aplos-nca-saas-sdk 1.0.0__py3-none-any.whl

aplos_nca_saas_sdk/aws_resources/aws_cognito.py

@@ -0,0 +1,188 @@
+"""
+Copyright 2024 Aplos Analytics
+All Rights Reserved.   www.aplosanalytics.com   LICENSED MATERIALS
+Property of Aplos Analytics, Utah, USA
+"""
+
+import boto3
+import jwt as jwt_lib
+from typing import Optional
+from aplos_nca_saas_sdk.nca_resources.nca_app_configuration import (
+    NCAAppConfiguration,
+)
+
+
+class CognitoAuthenication:
+    """
+    Cognito Authentication
+
+    """
+
+    def __init__(
+        self,
+        *,
+        client_id: Optional[str] = None,
+        region: Optional[str] = None,
+        aplos_domain: Optional[str] = None,
+    ) -> None:
+        # setup the client id
+        self.__client_id: Optional[str] = client_id
+        self.__jwt: Optional[str] = None
+        self.__access_token: Optional[str] = None
+        self.__refresh_token: Optional[str] = None
+        self.__region: str = region or "us-east-1"
+        self.__client: Optional[boto3.client] = None
+        self.__user_id: Optional[str] = None
+        self.__tenant_id: Optional[str] = None
+        self.__config: Optional[NCAAppConfiguration] = None
+        self.__aplos_domain: Optional[str] = aplos_domain
+
+        self.__validate_parameters()
+
+    @property
+    def client(self) -> boto3.client:
+        """
+        Get the boto3 client
+
+        Returns:
+            boto3.client: the boto3 client
+        """
+        if self.__client is None:
+            self.__client = boto3.client("cognito-idp", region_name=self.region)
+
+        return self.__client
+
+    @property
+    def client_id(self) -> str:
+        """
+        Client Id
+        Returns:
+            str: the client id
+        """
+        return self.__client_id
+
+    @property
+    def region(self) -> str:
+        """
+        Region
+        Returns:
+            str: the region
+        """
+        return self.__region
+
+    def __validate_parameters(self) -> None:
+        if self.__client_id is None and self.__aplos_domain is not None:
+            self.__config = NCAAppConfiguration(aplos_saas_domain=self.__aplos_domain)
+            self.__client_id = self.__config.cognito_client_id
+            self.__region = self.__config.cognito_region
+
+        if self.__client_id is None:
+            raise RuntimeError(
+                "Missing Cognito Client Id. "
+                "Pass in a client_id as a command arg or set the COGNITO_CLIENT_ID enviornment var. "
+                "Alternatively, set the aplos_domain to automatically get the client_id and region."
+            )
+
+        if self.__region is None:
+            raise RuntimeError(
+                "Missing Cognito Region"
+                "Pass in a region as a command arg or set the COGNITO_REGION enviornment var. "
+                "Alternatively, set the aplos_domain to automatically get the client_id and region."
+            )
+
+    def login(self, username: str, password: str) -> str:
+        """
+        Get a JWT (JSON Web Token)
+
+        Args:
+            username (str): username (email address)
+            password (str): password
+            client_id (str): cognito client/application id
+
+        Returns:
+            str | None: json web token (jwt)
+        """
+
+        if not self.client_id:
+            raise RuntimeError("Missing Cognito Client Id")
+
+        auth_response = self.client.initiate_auth(
+            ClientId=self.client_id,
+            # user USER_PASSWORD_AUTH flow for this type of login
+            AuthFlow="USER_PASSWORD_AUTH",
+            AuthParameters={"USERNAME": username, "PASSWORD": password},
+        )
+
+        if "ChallengeName" in auth_response:
+            # depending on your setup, it's possible you will get challenged for a
+            # password change. contact support if this happens
+            raise RuntimeError(
+                "New password required before a token can be provided. Please contact support or your Aplos Administrator."
+            )
+
+        # Extract the session tokens
+        # id_token is the JWT token
+        # typical tokens last for 30 minutes to 1 hour by default
+        self.__jwt = auth_response["AuthenticationResult"]["IdToken"]
+        # access token is if you have direct access to aws resources
+        # you probably won't ever need this
+        self.__access_token = auth_response["AuthenticationResult"]["AccessToken"]  # noqa: F814, F841, pylint: disable=W0612
+        # refresh token if needed
+        # you can use refresh tokens to "refresh" your jwt or simply login again
+        # refresh tokens are typically good for 30 days by default
+        self.__refresh_token = auth_response["AuthenticationResult"]["RefreshToken"]  # noqa: F814, F841, pylint: disable=w0612
+
+        # return the jwt token
+        if isinstance(self.__jwt, str):
+            self.__parse_jwt(self.__jwt)
+            return self.__jwt
+
+        raise RuntimeError("Failed to get a JWT token")
+
+    def __parse_jwt(self, encoded_jwt: str) -> None:
+        # Decode the payload (second part) from Base64
+        decoded_jwt: dict = jwt_lib.decode(
+            encoded_jwt, options={"verify_signature": False}
+        )
+        self.__user_id = decoded_jwt.get("custom:aplos_user_id")
+        self.__tenant_id = decoded_jwt.get("custom:aplos_user_tenant_id")
+
+    @property
+    def jwt(self) -> str:
+        """Get the JWT JSON Web Token"""
+        if isinstance(self.__jwt, str):
+            return self.__jwt
+
+        raise RuntimeError("Failed to get a JWT token")
+
+    @property
+    def user_id(self) -> str:
+        """Get the authenticated User Id"""
+        if isinstance(self.__user_id, str):
+            return self.__user_id
+
+        raise RuntimeError("Failed to get a user id")
+
+    @property
+    def tenant_id(self) -> str:
+        """Get the authenticated Tenant Id"""
+        if isinstance(self.__tenant_id, str):
+            return self.__tenant_id
+
+        raise RuntimeError("Failed to get a tenant id")
+
+    @property
+    def access_token(self) -> str:
+        """Get the AWS Access Token"""
+        if isinstance(self.__access_token, str):
+            return self.__access_token
+
+        raise RuntimeError("Failed to get an access token")
+
+    @property
+    def refresh_token(self) -> str:
+        """Get the AWS Cognito Refresh Token"""
+        if isinstance(self.__refresh_token, str):
+            return self.__refresh_token
+
+        raise RuntimeError("Failed to get a refresh token")

