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https://github.com/openphacts/OPS_LinkedDataApi

A repository to host API configuration files, and code extensions
https://github.com/openphacts/OPS_LinkedDataApi

Last synced: 5 days ago
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A repository to host API configuration files, and code extensions

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README 

        
# OPS LinkedDataApi



The Linked Data API for [Open PHACTS](http://www.openphacts.org/).



Based on the [Puelia PHP](https://code.google.com/p/puelia-php/) implementation

of the [Linked Data API](https://github.com/UKGovLD/linked-data-api/blob/wiki/Specification.md) specification.



This is a repository to host [API configuration files](api-config-files/)

 and code extensions



Requirements are php 5.2, with `php_xsl`, `lib_curl`, and `mod_rewrite` and `.htaccess` override enabled.



Make sure that Apache's `DocumentRoot` directory and (all parent directories from /var/ forward) are writable by the user running Apache



The sparql endpoint is set from environment variable `OPS_SPARQL_ENDPOINT` eg `export OPS_SPARQL_ENDPOINT=http://sparql-endpoint:8890/sparql` and read in `deployment.settings.php`.



The IMS API endpoint is set from environment variable `IMS_ENDPOINT` eg `export IMS_ENDPOINT=http://ims-endpoint:8000` and read in `deployment.settings.php`.



The OPS Search API endpoint is set from environment variable `OPS_SEARCH_ENDPOINT` eg `export OPS_SEARCH_ENDPOINT=http://somewhere.com:8839` and read in `deployment.settings.php`.



Memcache location is set from environment variable `MEMCACHE_ENDPOINT` eg `export MEMCACHE_ENDPOINT=localhost`.



By default memcache is not used, to enable it set environment variable `USE_MEMCACHE` eg `export USE_MEMCACHE=TRUE`.



You can also run on localhost without Apache using php -S localhost:3000. Note that this address will only work on localhost on your machine.



You can also run on localhost without Apache using php -S localhost:3000.



## Docker image



This application is also available as a [Docker](https://www.docker.com/) image:

[openphacts/ops-linkeddataapi](https://registry.hub.docker.com/u/openphacts/ops-linkeddataapi/)



This image will provide the Open PHACTS API on HTTP port `80`, which can be exposed

using the `-p` docker parameter.



This image relies on linking to these other docker images as the following aliases:



 * `memcached`: [memcached](https://hub.docker.com/_/memcached/)

 * `ims`: [openphacts/identitymappingservice/](https://hub.docker.com/r/openphacts/identitymappingservice/)

 * `sparql`: [stain/virtuoso](https://hub.docker.com/r/stain/virtuoso/)



Details about starting and populating those are provided at their respective READMEs.

The simplest option to start up the Open PHACTS platform is usually the

[ops-platform-setup](https://github.com/openphacts/ops-platform-setup/tree/master/docker) configuration for [Docker Compose](https://docs.docker.com/compose/).



Additionally these environment variables define the external services for

[ConceptWiki](http://conceptwiki.org/) and

[Chemical Resolution Service](https://chemistry.openphacts.org/) (these are not

currently available as Docker containers):



 * `CRS` (default: https://crs/api/v1/)

 * `CONCEPTWIKI` (default: http://conceptwiki:8080/web-ws/concept)

 * `USE_MEMCACHE` (TRUE or FALSE - default FALSE)

 * `MEMCACHE_ENDPOINT` (default 'localhost')

 * `IMS_ENDPOINT` (default: 'localhost:3004')

 * `OPS_SPARQL_ENDPOINT` (default: none, assumed to be defined in the config settings for each API call)

 * `OPS_SEARCH_ENDPOINT` (default: none, assumed to be defined in the config settings for the OPS search API call)



The default values for `CRS` and `CONCEPTWIKI` access the aliases `crs` and `conceptwiki`, but

if you don't have your own installation of these services, you might use the

public services, by adding the following to `docker run`:



    --env CRS=https://chemistry.openphacts.org/api/v1/ \

    --env CONCEPTWIKI=http://www.conceptwiki.org/web-ws/concept



You can also add settings for memcache:



 * 'USE_MEMCACHE' (TRUE or FALSE - default FALSE)

 * 'MEMCACHE_ENDPOINT' (default 'localhost')



    --env USE_MEMCACHE=TRUE

    --env MEMCACHE_ENDPOINT=my-memcache



You can also tell the LDAPI where to find the IMS and the sparql endpoint:



    --env IMS_ENDPOINT=http://a.b.c:3000

    --env OPS_SPARQL_ENDPOINT=http://d.e.f:8000

    

You can also set the endpoint to use for searches that will use the  [OPS Search component](https://github.com/openphacts/ops-search/) via the LDAPI:



     --env OPS_SEARCH_ENDPOINT=http://localhost:8839

     

If `OPS_SEARCH_ENDPOINT` is not set then it will use whatever is in the config files.



If using memcache or the OPS Search component via docker then you need to ensure that both the LDAPI and these containers are on the same docker network:



  `docker network create ops-ldapi-network`



then you can refer to the `MEMCACHE_ENDPOINT` or `OPS_SEARCH_ENDPOINT` by it's internal docker network DNS eg `my-memcache`. OPS Search can also have the port included eg `ops-search:8839`.



### Example Docker run



To run (note that this example uses the deprecated docker `--link` command):



    docker run --name ops-linkeddataapi -p 8081:80 \

      --network=ops-ldapi-network \

      --env CRS=https://chemistry.openphacts.org/api/v1/ \

      --env CONCEPTWIKI=http://www.conceptwiki.org/web-ws/concept \

      --env OPS_SEARCH_ENDPOINT=http://localhost:8839 \

      --env USE_MEMCACHE=TRUE \

      --env MEMCACHE_ENDPOINT=my-memcache \

      --link memcached:memcached \

      --link identitymappingservice:ims \

      --link virtuoso:sparql \

      -d openphacts/ops-linkeddataapi



The above will expose the Open PHACTS Linked Data API on

[http://localhost:8081](http://localhost:8081) (or equivalent)

and link to existing Docker containers `memcached`, `identitymappingservice`

and `virtuoso` (which must already be running), and the

public APIs for [CRS](https://chemistry.openphacts.org/) and

[ConceptWiki](http://www.conceptwiki.org/). It will also tell the LDAPI to use the memcache container called `my-memcache` on the docker network `ops-ldapi-network`.



If using a docker network then there is no need to `link` the containers but you must ensure that they are on the same docker network. You can either attach the container at run time (as in the example above) or add it afterwards eg. `docker network connect ops-ldapi-network ops-linkeddataapi`.



## Swagger



The API includes a [Swagger](http://swagger.io/) definition in JSON

for the exposed services, available at `/swagger` - for example

http://localhost:8081/swagger. This file is in `api-config-files/swagger.json`.

The swagger files for previous API versions can be found in `api-config-files/swagger/old/`.

The swagger file for the current API can also be found in `api-config-files/swagger/current/`.



Note that the hostname and port returned as `basePath` here

depends on the URL the swagger file is accessed at. If you are

exposing the API via a proxy, the swagger definition might be

wrongly exposing the internal URI.



To override the `basePath`, set the `BASE_PATH` environment variable.



For example:



    docker run -p 8081:80 \

      --env BASE_PATH=http://cool.example.com/ \

      -d openphacts/ops-linkeddataapi