dg-mol-track-client 0.0.1

Python Client SDK Generated by Speakeasy.

dg-mol-track-client

Summary

MolTrack API: API for managing chemical compounds and batches

Table of Contents

• dg-mol-track-client
  • SDK Installation
  • IDE Support
  • SDK Example Usage
  • Available Resources and Operations
  • File uploads
  • Retries
  • Error Handling
  • Custom HTTP Client
  • Resource Management
  • Debugging
• Development
  • Maturity
  • Contributions

SDK Installation

[!TIP] To finish publishing your SDK to PyPI you must run your first generation action.

[!NOTE] Python version upgrade policy

Once a Python version reaches its official end of life date, a 3-month grace period is provided for users to upgrade. Following this grace period, the minimum python version supported in the SDK will be updated.

The SDK can be installed with uv, pip, or poetry package managers.

uv

uv is a fast Python package installer and resolver, designed as a drop-in replacement for pip and pip-tools. It's recommended for its speed and modern Python tooling capabilities.

uv add git+<UNSET>.git

PIP

PIP is the default package installer for Python, enabling easy installation and management of packages from PyPI via the command line.

pip install git+<UNSET>.git

Poetry

Poetry is a modern tool that simplifies dependency management and package publishing by using a single pyproject.toml file to handle project metadata and dependencies.

poetry add git+<UNSET>.git

Shell and script usage with uv

You can use this SDK in a Python shell with uv and the uvx command that comes with it like so:

uvx --from dg-mol-track-client python

It's also possible to write a standalone Python script without needing to set up a whole project like so:

#!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.9"
# dependencies = [
#     "dg-mol-track-client",
# ]
# ///

from dg_mol_track_client import MolTrackClient

sdk = MolTrackClient(
  # SDK arguments
)

# Rest of script here...

Once that is saved to a file, you can run it with uv run script.py where script.py can be replaced with the actual file name.

IDE Support

PyCharm

Generally, the SDK will work well with most IDEs out of the box. However, when using PyCharm, you can enjoy much better integration with Pydantic by installing an additional plugin.

• PyCharm Pydantic Plugin

SDK Example Usage

Example

# Synchronous Example
from dg_mol_track_client import MolTrackClient


with MolTrackClient(
    server_url="https://api.example.com",
) as mol_track_client:

    res = mol_track_client.auto_map_columns.create(entity_type="ASSAY_RUN", columns=[
        "<value 1>",
    ])

    # Handle response
    print(res)

The same SDK client can also be used to make asynchronous requests by importing asyncio.

# Asynchronous Example
import asyncio
from dg_mol_track_client import MolTrackClient

async def main():

    async with MolTrackClient(
        server_url="https://api.example.com",
    ) as mol_track_client:

        res = await mol_track_client.auto_map_columns.create_async(entity_type="ASSAY_RUN", columns=[
            "<value 1>",
        ])

        # Handle response
        print(res)

asyncio.run(main())

Available Resources and Operations

Available methods

additions

• get - Read Additions V1
• create - Create Additions
• get_salts - Read Additions Salts V1
• get_solvates - Read Additions Solvates V1
• fetch_specific - Read Addition V1
• update - Update Addition V1
• delete - Delete Addition

admin

• update_standardization_config - Update Standardization Config

admin.settings

• update - Update Settings

assay_results

• get - Get Assay Results
• create - Create Assay Results
• search - Search Assay Results Advanced

assay_runs

• get - Get Assay Runs
• create - Create Assay Runs
• get_by_id - Get Assay Run By Id

assays

• create - Create Assays
• get - Get Assays
• get_by_id - Get Assay By Id

auto_map_columns

• create - Auto Map Columns

batches

• get - Get Batches
• register - Register Batches
• get_by_any_synonym - Get Batch By Any Synonym
• get_properties - Get Batch Properties
• get_synonyms - Get Batch Synonyms
• get_additions - Get Batch Additions
• delete_by_synonym - Delete Batch By Any Synonym

compounds

• schema_get_synonyms - Get Schema Compound Synonyms
• get - Get Compounds
• register - Register Compounds
• get_by_synonym - Get Compound By Any Synonym
• get_synonyms - Get Compound Synonyms
• get_properties - Get Compound Properties
• update_by_id - Update Compound By Id
• delete_by_id - Delete Compound By Id
• search_advanced - Search Compounds Advanced

