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_all_projects())

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

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

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.

Endpoints

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

Project Endpoints

• Get All Projects: get_all_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) -> Project

  • Updates an existing project.

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

  • Deletes a project by its ID.

Organization Endpoints

• Get Organization: get_organization() -> Organization

  • Retrieves the details of the organization.

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

  • Updates the organization's name.

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

  • Invites a new member to the organization.

FASTA Endpoints

• Get All FASTA Databases: get_all_fastas() -> List[Fasta]

  • Retrieves a list of all FASTA databases.

• Get FASTA Database by ID: get_fasta(fasta_id: str) -> Fasta

  • Retrieves a specific FASTA database by its ID.

• Update FASTA Database: update_fasta(fasta_id: str, name: str, organism: str, decoy_tag: Optional[str]) -> Fasta

  • Updates an existing FASTA database.

• Create FASTA Database: create_fasta() -> Fasta

  • Creates a new FASTA database. (Not implemented)

• Delete FASTA Database: delete_fasta(fasta_id: str) -> None

  • Deletes a FASTA database by its ID.

Search Result Endpoints

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

  • Retrieves a list of all search results.

• 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.