Revision as of 15:06, 13 October 2016

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GCube Data Catalogue: support for GRSF

In this page are reported the relevant information about the GRSF Data Catalogue, which is available here. This page is somehow an extension of the main gCube Data Catalogue guide, you are suggested to read before continue.

The GRFS Data Catalogue stores, as well as allows the publication of products of two types: Stock and Fishery. Apart from the default set of metadata, each type of product will also have specific fields. Some of them will also become automatically tags of the product. The same reasoning applies for group associations. In fact a set of groups was already available and each product will be automatically associated to them during publication, if that is the case. Fields that fire tags creation or groups association are documented below.

The publication phase is performed by means of a RESTful service whose publish methods accept JSON objects.

Metadata

Common Metadata

The following table shows the set of core metadata, that is the ones shared by both Stock and Fishery types. Some of them are automatically filled. The values given to some fields are automatically used to tag the product. Check the 'Is Tag' column of the table below. Other fields have a controlled vocabulary (that is, they can assume values selected from a defined set), and the value assigned to these fields allow to automatically determine to which group assign the product. Check the 'Is Group' column below.

mandatory fields are marked with an asterisk (*)

Stock Metadata

The Stock product type also supports the following list of fields.

mandatory fields are marked with an asterisk (*)

Fishery Metadata

The Fishery product type also supports the following list of fields.

mandatory fields are marked with an asterisk (*)

GRSF Publication Web Service

Publication of products is performed by means of a RESTful web service. Each call to the service requires the security token of the user for the context in which he wish to publish or exploit the other functionalities. Please note that in case of product publication it is needed that the user has enough privileges. The list of roles and associated privileges for the catalogue users is reported here. The VRE Manager assignes them.

In order to retrieve your security token you can use the token generator portlet.

The right address for contacting the service can be discovered by means of the Information System. For testing purpose, a running instance can be contacted at the following address.

https://next.d4science.org/grsf-publisher-ws/rest/  (base_url)

The token for testing purpose can be retrieved from the portal at this url https://next.d4science.org/group/next

Check Service Availability

To check that the stock/fishery service is up and running, just put the url below in your browser, together with your security token

base_url/fishery/hello?gcube-token=YOUR_TOKEN

or

base_url/stock/hello?gcube-token=YOUR_TOKEN

The response should look like

Hello.. Fishery service is here

or

Hello.. Stock service is here

Retrieve the licenses list

The default license that will be associated to the products, if not specified, is the CC-BY-SA-4.0 one. However, if it doesn't feet your needs, you can use one of the others available and retrievable by contacting the service(s) this way

base_url/fishery/get-licenses?gcube-token=YOUR_TOKEN

or, for stock

base_url/stock/get-licenses?gcube-token=YOUR_TOKEN

The response is a JSON object, containing couples <license key, license name>, which looks like

{
    "AFL-3.0": "Academic Free License 3.0",
    "RPSL-1.0": "RealNetworks Public Source License 1.0",
    "ODC-BY-1.0": "Open Data Commons Attribution License 1.0",
    "IPL-1.0": "IBM Public License 1.0",
    "ODbL-1.0": "Open Data Commons Open Database License 1.0",
    "PostgreSQL": "PostgreSQL License",
    "W3C": "W3C License",
    "other-open": "Other (Open)",
    "GPL-2.0": "GNU General Public License 2.0",
    "PHP-3.0": "PHP License 3.0",
    "OGL-UK-2.0": "Open Government Licence 2.0 (United Kingdom)",
    "LPL-1.0": "Lucent Public License (\"Plan9\") 1.0",
    "Artistic-2.0": "Artistic License 2.0",
    "Entessa": "Entessa Public License",
    "SPL-1.0": "Sun Public License 1.0",
    "other-at": "Other (Attribution)",
    "CC-BY-NC-SA-4.0": "Creative Commons Attribution-NonCommercial-ShareAlike 4.0",
    "MS-RL": "Microsoft Reciprocal License",
    "OSL-3.0": "Open Software License 3.0",
    "other-nc": "Other (Non-Commercial)",
    "LGPL-2.1": "GNU Lesser General Public License 2.1",
    "BSD-3-Clause": "BSD 3-Clause \"New\" or \"Revised\" License (BSD-3-Clause)",
    "CC-BY-NC-ND-4.0": "Creative Commons Attribution-NonCommercial-NoDerivatives 4.0",
    "VSL-1.0": "Vovida Software License 1.0",
    "AAL": "Attribution Assurance Licenses",
    "CPAL-1.0": "Common Public Attribution License 1.0",
    "Watcom-1.0": "Sybase Open Watcom Public License 1.0",
    "OGTSL": "Open Group Test Suite License",
    "EPL-1.0": "Eclipse Public License 1.0"
}