aplos_nca_saas_sdk/aws_resources/aws_s3_presigned_payload.py

@@ -0,0 +1,49 @@
+"""
+Copyright 2024 Aplos Analytics
+All Rights Reserved.   www.aplosanalytics.com   LICENSED MATERIALS
+Property of Aplos Analytics, Utah, USA
+"""
+
+
+class S3PresignedPayload:
+    """S3PresignedPayload"""
+
+    def __init__(self, payload: dict | None = None) -> None:
+        self.url: str | None = None
+        self.form_data: dict = {}
+        self.raw_payload: dict | None = payload
+        self.file_id: str | None = None
+        if payload:
+            self.__load(payload)
+
+    def __load(self, payload: dict):
+        if "presigned" not in payload:
+            raise KeyError("Missing key 'presigned' in response payload.")
+        self.url = payload["presigned"]["url"]
+        self.form_data = self.__get_presigned_form_data(payload=payload)
+
+        filed_id = payload.get("file", {}).get("id", None)
+        if not filed_id:
+            raise KeyError("Missing key 'file.id' in response payload.")
+        self.file_id = filed_id
+
+    def __get_presigned_form_data(self, payload: dict) -> dict:
+        """
+        Generates the form data need for an s3 presigned url upload
+        NOTE: the order of the items below are important.  s3 presigned url uploads are
+        very picky in the way the process the data.  if they are out of order you may get
+        errors that the "keys" are not present.  It's best to centralize this into a library
+        """
+        form_data = {
+            "key": payload["presigned"]["fields"]["key"],
+            "x-amz-algorithm": payload["presigned"]["fields"]["x-amz-algorithm"],
+            "x-amz-credential": payload["presigned"]["fields"]["x-amz-credential"],
+            "x-amz-date": payload["presigned"]["fields"]["x-amz-date"],
+            "x-amz-security-token": payload["presigned"]["fields"][
+                "x-amz-security-token"
+            ],
+            "policy": payload["presigned"]["fields"]["policy"],
+            "x-amz-signature": payload["presigned"]["fields"]["x-amz-signature"],
+        }
+
+        return form_data

