GRAPH-PLATER


NameGRAPH-PLATER JSON
Version 1.0 PyPI version JSON
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home_pagehttp://github.com/YaphetKG/plater.git
SummaryTranslatorAPI Interface for graph databases.
upload_time2021-01-28 03:43:22
maintainer
docs_urlNone
author
requires_python
license
keywords knowledge network graph biomedical
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requirements No requirements were recorded.
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            See the Homepage for a better formatted version.
 ## PLATER

PLATER is a service to stand up REST endpoint over a neo4j or redis graph database.
There are some restrictions on the data structure of the Neo4j backend to be fully utilized through PLATER.

> **Data structure restrictions:**
> * All nodes should have an `id` to be searchable (Used in querying single Nodes)
> * All edges should have an `id` to be searchable (Used in generating ReasonerAPI)
> * Data is recommended to comply to the [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI).

### Installation

To run the web server directly:

#### Create a virtual Environment and activate.

    cd <PLATER-ROOT>
    python<version> -m venv venv
    source venv/bin/activate
    
#### Install dependencies
    
    pip install -r PLATER/requirements.txt
    
 
#### Configure PLATER settings
   
   Populate `.env-template` file with settings and save as `.env` in repo root dir.
   
   ```bash   
    WEB_HOST=0.0.0.0
    WEB_PORT=8080
    DB_HOST=<neo4j_or_redis_address>
    DB_USERNAME=<user name required for neo4j, empty for redis>
    DB_PASSWORD=''
    DB_PORT=<redis port or neo4j http port>
    DB_NAME=<db name for redis, uses default db for neo4j>
    DB_TYPE=<use values 'redis' or 'neo4j'>
    PLATER_TITLE='Plater'
    PLATER_VERSION='1.0.0'
    

   ```
   
  
#### Run Script
  
    ./main.sh
 
    
 ### DOCKER 
   Or build an image and run it. 
  
  ```bash
    cd PLATER
    docker build --tag <image_tag> .
    cd ../
  ```
  
  ```bash
   docker run --env-file .env\
    --name plater\
    -p 8080:8080\
    --network <network_where_neo4j_is_running>\
    plater-tst

  ```
 
 ### Clustering with [Automat Server](https://github.com/RENCI-AUTOMAT/Automat-server/) \[Optional\]
 You can also serve several instances of plater through a common gateway(Automat). On specific instructions 
 please refer to [AUTOMAT's readme](https://github.com/RENCI-AUTOMAT/Automat-server/blob/master/README.md)
  
 

 ### Miscellaneous
 ###### `/about` Endpoint 
 The `/about` endpoint can be used to present meta-data about the current PLATER instance. 
 This meta-data is served from `<repo-root>/PLATER/about.json` file. One can edit the contents of
 this file to suite needs. In containerized environment we recommend mounting this file as a volume.
 
 Eg:
 ```bash
docker run -p 0.0.0.0:8999:8080  \
               --env DB_HOST=<your_db_host> \
               --env DB_PORT=<your_db_port> \
               --env DB_USERNAME=<db_user_name required for neo4j, ignored for redis> \
               --env DB_PASSWORD=<db_password> \
               --env DB_NAME=<required for redis> \ 
               --env DB_TYPE=<redis or neo4j> \  
               --env WEB_HOST=0.0.0.0 \
               -v <your-custom-about>:/<path-to-plater-repo-home>/plater/about.json \
               --network=<docker_network_neo4j_is_running_at> \    
                <image_tag>   
```
            

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    "description": "See the Homepage for a better formatted version.\n ## PLATER\n\nPLATER is a service to stand up REST endpoint over a neo4j or redis graph database.\nThere are some restrictions on the data structure of the Neo4j backend to be fully utilized through PLATER.\n\n> **Data structure restrictions:**\n> * All nodes should have an `id` to be searchable (Used in querying single Nodes)\n> * All edges should have an `id` to be searchable (Used in generating ReasonerAPI)\n> * Data is recommended to comply to the [Translator Reasoner API](https://github.com/NCATSTranslator/ReasonerAPI).\n\n### Installation\n\nTo run the web server directly:\n\n#### Create a virtual Environment and activate.\n\n    cd <PLATER-ROOT>\n    python<version> -m venv venv\n    source venv/bin/activate\n    \n#### Install dependencies\n    \n    pip install -r PLATER/requirements.txt\n    \n \n#### Configure PLATER settings\n   \n   Populate `.env-template` file with settings and save as `.env` in repo root dir.\n   \n   ```bash   \n    WEB_HOST=0.0.0.0\n    WEB_PORT=8080\n    DB_HOST=<neo4j_or_redis_address>\n    DB_USERNAME=<user name required for neo4j, empty for redis>\n    DB_PASSWORD=''\n    DB_PORT=<redis port or neo4j http port>\n    DB_NAME=<db name for redis, uses default db for neo4j>\n    DB_TYPE=<use values 'redis' or 'neo4j'>\n    PLATER_TITLE='Plater'\n    PLATER_VERSION='1.0.0'\n    \n\n   ```\n   \n  \n#### Run Script\n  \n    ./main.sh\n \n    \n ### DOCKER \n   Or build an image and run it. \n  \n  ```bash\n    cd PLATER\n    docker build --tag <image_tag> .\n    cd ../\n  ```\n  \n  ```bash\n   docker run --env-file .env\\\n    --name plater\\\n    -p 8080:8080\\\n    --network <network_where_neo4j_is_running>\\\n    plater-tst\n\n  ```\n \n ### Clustering with [Automat Server](https://github.com/RENCI-AUTOMAT/Automat-server/) \\[Optional\\]\n You can also serve several instances of plater through a common gateway(Automat). On specific instructions \n please refer to [AUTOMAT's readme](https://github.com/RENCI-AUTOMAT/Automat-server/blob/master/README.md)\n  \n \n\n ### Miscellaneous\n ###### `/about` Endpoint \n The `/about` endpoint can be used to present meta-data about the current PLATER instance. \n This meta-data is served from `<repo-root>/PLATER/about.json` file. One can edit the contents of\n this file to suite needs. In containerized environment we recommend mounting this file as a volume.\n \n Eg:\n ```bash\ndocker run -p 0.0.0.0:8999:8080  \\\n               --env DB_HOST=<your_db_host> \\\n               --env DB_PORT=<your_db_port> \\\n               --env DB_USERNAME=<db_user_name required for neo4j, ignored for redis> \\\n               --env DB_PASSWORD=<db_password> \\\n               --env DB_NAME=<required for redis> \\ \n               --env DB_TYPE=<redis or neo4j> \\  \n               --env WEB_HOST=0.0.0.0 \\\n               -v <your-custom-about>:/<path-to-plater-repo-home>/plater/about.json \\\n               --network=<docker_network_neo4j_is_running_at> \\    \n                <image_tag>   \n```",
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