During the publication phase, the identifier of the license chosen must be passed.

Stock Publication Example

The publish method to invoke to publish a stock is the following

base_url/stock/publish-product?gcube-token=YOUR_TOKEN

The JSON object you must provide in input has the following structure (of course, not all fields are mandatory)

{
   "description": ...,
   "license_id": ...,
   "version": ...,
   "maintainer": ...,
   "maintainer_contact": ...,
   "catches_or_landings": ...,
   "database_sources": [{...}, ...],
   "source_of_information": [{...}, ...],
   "data_owner": ...,
   "type": ...,
   "stock_name": ...,
   "stock_id": ...,
   "species_scientific_name": ...,
   "assessment_distribution_area": ...,
   "exploiting_fishery": ...,
   "management_entity": ...,
   "assessment_methods": ...,
   "state_of_marine_resource": ...,
   "exploitation_rate": ...,
   "abundance_level": ...,
   "narrative_state_and_trend": ...,
   "scientific_advice": ...,
   "reporting_entity": ...,
   "reporting_year": ...,
   "status": ...
}

Fishery Publication Example

The publish method to invoke to publish a fishery product is the following

base_url/stock/publish-product?gcube-token=YOUR_TOKEN

The JSON object you must provide in input has the following structure (of course, not all fields are mandatory)

{
   "description": ...,
   "license_id": ...,
   "version": ...,
   "maintainer": ...,
   "maintainer_contact": ...,
   "catches_or_landings": ...,
   "database_sources": [{...}, ...],
   "source_of_information": [{...}, ...],
   "data_owner": ...,
   "type": ...,
   "fishery_name": ...,
   "fishery_id": ...,
   "scientific_name": ...,
   "fishing_area": ...,
   "exploited_stocks": ...,
   "management_entity": ...,
   "jurisdiction_area": ...,
   "production_system_type": ...,
   "flag_state": ...,
   "fishing_gear": ...,
   "status":...,
   "environment":..
}

How To Publish a GRSF product using JAVA

Below you find a simple Java application publishing a GRSF product (i.e. a stock).

package [YOUR PACKAGE];

import org.apache.commons.httpclient.HttpClient;
import org.apache.commons.httpclient.HttpException;
import org.apache.commons.httpclient.MultiThreadedHttpConnectionManager;
import org.apache.commons.httpclient.methods.ByteArrayRequestEntity;
import org.apache.commons.httpclient.methods.PostMethod;
import org.apache.http.HttpStatus;
import org.apache.log4j.Logger;

/**
 * The Class GRSFPublishMetadata.
 *
 * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
 * Oct 13, 2016
 */
public class GRSFPublishMetadata {

	public static final Logger logger = Logger.getLogger(GRSFPublishMetadata.class);
	private static final String GRSF_PUBLISHER_REST_SERVICE_BASE_URL = "https://next.d4science.org/grsf-publisher-ws/rest/";