aplos_nca_saas_sdk/aws_resources/aws_s3_presigned_upload.py

@@ -0,0 +1,116 @@
+"""
+Copyright 2024 Aplos Analytics
+All Rights Reserved.   www.aplosanalytics.com   LICENSED MATERIALS
+Property of Aplos Analytics, Utah, USA
+"""
+
+import json
+import os
+
+import requests
+from aplos_nca_saas_sdk.aws_resources.aws_s3_presigned_payload import (
+    S3PresignedPayload,
+)
+from aplos_nca_saas_sdk.utilities.http_utility import HttpUtilities, Routes
+
+
+class S3PresignedUpload:
+    """S3PresignedUpload"""
+
+    def __init__(self, jwt: str, api_url: str) -> None:
+        self.api_url = api_url
+        self.jwt = jwt
+
+    def upload_file(self, input_file: str) -> S3PresignedPayload:
+        """
+        Uploads a file to your Aplos Cloud Account in AWS
+
+        Args:
+            input_file (str): path to the analysis file you are uploading
+
+        Returns:
+            S3PresignedPayload: an instance of S3PresignedPayload
+        """
+
+        # get the presigned url for uploading
+        paylod: S3PresignedPayload = self.__get_presigned_upload_info(
+            input_file=input_file
+        )
+        # upload the files
+        self.__upload_file_to_s3(paylod, input_file=input_file)
+
+        return paylod
+
+    def __get_presigned_upload_info(self, input_file: str) -> S3PresignedPayload:
+        """
+        Performs all the necessary steps for creating a presigned url to upload a file to S3.
+        We're using AWS S3 presigned urls for security as well as allowing for very large files if requried.
+        Args:
+            input_file (str): the path to the input (analysis) file
+
+        Returns:
+            S3PresignedPayload: instance of S3PresignedPayload
+        """
+
+        url = f"{self.api_url}/{Routes.NCA_GENERATE_UPLOAD}"
+        headers = HttpUtilities.get_headers(self.jwt)
+
+        body = {"file_name": input_file, "method_type": "post"}
+        response = requests.post(
+            url=url, headers=headers, data=json.dumps(body), timeout=30
+        )
+
+        if response.status_code == 403:
+            raise PermissionError(
+                "Failed to get a presigned url. "
+                f"Status Code: {response.status_code }"
+                f"Reason: {response.reason} "
+                f"403 Errors can also occur if you have an invalid path."
+            )
+        elif response.status_code != 200:
+            raise RuntimeError(
+                "Failed to get a presigned url. "
+                f"Status Code: {response.status_code }"
+                f"Reason: {response.reason}"
+            )
+        result = response.json()
+
+        payload: S3PresignedPayload = S3PresignedPayload(result)
+
+        return payload
+
+    def __upload_file_to_s3(self, payload: S3PresignedPayload, input_file: str) -> bool:
+        """
+        Peforms the actual uploading via a presigned url for S3 bucket storage
+        Args:
+            payload (S3PresignedPayload): instance of S3PresignedPayload with all the data needed
+            input_file (str): the path to a file being uploaded
+
+        Raises:
+            FileNotFoundError: If the file is not found
+
+        Returns:
+            bool: True on success, False if not
+        """
+
+        if not os.path.exists(input_file):
+            raise FileNotFoundError(
+                "The input file you are submitting cannot be found.  Please check the path and try again."
+            )
+
+        with open(input_file, "rb") as file:
+            files = {"file": (input_file, file)}
+            # upload to s3 with the presigned url
+            upload_response = requests.post(
+                str(payload.url), data=payload.form_data, files=files, timeout=30
+            )
+
+        # Check the response: 204 is a success in this case
+        if upload_response and upload_response.status_code == 204:
+            return True
+        else:
+            raise RuntimeError(
+                "Error uploading the file. "
+                f"Status Code: {upload_response.status_code}"
+                f"Response: {upload_response.reason}"
+            )

