phenoml 0.0.1__py3-none-any.whl

phenoml/tools/types/__init__.py

@@ -0,0 +1,25 @@
+# This file was auto-generated by Fern from our API Definition.
+
+# isort: skip_file
+
+from .cohort_request_provider import CohortRequestProvider
+from .cohort_response import CohortResponse
+from .fhir_client_config import FhirClientConfig
+from .lang2fhir_and_create_request_provider import Lang2FhirAndCreateRequestProvider
+from .lang2fhir_and_create_request_resource import Lang2FhirAndCreateRequestResource
+from .lang2fhir_and_create_response import Lang2FhirAndCreateResponse
+from .lang2fhir_and_search_request_provider import Lang2FhirAndSearchRequestProvider
+from .lang2fhir_and_search_response import Lang2FhirAndSearchResponse
+from .search_concept import SearchConcept
+
+__all__ = [
+    "CohortRequestProvider",
+    "CohortResponse",
+    "FhirClientConfig",
+    "Lang2FhirAndCreateRequestProvider",
+    "Lang2FhirAndCreateRequestResource",
+    "Lang2FhirAndCreateResponse",
+    "Lang2FhirAndSearchRequestProvider",
+    "Lang2FhirAndSearchResponse",
+    "SearchConcept",
+]

phenoml/tools/types/cohort_request_provider.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+CohortRequestProvider = typing.Union[typing.Literal["medplum", "google_healthcare", "canvas", "hapi"], typing.Any]

phenoml/tools/types/cohort_response.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+import typing_extensions
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+from ...core.serialization import FieldMetadata
+from .search_concept import SearchConcept
+
+
+class CohortResponse(UniversalBaseModel):
+    success: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether the cohort analysis was successful
+    """
+
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Status message with details about the analysis
+    """
+
+    patient_ids: typing_extensions.Annotated[typing.Optional[typing.List[str]], FieldMetadata(alias="patientIds")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    Array of patient IDs that match the cohort criteria
+    """
+
+    patient_count: typing_extensions.Annotated[typing.Optional[int], FieldMetadata(alias="patientCount")] = (
+        pydantic.Field(default=None)
+    )
+    """
+    Total number of patients in the cohort
+    """
+
+    queries: typing.Optional[typing.List[SearchConcept]] = pydantic.Field(default=None)
+    """
+    Individual search concepts that were identified and executed
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/tools/types/fhir_client_config.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class FhirClientConfig(UniversalBaseModel):
+    """
+    Provider-specific configuration and metadata
+    """
+
+    fhir_store_id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    FHIR store ID for Google Healthcare provider
+    """
+
+    on_behalf_of_email: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Email address to use for On-Behalf-Of requests (Medplum only). If provided, the request will be made on behalf of the Patient or Practitioner with this email address.
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/tools/types/lang2fhir_and_create_request_provider.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+Lang2FhirAndCreateRequestProvider = typing.Union[
+    typing.Literal["medplum", "google_healthcare", "canvas", "hapi"], typing.Any
+]

phenoml/tools/types/lang2fhir_and_create_request_resource.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+Lang2FhirAndCreateRequestResource = typing.Union[
+    typing.Literal[
+        "auto",
+        "appointment",
+        "condition-encounter-diagnosis",
+        "medicationrequest",
+        "careplan",
+        "condition-problems-health-concerns",
+        "coverage",
+        "encounter",
+        "observation-clinical-result",
+        "observation-lab",
+        "patient",
+        "procedure",
+        "questionnaire",
+        "questionnaireresponse",
+        "simple-observation",
+        "vital-signs",
+    ],
+    typing.Any,
+]

phenoml/tools/types/lang2fhir_and_create_response.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class Lang2FhirAndCreateResponse(UniversalBaseModel):
+    fhir_resource: typing.Optional[typing.Dict[str, typing.Optional[typing.Any]]] = pydantic.Field(default=None)
+    """
+    The created FHIR resource
+    """
+
+    fhir_id: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    ID of the resource in the FHIR server (if successfully stored)
+    """
+
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Status message
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/tools/types/lang2fhir_and_search_request_provider.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+Lang2FhirAndSearchRequestProvider = typing.Union[
+    typing.Literal["medplum", "google_healthcare", "canvas", "hapi"], typing.Any
+]

phenoml/tools/types/lang2fhir_and_search_response.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class Lang2FhirAndSearchResponse(UniversalBaseModel):
+    resource_type: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    The FHIR resource type identified for the search
+    """
+
+    search_params: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    FHIR search parameters in standard format
+    """
+
+    fhir_results: typing.Optional[typing.List[typing.Dict[str, typing.Optional[typing.Any]]]] = pydantic.Field(
+        default=None
+    )
+    """
+    Array of FHIR resources returned from the search
+    """
+
+    success: typing.Optional[bool] = None
+    message: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Status message
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/tools/types/search_concept.py

