GCube Data Catalogue for GRSF

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** THIS PAGE IS UNDER CONSTRUCTION **

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. The service allows also to publish records belonging to the original source records (i.e., "RAM", "FishSource" and "FIRMS") on which the aggregated GRSF records are build.

Metadata

Base 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.

The table also reports the column Type that shows how the field is mapped into the product, once it is published within the catalogue, i.e. as a simple field (key/value pair, possibly repeatable) or a resource (an object with a mandatory name, an optional description and a mandatory url).

IMPORTANT: Any other field that doesn't match one of the below ones will be managed as an object having a key and a value, both of String type, and attached to the product as a simple field.

Name Api Name (JSON) Display Section Mandatory (No, Aggregated, All) * Is Tag (Aggregated records only) Is Group Is Sensitive Type Example Guidelines/Comments
Title stock_name or fishery_name Top of the record All No No No Field Hippoglossoides platessoides - Atlantic, Northwest / 21.5.Y - Atlantic, Northwest / 21.5.Z - https://data.d4science.org/ctlg/GRSF_Admin/f6342402-b5fb-3457-9b49-c0a018f2ce72 The name of the stock or fishery
Description description Top of the record No No No No Field This product contains attributes of ... A brief description of the dataset written in plain language. It should provide a sufficiently comprehensive overview of the resource for anyone to understand its content origins and any continuing work on it.
License license_id Right panel All No No No Field CC-BY-SA-4.0 The list of licenses' ids can be retrieved by using the service (see below). By default the CC-BY-SA-4.0 will be used.
Author author Management Info No No No No Field Bloggs, Joe This field is automatically compiled by using the information of the caller entity.
Author contact author_contact Management Info No No No No Field joe.blogg@example.com This field is automatically compiled by using the information of the caller entity
Version version Management Info No No No No Field 1.0 Increase manually after editing
Maintainer maintainer Management Info No No No No Field A person: Bloggs, Joe. An authority: D4Science Mantainer of the dataset
Maintainer Contact maintainer_contact Management Info No No No No Field joe@example.com Contact details of the resource maintainer.
Extra Fields extras_fields Additional Info No No No No Field(s) "extras_fields":{"other_key":[{"value1", "value2", ...}], "other_keyN": [{"valueN" "valueM"}]} It is a map of objects <key, list of values> that allows to dynamically add extra fields if the list of recognized fields by the service doesn't fit some needs.
Extra Resources extras_resources Data and Resources No No No No Resources(s) "extras_resources":[{"url": "http:// .....", "name": "...", "description":"...."}, ....] It is a list of objects of the type {"url": ..., "name": ...., "description": ...} that allows to dynamically add extra resources if the list of recognized resources by the service doesn't fit some needs. Please note that "url" and "name" are mandatory.

* specifies if an attribute is not mandatory (No), mandatory for GRSF aggregated records (Aggregated) or is mandatory for every record (All)

Common Metadata

Besides the above common metadata, there is the following set of attributes that are captured for both Stock and Fishery records.