aplos_nca_saas_sdk/files/analysis_files/single_ev/configuration_single_ev.json

@@ -0,0 +1,51 @@
+{
+   "version": "2024-02-22",
+   "designations": {
+     "blq": "BLQ",
+     "missing": "NS",
+     "concentration_unit": "ng/mL"
+   },
+   "columns": {
+     "time": "time",
+     "unique_id": "subject",
+     "concentration": {
+       "observed": "conc.obs",
+       "analyzed": "conc"
+     },
+     "sorting": [
+       "subject",
+       "time"
+     ],
+     "grouping": [
+       "subject"
+     ]
+   },
+   "dosing": {
+     "amount": 10000,
+     "unit": "mg",
+     "frequency": "single",
+     "type": "ev"
+   },
+   "time": {
+     "unit": "hr",
+     "time_of_administration": 0,
+     "tau": 24,
+     "infusion": {
+       "protocol": "rate",
+       "amount": "1"
+     }
+   },
+   "kel_rules": {
+     "regression_statistic": "adj_r2",
+     "minimum_statistic": 0,
+     "maximum_extrapolation_linear": 0,
+     "maximum_extrapolation_logarithmic": 0,
+     "maximum_time_points": 0,
+     "minimum_span": 0,
+     "earliest_time_point": 0,
+     "tie": [
+       "kel_n",
+       "kel_lower"
+     ]
+   }
+ }

aplos_nca_saas_sdk/files/analysis_files/single_ev/meta_data.json

@@ -0,0 +1,17 @@
+{
+    "description": "meta data is optional.  contains any json or string you'd like.  json will give you structure.  example below",
+    "reason": "analysis for xyz",
+    "team": [
+        {
+            "name": "john doe",
+            "title": "lead analyst",
+            "company": "little pharma"
+        },
+        {
+            "name": "jane doe",
+            "title": "consultant",
+            "company": "acme consulting"
+        }
+    ]
+
+}

aplos_nca_saas_sdk/files/analysis_files/single_ev/single_ev.csv

@@ -0,0 +1,121 @@
+subject,sex,dose,time,conc,conc.obs,Dose.type,Dose.amt,Dose.unit,Dose.time,conc.unit,time.unit
+1,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,2,534,534,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,4,540,540,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,6,382,382,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,8,268,268,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,12,132,132,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,16,65.2,65.2,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,20,32.1,32.1,extravascular,10000,mg,0,mg/L,hr
+1,F,10000,24,15.8,15.8,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,2,144,144,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,4,231,231,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,6,197,197,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,8,168,168,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,12,122,122,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,16,88.2,88.2,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,20,64,64,extravascular,10000,mg,0,mg/L,hr
+2,F,10000,24,46.4,46.4,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,1,78.6,78.6,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,1.5,713,713,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,2,842,842,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,4,692,692,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,6,474,474,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,8,321,321,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,12,147,147,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,16,67.7,67.7,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,20,31,31,extravascular,10000,mg,0,mg/L,hr
+3,F,10000,24,14.2,14.2,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,1.5,1640,1640,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,2,1570,1570,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,4,531,531,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,6,154,154,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,8,44.4,44.4,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,12,3.69,3.69,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,16,0.307,0.307,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,20,,BLQ,extravascular,10000,mg,0,mg/L,hr
+4,F,10000,24,,BLQ,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,2,650,650,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,4,1080,1080,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,6,808,808,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,8,571,571,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,12,281,281,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,16,138,138,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,20,68,68,extravascular,10000,mg,0,mg/L,hr
+5,F,10000,24,33.5,33.5,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,2,1290,1290,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,4,1170,1170,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,6,589,589,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,8,287,287,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,12,67.5,67.5,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,16,15.9,15.9,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,20,3.74,3.74,extravascular,10000,mg,0,mg/L,hr
+6,F,10000,24,0.882,0.882,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,1.5,961,961,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,2,1240,1240,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,4,816,816,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,6,443,443,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,8,239,239,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,12,69.4,69.4,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,16,20.2,20.2,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,20,5.86,5.86,extravascular,10000,mg,0,mg/L,hr
+7,F,10000,24,1.7,1.7,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,2,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,4,1400,1400,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,6,777,777,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,8,391,391,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,12,97,97,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,16,24,24,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,20,5.96,5.96,extravascular,10000,mg,0,mg/L,hr
+8,F,10000,24,1.48,1.48,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,1.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,2,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,4,944,944,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,6,654,654,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,8,417,417,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,12,168,168,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,16,67.7,67.7,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,20,27.3,27.3,extravascular,10000,mg,0,mg/L,hr
+9,F,10000,24,11,11,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,0,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,0.5,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,1,0,BLQ,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,1.5,657,657,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,2,1130,1130,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,4,1000,1000,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,6,658,658,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,8,425,425,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,12,176,176,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,16,73.2,73.2,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,20,30.4,30.4,extravascular,10000,mg,0,mg/L,hr
+10,F,10000,24,12.6,12.6,extravascular,10000,mg,0,mg/L,hr