schema_

• get - Get Schema
• preload - Preload Schema
• get_direct - Get Schema Direct
• get_compounds - Get Schema Compounds
• get_batches - Get Schema Batches

schema_batches

• get_synonyms - Get Schema Batch Synonyms

search

• create_filter - Generate Search Filter

search.assay_runs

• advanced - Search Assay Runs Advanced

search.assays

• advanced - Search Assays Advanced

search.batches

• advanced - Search Batches Advanced

users

• get - Get Users

validators

• get - Get Validators
• register - Register Validators
• delete_by_name - Delete Validator By Name

File uploads

Certain SDK methods accept file objects as part of a request body or multi-part request. It is possible and typically recommended to upload files as a stream rather than reading the entire contents into memory. This avoids excessive memory consumption and potentially crashing with out-of-memory errors when working with very large files. The following example demonstrates how to attach a file stream to a request.

[!TIP]

For endpoints that handle file uploads bytes arrays can also be used. However, using streams is recommended for large files.

from dg_mol_track_client import MolTrackClient


with MolTrackClient(
    server_url="https://api.example.com",
) as mol_track_client:

    res = mol_track_client.compounds.register(file={
        "file_name": "example.file",
        "content": open("example.file", "rb"),
    })

    # Handle response
    print(res)

Retries

Some of the endpoints in this SDK support retries. If you use the SDK without any configuration, it will fall back to the default retry strategy provided by the API. However, the default retry strategy can be overridden on a per-operation basis, or across the entire SDK.

To change the default retry strategy for a single API call, simply provide a RetryConfig object to the call:

from dg_mol_track_client import MolTrackClient
from dg_mol_track_client.utils import BackoffStrategy, RetryConfig


with MolTrackClient(
    server_url="https://api.example.com",
) as mol_track_client:

    res = mol_track_client.auto_map_columns.create(entity_type="ASSAY_RUN", columns=[
        "<value 1>",
    ],
        RetryConfig("backoff", BackoffStrategy(1, 50, 1.1, 100), False))

    # Handle response
    print(res)

If you'd like to override the default retry strategy for all operations that support retries, you can use the retry_config optional parameter when initializing the SDK:

from dg_mol_track_client import MolTrackClient
from dg_mol_track_client.utils import BackoffStrategy, RetryConfig


with MolTrackClient(
    server_url="https://api.example.com",
    retry_config=RetryConfig("backoff", BackoffStrategy(1, 50, 1.1, 100), False),
) as mol_track_client:

    res = mol_track_client.auto_map_columns.create(entity_type="ASSAY_RUN", columns=[
        "<value 1>",
    ])

    # Handle response
    print(res)

Error Handling

MolTrackClientError is the base class for all HTTP error responses. It has the following properties:

Property	Type	Description
err.message	str	Error message
err.status_code	int	HTTP response status code eg 404
err.headers	httpx.Headers	HTTP response headers
err.body	str	HTTP body. Can be empty string if no body is returned.
err.raw_response	httpx.Response	Raw HTTP response
err.data		Optional. Some errors may contain structured data. See Error Classes.

Example

from dg_mol_track_client import MolTrackClient, errors


with MolTrackClient(
    server_url="https://api.example.com",
) as mol_track_client:
    res = None
    try:

        res = mol_track_client.auto_map_columns.create(entity_type="ASSAY_RUN", columns=[
            "<value 1>",
        ])

        # Handle response
        print(res)


    except errors.MolTrackClientError as e:
        # The base class for HTTP error responses
        print(e.message)
        print(e.status_code)
        print(e.body)
        print(e.headers)
        print(e.raw_response)

        # Depending on the method different errors may be thrown
        if isinstance(e, errors.HTTPValidationError):
            print(e.data.detail)  # Optional[List[models.ValidationError]]

Error Classes

Primary errors:

• MolTrackClientError: The base class for HTTP error responses.
  • HTTPValidationError: Validation Error. Status code 422. *

Less common errors (5)

Network errors:

• httpx.RequestError: Base class for request errors.
  • httpx.ConnectError: HTTP client was unable to make a request to a server.
  • httpx.TimeoutException: HTTP request timed out.