Name Api Name (JSON) Display Section Mandatory (No, Aggregated, All) * Is Tag (Aggregated records only) Is Group Is Sensitive Type Example Guidelines/Comments
GRSF Type grsf_type Fishery Identity/Stock Identity All Yes (Controlled vocabulary: "Fishing Unit", "Other Fishery", "Assessment Unit", "Marine Resource") No No Field Controlled vocabulary: "Fishing Unit", "Other Fishery", "Assessment Unit", "Marine Resource" Automatically compiled
Source N/A N/A Aggregated No No No Field Any combination of the following values: "FIRMS", "RAMS" or "FishSource". RAM/FishSource/FIRMS records don't have this property. Automatically compiled
Data Owner data_owner Fishery Data/Stock Data No No No Yes Field e.g. IATTC
Database Source database_sources Fishery Identity/Stock Identity Aggregated No No No Resource "database_sources": [{"name":"FIRMS", "description": "unknown", "url":"http://....."}, ...] A list of elements of the type {"name": "a name", "description": "a description", "url": "http://...."}. Name and url are mandatory. For the attribute name there is a controlled vocabulary: FIRMS, RAM, FishSource.
Source of Information source_of_information Data and Resources (Generate a Resource) No No No No Resource "source_of_information" : [{"name":"...", "description": "...", "url":"http://....."},...] A list of elements of the type {"name": "a name", "description": "a description", "url": "http://...."}. Name and url are mandatory.
Refers To refers_to Data and Resources (Generate a Resource) Aggregated No No No Resource Check the record http://data.d4science.org/ctlg/GRSF_Admin/f82393dd-d23a-3c26-98d3-ccc5f7910266 The JSON submitted by KB contains: "refers_to" : [ { "id" : "c29b2485-c33f-3c03-8790-55a1dcf045ed", "url" : "http://data.d4science.org/ctlg/GRSF_Admin/c29b2485-c33f-3c03-8790-55a1dcf045ed"}]. The reference is in the generated resource FIRMS A list of objects of the format {"url": "http://", "id": "..."} that allows the aggregated GRSF records to point to their source records already published in the catalogue. The URL and the id are both mandatory and are the ones returned by the services when a source record is published.
Short Name short_name Stock Identity/Fishery Identity Aggregated No No No Field American Plaice NAFO-5YZ - https://data.d4science.org/ctlg/GRSF_Admin/f6342402-b5fb-3457-9b49-c0a018f2ce72 A short name for this product
SDG Flag sdg_flag Additional Info Yes No Yes (The group is assigned only if the value is true - "GRSF SDG Flag":grsf-sdg-flag) No Field true or false Available only in record https://data.d4science.org/ctlg/GRSF/a676350b-c37c-3754-aa64-13ad407f829e
Status of the Record status_grsf_record Additional Info Aggregated No No No Field Pending Controlled vocabulary: Pending, Rejected, Confirmed, Archived, Hidden, Merged (i.e. when the aggregated record comes out from more than one source record)
Catch catches Stock Data/Fishery Data No No Yes (Catch) Yes Resource "catches": [{"unit" : "...", "value": "...", "year": "..."}, ...] A time series of value, unit and date
Landing landings Stock Data/Fishery Data No No Yes (Landing) Yes Resource "landings": [{"unit" : "...", "value": "...", "year": "..."}, ...] A time series of value, unit and date
Species species Stock Identity/Fishery Identity Aggregated Yes No No Field (repeatable) The multiple fields are mapped as multiple key/value pair fields in the catalogue.
Similar GRSF Record similar_grsf_records Stock Identity/Fishery Identity Aggregated No No No Field (repeatable)
Domain N/A Additional Info All No Yes (Stock or Fishery). The group is not generated using an annotation on domain field No Field Automatically set to Stock or Fishery.
GRSF UUID grsf_uuid Additional Info All No No No Field The id of this Stock/Fishery object into the Knowledge Base. It must be unique because will be used as name of the published product.
Management Body/Authority management_body_authorities Stock Identity/Fishery Identity Aggregated No No No Field
Geospatial spatial Additional Info No No No No Field 2005
Connected Record connected Stock Identity/Fishery Identity Aggregated No No No Field [ "https://data.d4science.org/ctlg/GRSF_Admin/331e1999-c640-3482-a905-ee8a27ead94e", ...., "https://data.d4science.org/ctlg/GRSF_Admin/695c64b9-425c-3fb9-8c17-a1948f5d3f5f" ] A list of URI fo connected records
N/A connections_indicator N/A Aggregated Yes (connected, not connected) No No Field "connections_indicator" : "not connected" OR "connections_indicator" : "connected", USED only for tagging. The indication if the record is connected or not. The above field (i.e. connected) is sufficient but this field allows automatic tagging because of service internals. https://support.d4science.org/issues/11766
Annotation annotations Additional Info No No No Yes Field {"annotation_message":"checked together with Paula Anton","admin":"Aureliano Gentile","time":"2018-07-27 14:58:13 CET"} The example is from record https://data.d4science.org/ctlg/GRSF_Admin/22657fbf-41fb-3c10-90bd-6244b38d4e05
N/A similarities_indicator N/A N/A Yes ("with similar records", "without similar records") No No N/A Tag values are: "with similar records", "without similar records" USED only for tagging.
Citation citation Additional Info + Top Button No No No No Field © D4Science.org. Hippoglossoides platessoides - Atlantic, Northwest / 21.5.Y - Atlantic, Northwest / 21.5.Z. In: Global Record of Stocks and Fisheries (GRSF). Consiglio Nazionale delle Ricerche, CNR. Version: 1.0. Updated: June 14, 2021. Accessed: [Date accessed and/or downloaded]. http://data.d4science.org/ctlg/GRSF_Admin/f6342402-b5fb-3457-9b49-c0a018f2ce72. Database sources: [FishSource, RAM] Using the button the part [Date accessed and/or downloaded] is replaced with the current time e.g. Fri Jan 21 2022 11:32:51 GMT+0100 (Central European Standard Time).

