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A Java client for Open PHACTS

This Java client is an incomplete client to the Open PHACTS 1.4 API. The goal is a small client with few dependencies and no Scala in particular. Dependencies are JUnit and Apache's HttpClient and Commons IO.

  • License: LGPL v2.1 or later
  • Authors: Egon Willighagen

Compiling and Testing

To compile and test this client, you need an Open PHACTS account and API key which you can get at http://dev.openphacts.org/.

Compile and test with:

mvn -Dserver=... -DappID=... -DappKey=... clean test install

The current beta test server can be tested against using:

-Dserver=https://beta.openphacts.org/1.4/

The documentation for this Open PHACTS API server can be found at https://dev.openphacts.org/docs/1.4

Example

Mapping client = Mapping.getInstance(server, appID, appKey);
String turtle = client.mapUri("http://identifiers.org/ensembl/ENSG00000100030");

Methods return a String with the content in Turtle format. If you want another format, use the ResponseFormat class:

Mapping client = Mapping.getInstance(server, appID, appKey);
String json = client.mapUri(
  "http://identifiers.org/ensembl/ENSG00000100030",
  ResponseFormat.JSON
);

Other formats include HTML, RDF, RDFJSON, and TSV.

Adding other filtration parameters to API-calls is handled by the Parameter and ParameterValue classes:

Targets client = Targets.getInstance(server, appID, appKey);
String json = client.classPharmacologyList(
  "http://purl.uniprot.org/enzyme/6.2.-.-", 1, 1, 
  ResponseFormat.JSON, 
  new ParameterValue(new Parameter("activity_type"), "IC50"),
  new ParameterValue(new Parameter("activity_relation"), "=")
);