_
 
         Returns:
-            Dict: {"file_id": id, "statu_code": 204}
+            Dict: {"file_id": id, "status_code": 204, ...}
+            204 Response staus_code is a success
         """
         if input_file_path is None or not input_file_path:
             raise ValueError("Valid input_file_path is required.")
@@ -67,12 +69,19 @@ class NCAFileDownload(NCAApiBaseClass):
         file_id: str,
         user_name: str | None = None,
         password: str | None = None,
+        wait_time_in_seconds: float = 5,
+        max_tries: float = 12,
+        required_workable_state: str = "ready",
     ) -> Dict[str, Any]:
         """
         Downloads a file from the Aplos NCA Cloud
 
         Args:
             file_id (str): the id of the file to download
+            user_name Optional(str): the username used to connect.  If not specified
+                the authenticator is required.
+            password Optional(str): the password used to connect.  If not specified
+                the authenticator is required.
 
         Raises:
             ValueError: _description_
@@ -94,12 +103,17 @@ class NCAFileDownload(NCAApiBaseClass):
                 )
             self.authenticator.authenticate(username=user_name, password=password)
 
-        max_wait_in_minutes: int = 3
         headers = HttpUtilities.get_headers(self.authenticator.cognito.jwt)
         current_time = datetime.now()
 
-        # Create a timedelta object representing 3 minutes
-        time_delta = timedelta(minutes=max_wait_in_minutes)
+        if max_tries < 0:
+            max_tries = 1
+        if wait_time_in_seconds < 0:
+            wait_time_in_seconds = 1
+
+        max_wait_time_in_seconds = wait_time_in_seconds * max_tries
+        # Create a timedelta object representing x seconds
+        time_delta = timedelta(seconds=max_wait_time_in_seconds)
         # Add the timedelta to the current time
         max_time = current_time + time_delta
 
@@ -113,16 +127,18 @@ class NCAFileDownload(NCAApiBaseClass):
             status = json_response.get("workable_state")
             complete = status == "ready"
 
+            if not required_workable_state or required_workable_state == "any":
+                break
             if status == "invalid" or len(errors) > 0:
                 break
             if complete:
                 break
             if not complete:
-                time.sleep(5)
+                time.sleep(wait_time_in_seconds)
             if datetime.now() > max_time:
                 error = (
-                    "Timeout attempting to get conversion file status. "
-                    f"The current timeout limit is {max_wait_in_minutes} minutes. "
+                    "Timeout attempting to get an analysis file. "
+                    f"The current timeout limit is {max_wait_time_in_seconds} seconds. "
                     "You may need to up the timeout period, or check for errors. "
                 )
                 raise RuntimeError(error)

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/run_analysis_execution.py

@@ -48,7 +48,7 @@ def main():
 
         wait_for_results = True
         max_wait_in_seconds = 900  # 15 minutes
-        resutls = analysis_api.execute(
+        results = analysis_api.execute(
             username=str(args.username),
             password=str(args.password),
             input_file_path=str(args.analysis_file),
@@ -60,7 +60,7 @@ def main():
         )
 
         if not wait_for_results:
-            exec_id = resutls.get("execution", {}).get("execution_id", "")
+            exec_id = results.get("execution", {}).get("execution_id", "")
             print(
                 "Analysis execution has been queued.  We're not waiting for the results."
             )
@@ -69,7 +69,7 @@ def main():
         print("🙌 Thank you for using the NCA API for an Analysis Execution Demo. 🙌")
     except Exception as e:  # pylint: disable=w0718
         print(
-            "🚨 An error occured ... exiting with an error.  Please check your settings and try again."
+            "🚨 An error occurred ... exiting with an error.  Please check your settings and try again."
         )
         print(
             "If you believe this is bug please create a support ticket and include the execution id (if available)."
@@ -83,7 +83,7 @@ def main():
 
 def optional_json_loads(data: str | dict) -> str | dict:
     """
-    Attempts to load the data as json, fails gracefull and retuns the data is if it fails
+    Attempts to load the data as json, fails graceful and returns the data is if it fails
     Args:
         data (str): data as string
 

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/utilities/commandline_args.py

@@ -39,7 +39,7 @@ class CommandlineArgs:
             "-c", "--config-file", required=False, help="Path to the configuration file"
         )
         self.parser.add_argument(
-            "-f", "--analyis-file", required=False, help="Path to the analysis file"
+            "-f", "--analysis-file", required=False, help="Path to the analysis file"
         )
         self.parser.add_argument(
             "-m", "--metadata-file", required=False, help="Path to the metadata file"
@@ -82,7 +82,7 @@ class CommandlineArgs:
         self.password: str | None = None
         self.host: str | None = None
 
-        # excuction setup
+        # execution setup
         self.config_file: str | None = None
         self.config_file_default: str | None = None
         self.analysis_file: str | None = None
@@ -102,21 +102,21 @@ class CommandlineArgs:
         Returns:
             bool: True if they are all valid
         """
-        # see if we have any aruments
+        # see if we have any arguments
         args = self.parser.parse_args()
 
         self.username = args.username
         self.password = args.password
         self.config_file = args.config_file
         # anything with a dash (in the args) is accessed with an underscore
-        self.analysis_file = args.analyis_file
+        self.analysis_file = args.analysis_file
         self.host = args.host
 
         self.metadata_file = args.metadata_file
         self.skip = args.skip
         self.output_directory = args.output_directory
         self.environment_file = args.environment_file
-        # no args check to see if they have them in the environmet
+        # no args check to see if they have them in the environment
 
         # if we have an environment file we'll want to load it before checking any defaults
         self.check_for_environment_config()

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/utilities/environment_services.py

@@ -103,7 +103,7 @@ class EnvironmentServices:
         if raise_error_if_not_found:
             searched_paths = "\n".join(paths)
             raise RuntimeError(
-                f"Failed to locate the moduel root: {MODULE_ROOT} in: \n {searched_paths}"
+                f"Failed to locate the module root: {MODULE_ROOT} in: \n {searched_paths}"
             )
 
         return None

{aplos_nca_saas_sdk-0.0.16 → aplos_nca_saas_sdk-0.0.17}/src/aplos_nca_saas_sdk/version.py

@@ -1,4 +1,4 @@
 # Aplos NCA SaaS SDK Version File
 # This is automatically generated during the build process. 
 # DO NOT UPDATE IT DIRECTLY. IT WILL BE OVERWRITTEN. 
-__version__ = '0.0.16'
+__version__ = '0.0.17'