brapi-proxy


Namebrapi-proxy JSON
Version 0.0.9 PyPI version JSON
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SummaryA BRAPI server instance that functions as a proxy to merge and combine endpoints from existing BRAPI services
upload_time2024-05-29 12:35:34
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authorNone
requires_python>=3.10
licenseMIT License Copyright (c) 2024 EU H2020 AGENT project 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.
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            # BrAPI proxy solution


A [BrAPI](https://brapi.org/) server instance that functions as a proxy to merge and combine endpoints from existing BrAPI services.

## Installation

- **Step 1: Install BrAPI Proxy**
  - To install the BrAPI Proxy, run the following command:
    ```sh
    pip install brapi_proxy
    ```
- **Step 2: Test the Installation (Optional)**
  - To ensure that the installation was successful, you can run the BrAPI Proxy in demo mode with the following command:
    ```sh
    brapi_proxy --demo
    ```
    This will start a [service on port 8080](http://localhost:8080/) from a configuration based on the [BrAPI Test Server](https://test-server.brapi.org/brapi/v2/)

## Usage

- **Step 1: Create Configuration File**
  - Create a file named config.ini.
  - Populate this file with the necessary configuration settings.

- **Step 2: Start the Service**
  - Start the service by running the command:
    ```sh
    brapi_proxy
    ```
  - If the config.ini file is located outside the working directory, use the --config option to specify its location. For example:
    ```sh
    brapi_proxy --config /path/to/config.ini
    ```
    
---

### Currently Supported

**BrAPI Versions**
- version 2.1

**Endpoints**

- BrAPI-Core
  - /commoncropnames
  - /lists
  - /lists/{listDbId}
  - /locations
  - /locations/{locationDbId}
  - /people
  - /people/{personDbId}
  - /programs
  - /programs/{programDbId}
  - /seasons
  - /seasons/{seasonDbId}
  - /studies
  - /studies/{studyDbId}
  - /trials
  - /trials/{trialDbId}
- BrAPI-Phenotyping
  - /ontologies
  - /ontologies/{ontologyDbId}
- BrAPI-Genotyping
  - /allelematrix
  - /callsets
  - /callsets/{callSetDbId}
  - /plates
  - /plates/{plateDbId}
  - /references
  - /references/{referenceDbId}
  - /referencesets
  - /referencesets/{referenceSetDbId}
  - /samples
  - /samples/{sampleDbId}
  - /variants
  - /variants/{variantDbId}
  - /variantsets
  - /variantsets/{variantSetDbId}
- BrAPI-Germplasm
  - /breedingmethods
  - /breedingmethods/{breedingMethodDbId}

### ToDo

- Implement additional endpoints
  
---

### Structure Configuration File

Create a `config.ini` file with the necessary configuration settings.

**Basic Configuration**

Include at least the `brapi` section:

```config
[brapi]
port=8080
host=0.0.0.0
location=/
threads=4
debug=False
version=2.1
```

**Optional: Serverinfo**

Optionally, provide `serverinfo` entries:

```
contactEmail=noreply@wur.nl
documentationURL=https://github.com/matthijsbrouwer/brapi-proxy/
location=Wageningen
organizationName=Wageningen University and Research
organizationURL=https://www.plantbreeding.wur.nl/
serverDescription=Demo-version proxy to combine multiple BrAPI services
serverName=BrAPI-Proxy
```

**Optional: Authorization**

Optionally, provide authentication tokens to restrict access in the `authorization` section:

```
[authorization]
john=tokenjohn123abc
mary=tokenmary456def
```

**Server Definitions**

Within sections prefixed with `server.`, define the underlying servers:

```
[server.test1]
url=https://test-server.brapi.org/brapi/v2
calls=commoncropnames,variants,allelematrix
authorization=XXXX
prefix.variants=barley:
prefix.variantsets=barley:
prefix.references=barley:
prefix.referencesets=barley:
prefix.callsets=barley:

[server.test2]
url=https://test-server.brapi.org/brapi/v2
calls=commoncropnames,variants,allelematrix
prefix.variants=wheat:
prefix.variantsets=wheat:
prefix.references=wheat:
prefix.referencesets=wheat:
prefix.callsets=wheat:

[server.test3]
url=https://test-server.brapi.org/brapi/v2
calls=samples,studies,plates,callsets,variantsets,referencesets,references
```

---
This software has been developed for the [AGENT](https://www.agent-project.eu/) project




            