* specifies if an attribute is not mandatory (No), mandatory for GRSF aggregated records (Aggregated) or is mandatory for every record (All)

Stock Metadata

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

Name API Name Display Section Mandatory (No, Aggregated, All) * Is Tag (Aggregated records only) Is Group Is Sensitive Type Example Guidelines/Comments
GRSF Stock Name stock_name Stock Identity + Top of the record All No No No Field Skipjack tuna - Eastern Pacific The title of the record/item.
GRSF Semantic Identifier grsf_semantic_identifier Stock Identity + Top of the record All No No No Field asfis:PLA+fao:21.5.Y;fao:21.5.Z
Assessment Area assessment_area Stock Identity No Yes No No Field (repeatable) "assessment_distribution_area": ["East Pacific Ocean",...] The multiple fields are mapped as multiple key/value pair fields in the catalogue.
Exploiting Fishery exploiting_fishery Stock Identity No No No No Field (repeatable) "exploiting_fishery": ["Tunas and billfishes fishery", ....] The multiple fields are mapped as multiple key/value pair fields in the catalogue.
Assessment Method assessment_methods Stock Data No No Yes (Group name: "Assessment Method") Yes Field Analytical assessment
Abundance Level (FIRMS Standard) firms_standard_abundance_level Stock Data No No Yes (Group name: "Abundance Level (FIRMS Standard)") Yes Resource "standard_abundance_level" : [{"year":2014, "value":"low abundance"}, {"year":2015, "value":"intermediate abundance"}, ...] Controlled vocabulary for "value": Not applicable, Intermediate abundance, Low abundance, Uncertain/Not assessed, Depleted
Abundance Level abundance_level Stock Data No No Yes (Group name: "Abundance Level") Yes Resource "abundance_level": [{"year":2014, "value":"low abundance", "unit": "..."}, {"year":2015, "value":"intermediate abundance", "unit": "..."}, ...]
Biomass biomass Stock Data No No Yes (Group name: "Biomass") Yes Resource "biomass": [{"year":2014, "value": 123, "unit": "..."}, {"year":2015, "value": 172, "unit": "..."}, ...]
Fishing Pressure (FIRMS Standard) firms_standard_fishing_pressure Stock Data No No Yes (Group name: "Fishing Pressure (FIRMS Standard)") Yes Resource "standard_fishing_pressure" : [{"year":2014, "value":"..."}, {"year":2015, "value":"..."}, ...]
Fishing Pressure fishing_pressure Stock Data No No Yes (Group name: "Fishing Pressure") Yes Resource "fishing_pressure": [{"year":2014, "value":"...", "unit": "..."}, {"year":2015, "value":"...", "unit": "..."}, ...]
State and Trend state_and_trend_of_marine_resources Stock Data No No Yes (Group name: "State and Trend") Yes Resource
FAO Stock Status Category fao_categories Stock Data No No Yes (Group name: "FAO Stock Status Category") Yes Resource e.g. overexploited [Ref. Year: 2011] Time Series
Scientific Advice scientific_advice Stock Data No No Yes(Group name: "Scientific Advice") Yes Field The indices of abundance from two longline fleets available for this stock present divergent trends over the last few years, the differences observed in targeting are not fully explained. e.g. overexploited [Ref. Year: 2011] A textual description.
Assessor assessor Stock Data No No No Yes Field GRP3
GRSF Type grsf_type Stock Identity All Yes (Controlled vocabulary: "Assessment Unit", "Marine Resource") No No Field Controlled vocabulary: "Assessment Unit", "Marine Resource" Automatically compiled

* specifies if an attribute is not mandatory (No), mandatory for GRSF aggregated records (Aggregated) or is mandatory for every record (All)