Inherit from MolTrackClientError:

• ResponseValidationError: Type mismatch between the response data and the expected Pydantic model. Provides access to the Pydantic validation error via the cause attribute.

* Check the method documentation to see if the error is applicable.

Custom HTTP Client

The Python SDK makes API calls using the httpx HTTP library. In order to provide a convenient way to configure timeouts, cookies, proxies, custom headers, and other low-level configuration, you can initialize the SDK client with your own HTTP client instance. Depending on whether you are using the sync or async version of the SDK, you can pass an instance of HttpClient or AsyncHttpClient respectively, which are Protocol's ensuring that the client has the necessary methods to make API calls. This allows you to wrap the client with your own custom logic, such as adding custom headers, logging, or error handling, or you can just pass an instance of httpx.Client or httpx.AsyncClient directly.

For example, you could specify a header for every request that this sdk makes as follows:

from dg_mol_track_client import MolTrackClient
import httpx

http_client = httpx.Client(headers={"x-custom-header": "someValue"})
s = MolTrackClient(client=http_client)

or you could wrap the client with your own custom logic:

from dg_mol_track_client import MolTrackClient
from dg_mol_track_client.httpclient import AsyncHttpClient
import httpx

class CustomClient(AsyncHttpClient):
    client: AsyncHttpClient

    def __init__(self, client: AsyncHttpClient):
        self.client = client

    async def send(
        self,
        request: httpx.Request,
        *,
        stream: bool = False,
        auth: Union[
            httpx._types.AuthTypes, httpx._client.UseClientDefault, None
        ] = httpx.USE_CLIENT_DEFAULT,
        follow_redirects: Union[
            bool, httpx._client.UseClientDefault
        ] = httpx.USE_CLIENT_DEFAULT,
    ) -> httpx.Response:
        request.headers["Client-Level-Header"] = "added by client"

        return await self.client.send(
            request, stream=stream, auth=auth, follow_redirects=follow_redirects
        )

    def build_request(
        self,
        method: str,
        url: httpx._types.URLTypes,
        *,
        content: Optional[httpx._types.RequestContent] = None,
        data: Optional[httpx._types.RequestData] = None,
        files: Optional[httpx._types.RequestFiles] = None,
        json: Optional[Any] = None,
        params: Optional[httpx._types.QueryParamTypes] = None,
        headers: Optional[httpx._types.HeaderTypes] = None,
        cookies: Optional[httpx._types.CookieTypes] = None,
        timeout: Union[
            httpx._types.TimeoutTypes, httpx._client.UseClientDefault
        ] = httpx.USE_CLIENT_DEFAULT,
        extensions: Optional[httpx._types.RequestExtensions] = None,
    ) -> httpx.Request:
        return self.client.build_request(
            method,
            url,
            content=content,
            data=data,
            files=files,
            json=json,
            params=params,
            headers=headers,
            cookies=cookies,
            timeout=timeout,
            extensions=extensions,
        )

s = MolTrackClient(async_client=CustomClient(httpx.AsyncClient()))

Resource Management

The MolTrackClient class implements the context manager protocol and registers a finalizer function to close the underlying sync and async HTTPX clients it uses under the hood. This will close HTTP connections, release memory and free up other resources held by the SDK. In short-lived Python programs and notebooks that make a few SDK method calls, resource management may not be a concern. However, in longer-lived programs, it is beneficial to create a single SDK instance via a context manager and reuse it across the application.

from dg_mol_track_client import MolTrackClient
def main():

    with MolTrackClient(
        server_url="https://api.example.com",
    ) as mol_track_client:
        # Rest of application here...


# Or when using async:
async def amain():

    async with MolTrackClient(
        server_url="https://api.example.com",
    ) as mol_track_client:
        # Rest of application here...

Debugging

You can setup your SDK to emit debug logs for SDK requests and responses.

You can pass your own logger class directly into your SDK.

from dg_mol_track_client import MolTrackClient
import logging

logging.basicConfig(level=logging.DEBUG)
s = MolTrackClient(server_url="https://example.com", debug_logger=logging.getLogger("dg_mol_track_client"))

You can also enable a default debug logger by setting an environment variable MOLTRACKCLIENT_DEBUG to true.