	/**
	 * The Enum PRODUCT_TYPE.
	 *
	 * @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
	 * Oct 13, 2016
	 */
	private static enum PRODUCT_TYPE{stock, fishery}
	private static final String PUBLISH_PRODUCT_REQUEST = "publish-product";
	private static final String GCUBE_TOKEN_PARAMETER = "gcube-token";
	private static final String GCUBE_TOKEN_VALUE = "XYZ"; //***********SET YOUR TOKEN************
	private static final String CONTENTTYPE = "application/json";
	private HttpClient httpClient = null;
	public static final int TIME_OUT_REQUESTS = 5000; //5 sec

	/**
	 * Instantiates a new GRSF publish metadata.
	 */
	public GRSFPublishMetadata() {
		MultiThreadedHttpConnectionManager connectionManager = new MultiThreadedHttpConnectionManager();
		connectionManager.getParams().setSoTimeout(TIME_OUT_REQUESTS);
		this.httpClient = new HttpClient(connectionManager);

	}

	/**
	 * Publish product.
	 *
	 * @param type the type
	 * @param body the body
	 * @return the string
	 * @throws Exception the exception
	 */
	public String publishProduct(PRODUCT_TYPE type, String body) throws Exception {
		// Create a method instance.
		String buildURL = GRSF_PUBLISHER_REST_SERVICE_BASE_URL + "/" + type.toString() +"/"+PUBLISH_PRODUCT_REQUEST +"?"+GCUBE_TOKEN_PARAMETER +"="+GCUBE_TOKEN_VALUE;
		PostMethod method = new PostMethod(buildURL);
		method.setRequestHeader("Content-type", CONTENTTYPE);
		logger.debug("call post to URI .... " + method.getURI());
		logger.debug("	the body is..." + body);
		method.setRequestEntity(new ByteArrayRequestEntity(body.getBytes()));
		byte[] responseBody = null;
		try {
			// Execute the method.
			int statusCode = httpClient.executeMethod(method);

			if (statusCode != HttpStatus.SC_OK && statusCode != HttpStatus.SC_CREATED) {
				logger.error("Method failed: " + method.getStatusLine()+"; Response bpdy: "+method.getResponseBody());
				method.releaseConnection();
				throw new Exception("Method failed: " + method.getStatusLine()+"; Response body: "+new String(method.getResponseBody()));
			}
			// Read the response body.
			responseBody = method.getResponseBody();

		} catch (HttpException e) {
			logger.error("Fatal protocol violation: ", e);
			method.releaseConnection();
			throw new Exception("Fatal protocol violation: " + e.getMessage());
		} catch (Exception e) {
			logger.error("Fatal transport error: ", e);
			method.releaseConnection();
			throw new Exception("Fatal transport error: " + e.getMessage());
		}
		method.releaseConnection();
		return new String(responseBody);
	}

	/**
	 * The main method.
	 *
	 * @param args the arguments
	 */
	public static void main(String[] args) {
		try {
			GRSFPublishMetadata grsfP = new GRSFPublishMetadata();
			String minimal_json_stock = "YOUR STOCK"; //***********SET YOUR STOCK************
			String response = grsfP.publishProduct(PRODUCT_TYPE.stock, minimal_json_stock);
			logger.info("The Response: "+response);
		}catch (Exception e) {
			e.printStackTrace();
		}
	}

}

You must use the following dependencies (if you are using Maven):

<!-- COMMONS HTTP -->
<dependency>
    <groupId>commons-httpclient</groupId>
    <artifactId>commons-httpclient</artifactId>
    <version>3.1</version>
</dependency>
<!-- LOGS -->
<dependency>
  <groupId>log4j</groupId>
  <artifactId>log4j</artifactId>
  <version>1.2.16</version>
</dependency>
<dependency>
  <groupId>org.slf4j</groupId>
  <artifactId>slf4j-log4j12</artifactId>
  <version>1.6.4</version>
</dependency>
<dependency>
  <groupId>org.slf4j</groupId>
  <artifactId>slf4j-api</artifactId>
  <version>1.6.4</version>
</dependency>