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    "description": "# BrAPI proxy solution\n\n\nA [BrAPI](https://brapi.org/) server instance that functions as a proxy to merge and combine endpoints from existing BrAPI services.\n\n## Installation\n\n- **Step 1: Install BrAPI Proxy**\n  - To install the BrAPI Proxy, run the following command:\n    ```sh\n    pip install brapi_proxy\n    ```\n- **Step 2: Test the Installation (Optional)**\n  - To ensure that the installation was successful, you can run the BrAPI Proxy in demo mode with the following command:\n    ```sh\n    brapi_proxy --demo\n    ```\n    This will start a [service on port 8080](http://localhost:8080/) from a configuration based on the [BrAPI Test Server](https://test-server.brapi.org/brapi/v2/)\n\n## Usage\n\n- **Step 1: Create Configuration File**\n  - Create a file named config.ini.\n  - Populate this file with the necessary configuration settings.\n\n- **Step 2: Start the Service**\n  - Start the service by running the command:\n    ```sh\n    brapi_proxy\n    ```\n  - If the config.ini file is located outside the working directory, use the --config option to specify its location. For example:\n    ```sh\n    brapi_proxy --config /path/to/config.ini\n    ```\n    \n---\n\n### Currently Supported\n\n**BrAPI Versions**\n- version 2.1\n\n**Endpoints**\n\n- BrAPI-Core\n  - /commoncropnames\n  - /lists\n  - /lists/{listDbId}\n  - /locations\n  - /locations/{locationDbId}\n  - /people\n  - /people/{personDbId}\n  - /programs\n  - /programs/{programDbId}\n  - /seasons\n  - /seasons/{seasonDbId}\n  - /studies\n  - /studies/{studyDbId}\n  - /trials\n  - /trials/{trialDbId}\n- BrAPI-Phenotyping\n  - /ontologies\n  - /ontologies/{ontologyDbId}\n- BrAPI-Genotyping\n  - /allelematrix\n  - /callsets\n  - /callsets/{callSetDbId}\n  - /plates\n  - /plates/{plateDbId}\n  - /references\n  - /references/{referenceDbId}\n  - /referencesets\n  - /referencesets/{referenceSetDbId}\n  - /samples\n  - /samples/{sampleDbId}\n  - /variants\n  - /variants/{variantDbId}\n  - /variantsets\n  - /variantsets/{variantSetDbId}\n- BrAPI-Germplasm\n  - /breedingmethods\n  - /breedingmethods/{breedingMethodDbId}\n\n### ToDo\n\n- Implement additional endpoints\n  \n---\n\n### Structure Configuration File\n\nCreate a `config.ini` file with the necessary configuration settings.\n\n**Basic Configuration**\n\nInclude at least the `brapi` section:\n\n```config\n[brapi]\nport=8080\nhost=0.0.0.0\nlocation=/\nthreads=4\ndebug=False\nversion=2.1\n```\n\n**Optional: Serverinfo**\n\nOptionally, provide `serverinfo` entries:\n\n```\ncontactEmail=noreply@wur.nl\ndocumentationURL=https://github.com/matthijsbrouwer/brapi-proxy/\nlocation=Wageningen\norganizationName=Wageningen University and Research\norganizationURL=https://www.plantbreeding.wur.nl/\nserverDescription=Demo-version proxy to combine multiple BrAPI services\nserverName=BrAPI-Proxy\n```\n\n**Optional: Authorization**\n\nOptionally, provide authentication tokens to restrict access in the `authorization` section:\n\n```\n[authorization]\njohn=tokenjohn123abc\nmary=tokenmary456def\n```\n\n**Server Definitions**\n\nWithin sections prefixed with `server.`, define the underlying servers:\n\n```\n[server.test1]\nurl=https://test-server.brapi.org/brapi/v2\ncalls=commoncropnames,variants,allelematrix\nauthorization=XXXX\nprefix.variants=barley:\nprefix.variantsets=barley:\nprefix.references=barley:\nprefix.referencesets=barley:\nprefix.callsets=barley:\n\n[server.test2]\nurl=https://test-server.brapi.org/brapi/v2\ncalls=commoncropnames,variants,allelematrix\nprefix.variants=wheat:\nprefix.variantsets=wheat:\nprefix.references=wheat:\nprefix.referencesets=wheat:\nprefix.callsets=wheat:\n\n[server.test3]\nurl=https://test-server.brapi.org/brapi/v2\ncalls=samples,studies,plates,callsets,variantsets,referencesets,references\n```\n\n---\nThis software has been developed for the [AGENT](https://www.agent-project.eu/) project\n\n\n\n",
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