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+# This file was auto-generated by Fern from our API Definition.
+
+import typing
+
+import pydantic
+from ...core.pydantic_utilities import IS_PYDANTIC_V2, UniversalBaseModel
+
+
+class SearchConcept(UniversalBaseModel):
+    """
+    A single search concept detected in cohort mode
+    """
+
+    resource_type: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    The FHIR resource type identified for this concept
+    """
+
+    search_params: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    FHIR search parameters for this concept
+    """
+
+    concept: typing.Optional[str] = pydantic.Field(default=None)
+    """
+    Description of what this search represents
+    """
+
+    exclude: typing.Optional[bool] = pydantic.Field(default=None)
+    """
+    Whether this is an exclusion criteria
+    """
+
+    if IS_PYDANTIC_V2:
+        model_config: typing.ClassVar[pydantic.ConfigDict] = pydantic.ConfigDict(extra="allow", frozen=True)  # type: ignore # Pydantic v2
+    else:
+
+        class Config:
+            frozen = True
+            smart_union = True
+            extra = pydantic.Extra.allow

phenoml/version.py

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+from importlib import metadata
+
+__version__ = metadata.version("phenoml")

phenoml/wrapper_client.py

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+"""
+Simple wrapper that extends the base client with automatic token generation.
+"""
+
+import httpx
+from typing import Optional, Union, Callable
+
+from .client import phenoml, Asyncphenoml
+from .environment import phenomlEnvironment
+from .authtoken.client import AuthtokenClient, AsyncAuthtokenClient
+from .core.client_wrapper import SyncClientWrapper, AsyncClientWrapper
+
+
+class PhenoMLClient(phenoml):
+    """
+    Extends the base client with automatic token generation from username/password.
+    """
+    
+    def __init__(
+        self,
+        *,
+        token: Optional[Union[str, Callable[[], str]]] = None,
+        username: Optional[str] = None,
+        password: Optional[str] = None,
+        **kwargs
+    ):
+        # Validate authentication
+        if token is None and (username is None or password is None):
+            raise ValueError("Must provide either 'token' or both 'username' and 'password'")
+        
+        if token is not None and (username is not None or password is not None):
+            raise ValueError("Cannot provide both 'token' and 'username'/'password'")
+        
+        # Generate token if needed
+        if token is None:
+            if username is None or password is None:
+                raise ValueError("Must provide both 'username' and 'password'")
+            base_url = kwargs.get('base_url')
+            if base_url is None:
+                raise ValueError("Must provide 'base_url' when using username/password")
+            token = self._generate_token(username, password, base_url)
+        
+        # Call parent constructor with the resolved token and all kwargs
+        super().__init__(token=token, **kwargs)
+    
+    def _generate_token(self, username: str, password: str, base_url: str) -> str:
+        """Generate token using the auth client."""
+        # Create a simple client wrapper without authentication
+        client_wrapper = SyncClientWrapper(
+            token="",  # No auth needed since we're using basic auth in the request
+            base_url=base_url,
+            httpx_client=httpx.Client()
+        )
+        
+        # Create the auth client using the existing SDK
+        auth_client = AuthtokenClient(client_wrapper=client_wrapper)
+        
+        print(f"Generating token for {username} using auth client")
+        response = auth_client.auth.generate_token(username=username, password=password)
+        print(f"Token response: {response}")
+        return response.token
+
+
+class AsyncPhenoMLClient(Asyncphenoml):
+    """
+    Extends the async base client with automatic token generation from username/password.
+    """
+    
+    def __init__(
+        self,
+        *,
+        token: Optional[Union[str, Callable[[], str]]] = None,
+        username: Optional[str] = None,
+        password: Optional[str] = None,
+        **kwargs
+    ):
+        # Validate authentication
+        if token is None and (username is None or password is None):
+            raise ValueError("Must provide either 'token' or both 'username' and 'password'")
+        
+        if token is not None and (username is not None or password is not None):
+            raise ValueError("Cannot provide both 'token' and 'username'/'password'")
+        
+        # Store for async token generation (needed for initialize)
+        self._username = username
+        self._password = password
+        self._base_url = kwargs.get('base_url')
+        if self._base_url is None:
+            raise ValueError("Must provide 'base_url' when using username/password")
+        
+        # Create with temporary token if needed
+        self._current_token = ""
+        super().__init__(token=token or (lambda: self._current_token), **kwargs)
+    
+    async def initialize(self) -> None:
+        """Generate token if username/password was provided."""
+        if self._username and self._password:
+            token = await self._generate_token()
+            # Update the token on the existing instance instead of recreating
+            # This is a workaround since we can't easily recreate the instance
+            self._current_token = token
+    
+    async def _generate_token(self) -> str:
+        """Generate token using the auth client."""
+        # Ensure base_url is a string
+        if self._base_url is None:
+            raise ValueError("Base URL must be provided")
+        
+        # Create a simple client wrapper without authentication
+        client_wrapper = AsyncClientWrapper(
+            token="",  # No auth needed since we're using basic auth in the request
+            base_url=self._base_url,
+            httpx_client=httpx.AsyncClient()
+        )
+        
+        # Create the auth client using the existing SDK
+        auth_client = AsyncAuthtokenClient(client_wrapper=client_wrapper)
+        
+        if self._username is None or self._password is None:
+            raise ValueError("Username and password must be provided")
+        
+        response = await auth_client.auth.generate_token(username=self._username, password=self._password)
+        return response.token 

