| Name | chaparralapi JSON |
| Version |
0.1.1
JSON |
| download |
| home_page | None |
| Summary | An API for the Chaparral platform |
| upload_time | 2024-07-24 00:53:13 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
chaparral
api
bioinformatics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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No Travis.
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No coveralls.
|
## 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:
```bash
pip install chaparralapi
```
## Example Usage
Here's a quick example of how to use the Chaparral API client:
```python
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](https://chaparral.ai).
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.
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"description": "## Chaparral Python API\n\nThis Python package is a wrapper for the Chaparral API. It provides a simple and convenient interface for interacting with the Chaparral platform.\n\n**Note:** Currently, it supports a limited number of API endpoints. More endpoints will be added in future releases.\n\n## Installation\n\nTo install the package, use pip:\n\n```bash\npip install chaparralapi\n```\n\n## Example Usage\n\nHere's a quick example of how to use the Chaparral API client:\n\n```python\nfrom chaparralapi import Client\n\ntoken = 'XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX'\napi = Client(token)\n\n# Fetch and print all projects\nprint(api.get_projects())\n\n# Fetch and print organization details\nprint(api.get_organization())\n\n# Fetch and print all FASTA databases\nprint(api.get_databases())\n```\n\n## Obtaining the API Token\n\nTo get your Chaparral API token, follow these steps:\n\n1. Go to the [Chaparral website](https://chaparral.ai).\n2. Open the browser's developer tools (usually F12 or right-click and select \"Inspect\").\n3. Navigate to the \"Network\" tab.\n4. Look for a REST API call and inspect its headers.\n5. Copy the token from the `Authorization` header.\n6. 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Creates a new database.\n\n- **Delete Database:** `delete_database(database_id: str) -> None`\n - Deletes a database by its ID.\n\n#### Search Result Endpoints\n\n- **Get All Search Results:** `get_search_results() -> List[SearchResult]`\n - Retrieves a list of all search results.\n\n- **Get Search Result by ID:** `get_search_result(search_result_id: str) -> Optional[SearchResult]`\n - Retrieves a specific search result by its ID.\n\n- **Get Search Result Download:** `get_search_result_download(search_result_id: str) -> SearchResultDownload`\n - Retrieves the download URLs for a specific search result.\n\n- **Fetch Config JSON:** `fetch_config_json(search_result_id: str) -> str`\n - Fetches the config JSON file for a specific search result.\n\n- **Fetch Matched Fragments Parquet:** `fetch_matched_fragments_parquet(search_result_id: str) -> str`\n - Fetches the matched fragments parquet file for a specific search result.\n\n- **Fetch Peptide CSV:** `fetch_peptide_csv(search_result_id: str) -> str`\n - 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