aplos_nca_saas_sdk/integration_testing/integration_test_base.py

@@ -0,0 +1,34 @@
+"""
+Copyright 2024 Aplos Analytics
+All Rights Reserved.   www.aplosanalytics.com   LICENSED MATERIALS
+Property of Aplos Analytics, Utah, USA
+"""
+
+from typing import Dict, Any
+from aplos_nca_saas_sdk.utilities.environment_vars import EnvironmentVars
+from aplos_nca_saas_sdk.nca_resources.nca_endpoints import NCAEndpoints
+
+
+class IntegrationTestBase:
+    """
+    Integration Test Base Class
+    """
+
+    def __init__(self, name: str, index: int = 0):
+        self.name = name
+        self.index = index
+        self.env_vars: EnvironmentVars = EnvironmentVars()
+
+        if not self.env_vars.api_domain:
+            raise RuntimeError(
+                "APLOS_API_DOMAIN environment variable is not set. "
+                "This is required to run the tests"
+            )
+
+        self.endpoints: NCAEndpoints = NCAEndpoints(
+            aplos_saas_domain=self.env_vars.api_domain,
+        )
+
+    def test(self) -> Dict[str, Any] | None:
+        """Run the Test"""
+        raise RuntimeError("This should be implemented by the subclass.")

aplos_nca_saas_sdk/integration_testing/integration_test_factory.py

@@ -0,0 +1,62 @@
+"""
+Copyright 2024 Aplos Analytics
+All Rights Reserved.   www.aplosanalytics.com   LICENSED MATERIALS
+Property of Aplos Analytics, Utah, USA
+"""
+
+import os
+from typing import List
+from pathlib import Path
+import importlib
+import inspect
+from aplos_nca_saas_sdk.integration_testing.integration_test_base import (
+    IntegrationTestBase,
+)
+
+
+class IntegrationTestFactory:
+    """
+    Integration Test Factory
+    Loads all the integration tests from the tests directory and registers them for execution
+    """
+
+    def __init__(self):
+        self.__test_classes: List[IntegrationTestBase] = []
+        self.__load_all_classes()
+
+    def __load_all_classes(self):
+        # find all files in the test directory that end in _test.py
+        test_directory = os.path.join(Path(__file__).parent, "tests")
+        potential_test_files = os.listdir(test_directory)
+        test_files = [
+            f
+            for f in potential_test_files
+            if f.endswith("_test.py") and f != "__init__.py"
+        ]
+
+        # load the class dynamically
+        for test_file in test_files:
+            module_name = (
+                f"aplos_nca_saas_sdk.integration_testing.tests.{test_file[:-3]}"
+            )
+            module = importlib.import_module(module_name)
+
+            # Iterate over all attributes in the module
+            for _, obj in inspect.getmembers(module, inspect.isclass):
+                # Check if the class inherits from the specified base class
+                if (
+                    issubclass(obj, IntegrationTestBase)
+                    and obj is not IntegrationTestBase
+                ):
+                    # Instantiate the class and store it
+                    self.register_test_class(obj())
+
+    @property
+    def test_classes(self) -> List[IntegrationTestBase]:
+        """Get the test classes"""
+        self.__test_classes.sort(key=lambda x: x.index)
+        return self.__test_classes
+
+    def register_test_class(self, test_class: IntegrationTestBase):
+        """Register a test class"""
+        self.__test_classes.append(test_class)