phenoml-0.0.1.dist-info/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 PhenoML
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

phenoml-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.1
+Name: phenoml
+Version: 0.0.1
+Summary: 
+Requires-Python: >=3.8,<4.0
+Classifier: Intended Audience :: Developers
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: OS Independent
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Typing :: Typed
+Requires-Dist: httpx (>=0.21.2)
+Requires-Dist: pydantic (>=1.9.2)
+Requires-Dist: pydantic-core (>=2.18.2)
+Requires-Dist: typing_extensions (>=4.0.0)
+Description-Content-Type: text/markdown
+
+# Phenoml Python Library
+
+[![fern shield](https://img.shields.io/badge/%F0%9F%8C%BF-Built%20with%20Fern-brightgreen)](https://buildwithfern.com?utm_source=github&utm_medium=github&utm_campaign=readme&utm_source=https%3A%2F%2Fgithub.com%2Ffern-demo%2Fphenoml-python-sdk)
+[![pypi](https://img.shields.io/pypi/v/phenoml)](https://pypi.python.org/pypi/phenoml)
+
+The Phenoml Python library provides convenient access to the Phenoml API from Python.
+
+## Installation
+
+```sh
+pip install phenoml
+```
+
+## Reference
+
+A full reference for this library is available [here](https://github.com/phenoml/phenoml-python-sdk/blob/HEAD/./reference.md).
+
+## Usage
+
+Instantiate and use the client with the following:
+
+```python
+from phenoml import Client
+
+client = Client(
+    username="your_username",
+    password="your_password",
+    base_url="https://your-phenoml-instance.com"
+)
+
+client.agent.create(
+    name="name",
+    prompts=["prompt_123", "prompt_456"],
+    is_active=True,
+)
+```
+
+## Async Client
+
+The SDK also exports an `async` client so that you can make non-blocking calls to our API.
+
+```python
+import asyncio
+
+from phenoml import AsyncClient
+
+client = AsyncClient(
+    username="your_username",
+    password="your_password",
+    base_url="https://your-phenoml-instance.com"
+)
+
+
+async def main() -> None:
+    await client.initialize()  # Generate token from username/password
+    await client.agent.create(
+        name="name",
+        prompts=["prompt_123", "prompt_456"],
+        is_active=True,
+    )
+
+
+asyncio.run(main())
+```
+
+## Exception Handling
+
+When the API returns a non-success status code (4xx or 5xx response), a subclass of the following error
+will be thrown.
+
+```python
+from phenoml.core.api_error import ApiError
+
+try:
+    client.agent.create(...)
+except ApiError as e:
+    print(e.status_code)
+    print(e.body)
+```
+
+## Advanced
+
+### Access Raw Response Data
+
+The SDK provides access to raw response data, including headers, through the `.with_raw_response` property.
+The `.with_raw_response` property returns a "raw" client that can be used to access the `.headers` and `.data` attributes.
+
+```python
+from phenoml import phenoml
+
+client = phenoml(
+    ...,
+)
+response = client.agent.with_raw_response.create(...)
+print(response.headers)  # access the response headers
+print(response.data)  # access the underlying object
+```
+
+### Retries
+
+The SDK is instrumented with automatic retries with exponential backoff. A request will be retried as long
+as the request is deemed retryable and the number of retry attempts has not grown larger than the configured
+retry limit (default: 2).
+
+A request is deemed retryable when any of the following HTTP status codes is returned:
+
+- [408](https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/408) (Timeout)
+- [429](https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/429) (Too Many Requests)
+- [5XX](https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/500) (Internal Server Errors)
+
+Use the `max_retries` request option to configure this behavior.
+
+```python
+client.agent.create(..., request_options={
+    "max_retries": 1
+})
+```
+
+### Timeouts
+
+The SDK defaults to a 60 second timeout. You can configure this with a timeout option at the client or request level.
+
+```python
+
+from phenoml import phenoml
+
+client = phenoml(
+    ...,
+    timeout=20.0,
+)
+
+
+# Override timeout for a specific method
+client.agent.create(..., request_options={
+    "timeout_in_seconds": 1
+})
+```
+
+### Custom Client
+
+You can override the `httpx` client to customize it for your use-case. Some common use-cases include support for proxies
+and transports.
+
+```python
+import httpx
+from phenoml import phenoml
+
+client = phenoml(
+    ...,
+    httpx_client=httpx.Client(
+        proxies="http://my.test.proxy.example.com",
+        transport=httpx.HTTPTransport(local_address="0.0.0.0"),
+    ),
+)
+```
+
+## Contributing
+
+While we value open-source contributions to this SDK, this library is generated programmatically.
+Additions made directly to this library would have to be moved over to our generation code,
+otherwise they would be overwritten upon the next generated release. Feel free to open a PR as
+a proof of concept, but know that we will not be able to merge it as-is. We suggest opening
+an issue first to discuss with us!
+
+On the other hand, contributions to the README are always very welcome!
+