Chaparral Python API

This Python package is a wrapper for the Chaparral API. It provides a simple and convenient interface for interacting with the Chaparral platform.

Note: Currently, it supports a limited number of API endpoints. More endpoints will be added in future releases.

Installation

To install the package, use pip:

pip install chaparralapi

Example Usage

Here's a quick example of how to use the Chaparral API client:

from chaparralapi import Client

token = 'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'
api = Client(token)

# Fetch and print all projects
print(api.get_projects())

# Fetch and print organization details
print(api.get_organization())

# Fetch and print all FASTA databases
print(api.get_databases())

Obtaining the API Token

To get your Chaparral API token, follow these steps:

1. Go to the Chaparral website.
2. Open the browser's developer tools (usually F12 or right-click and select "Inspect").
3. Navigate to the "Network" tab.
4. Look for a REST API call and inspect its headers.
5. Copy the token from the Authorization header.
6. The token will be valid for 8 hours.

Sure, here is the updated README to include the new endpoints in the Client class:

Endpoints

This section describes the endpoints available in the Client class for interacting with the Chaparral API.

Project Endpoints

• Get All Projects: get_projects() -> List[Project]

  • Retrieves a list of all projects.

• Get Project by ID: get_project(project_id: str) -> Project

  • Retrieves a specific project by its ID.

• Create Project: create_project(name: str, description: str) -> Project

  • Creates a new project.

• Update Project: update_project(project_id: str, name: str, description: str, tags: List[str]) -> Project

  • Updates an existing project.

• Delete Project: delete_project(project_id: str) -> None

  • Deletes a project by its ID.

• Tag Projects: tag_projects(project_ids: List[str], tags: List[str]) -> List[Project]

  • Adds tags to multiple projects.

• Get Projects by Tag: get_projects_by_tag(tag: str) -> List[Project]

  • Retrieves projects that have a specific tag.

Organization Endpoints

• Get Organization: get_organization() -> Organization

  • Retrieves the details of the organization.

• Update Organization: update_organization(organization_id: str, name: str) -> Organization

  • Updates the organization's name.

• Invite to Organization: invite_to_organization(email: str) -> None

  • Invites a new member to the organization.

• Get Resource Usage: get_resource_usage() -> OrganizationUsage

  • Retrieves the resource usage of the organization.

Database Endpoints

• Get All Databases: get_databases() -> List[Database]

  • Retrieves a list of all databases.

• Get Database by ID: get_database(database_id: str) -> Database

  • Retrieves a specific database by its ID.

• Update Database: update_database(database_id: str, name: str, organism: str, decoy_tag: Optional[str]) -> Database

  • Updates an existing database.

• Create Database: create_database(database_bytes: bytes, filename: str) -> Database

  • Creates a new database.

• Delete Database: delete_database(database_id: str) -> None

  • Deletes a database by its ID.

Search Result Endpoints

• Get All Search Results: get_search_results() -> List[SearchResult]

  • Retrieves a list of all search results.

• Get Search Result by ID: get_search_result(search_result_id: str) -> Optional[SearchResult]

  • Retrieves a specific search result by its ID.

• Get Search Result Download: get_search_result_download(search_result_id: str) -> SearchResultDownload

  • Retrieves the download URLs for a specific search result.

• Fetch Config JSON: fetch_config_json(search_result_id: str) -> str

  • Fetches the config JSON file for a specific search result.

• Fetch Matched Fragments Parquet: fetch_matched_fragments_parquet(search_result_id: str) -> str

  • Fetches the matched fragments parquet file for a specific search result.

• Fetch Peptide CSV: fetch_peptide_csv(search_result_id: str) -> str

  • Fetches the peptide CSV file for a specific search result.

• Fetch Proteins CSV: fetch_proteins_csv(search_result_id: str) -> str

  • Fetches the proteins CSV file for a specific search result.

• Fetch Results JSON: fetch_results_json(search_result_id: str) -> str

  • Fetches the results JSON file for a specific search result.

• Fetch Results Parquet: fetch_results_parquet(search_result_id: str) -> str

  • Fetches the results parquet file for a specific search result.

QC Endpoints

• Get QC Scores: get_qc_scores(search_result_id: str) -> List[QcScore]

  • Retrieves the QC scores for a specific search result.

• Get QC IDs: get_qc_ids(search_result_id: str) -> List[QcId]

  • Retrieves the QC IDs for a specific search result.

• Get QC Precursors: get_qc_precursors(search_result_id: str) -> List[QcPrecursor]

  • Retrieves the QC precursors for a specific search result.

User Profile Endpoints

• Get User Profile: get_user_profile() -> Profile

  • Retrieves the user's profile information.

• Update User Profile: update_user_profile(first_name: str, last_name: str) -> Profile

  • Updates the user's profile information.

Project File Endpoints

• Get Project Files: get_project_files(project_id: str) -> List[ProjectFile]

  • Retrieves the files for a specific project.

• Get Project File: get_project_file(project_id: str, file_id: str) -> ProjectFile

  • Retrieves a specific file from a project by its ID.

• Upload Project File: upload_project_file(project_id: str, file_bytes: bytes, filename: str)

  • Uploads a file to a specific project.

Search Submission Endpoints

• Submit Search: submit_search(project_id: str, search_settings: Dict) -> None
  • Submits a search request for a specific project.