Fishery Metadata

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

Name API Name Display Section Mandatory (No, Aggregated, All) * Is Tag (Aggregated records only) Is Group Is Sensitive Type Example Guidelines/Comments
GRSF Fishery Name fishery_name Fishery Identity + Top of the record All No No No Field NAFO Flemish Cap groundfish fisheries The title of the record/item.
GRSF Semantic identifier grsf_semantic_identifier Fishery Identity + Top of the record All No No No Field unk:GOLDEYE+fao:2+authority:NAT:CAN+iso3:CAN+isscfg:07.9 Example from https://data.d4science.org/ctlg/GRSF_Admin/de98c17e-6418-4cd0-8929-4ad0f63dbff8
Traceability Flag traceability_flag Fishery Identity Aggregated No Yes (The group is assigned only if the value is true - "GRSF Traceability Flag":grsf-traceability-flag) No Field A boolean value
Fishing Area fishing_area Fishery Identity No Yes No No Field (repeatable) "fishing_area": ["North Atlantic", .... ] A list of values. If missing then Jurisdiction Area cannot be null
Jurisdiction Area jurisdiction_area Fishery Identity No Yes No No Field (repeatable) "jurisdiction_area": ["Senegal", "..."] If missing then Fishing Area cannot be null
Resources Exploited resources_exploited Fishery Identity No No No No Field (repeatable)
Flag State flag_state Fishery Identity No Yes No No Field (Repeatable in case of RAM, FIRMS, FishSource records, a single value for GRSF records) Example field is "Code: PHL, System: iso3, Name: Philippines". The tag will be "Code PHL System iso3 Name Philippines".
Fishing Gear fishing_gear Fishery Identity No Yes No No Field (Repeatable in case of RAM, FIRMS, FishSource records, a single value for GRSF records) Example is "Code: SFP-16, System: sfp, Name: FAD-free purse seining". The tag will be "Code SFP-16 System sfp Name FAD-free purse seining".
GRSF Type grsf_type Fishery Identity All Yes (Controlled vocabulary: "Fishing Unit", "Other Fishery") No No Field Controlled vocabulary: "Fishing Unit", "Other Fishery" Automatically compiled

* specifies if an attribute is not mandatory (No), mandatory for GRSF aggregated records (Aggregated) or is mandatory for every record (All)

GRSF Publication Web Service

Records publication is performed by means of a RESTful web service running over SmartGears. Almost every call to the service requires the security token of the user for the context in which he/she wants 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 GRSF service in a context can be discovered by means of the Information System [1]. You need the following parameters

Service Name = GRSFPublisher
Service Class = Data-Catalogue
Entry Name = jersey-servlet

For testing purpose, a running instance can be contacted at the following address

https://smart-grsf-d-d4s.d4science.org/grsf-publisher-ws/rest/  [GRSF_PUBLISHER_WS_BASE_URL]

The token for testing purpose can be retrieved from the VRE at this url https://next.d4science.org/group/nextnext/home (register yourself if needed). In the following, every time you perform a request you must specify the type of record for which it will be valid, i.e., in the request path you need to specify a value among:

  • grsf;
  • fishsource;
  • ram;
  • firms.

Please check the Troubleshooting section in case of errors on publication phase.

Check Service Availability

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

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/fishery/hello

Specify the record type by replacing {...}. The response should look like

Hello.. Fishery service is here

or

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/stock/hello

and the response should look like

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

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/fishery/get-licenses?gcube-token=YOUR_TOKEN

or, for stock

[GRSF_PUBLISHER_WS_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",
    ....
}

During the publication phase, the identifier of the license chosen should be provided.

Stock Publication Example

The publish method to invoke to publish a stock for rams, grsf, fishsource or ram is the following

[GRSF_PUBLISHER_WS_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":...,
    "database_sources":[...],
    "source_of_information":[...],
    "uuid_knowledge_base":...,
    "traceability_flag":..,
    "data_owner":...,
    "type":...,
    "stock_name":...,
    "stock_id":...,
    "stock_uri":...,
    "species":[...],
    "assessment_distribution_area":[...],
    "exploiting_fishery":[...],
    "management_entity":...,
    "assessment_methods":...,
    "state_of_marine_resource":...,
    "standard_exploitation_rate":[...],
    "standard_abundance_level":[...],
    "water_area":[...],
    "narrative_state_and_trend":...,
    "scientific_advice":...,
    "reporting_entity":...,
    "reporting_year":...,
    "status":...,
    "short_title":...,
    "refers_to":[...]
}

The response of the method is a JSON object of this kind

{
   "id": ... , // identifier of the created product in the catalogue
   "knowledge_base_id" : .... // identifier of the product in the knowledge base
   "product_url": ..., // url of the created product
   "error": ... // in case of error, check this field
}

In case of success the HTTP code is 201 (CREATED) and the response contains the url and the unique identifier assigned to the product. In case of errors (BAD_REQUEST, INTERNAL_SERVER_ERROR, FORBIDDEN ... ) the "error" message of the above object reports what was wrong.

Example

A valid JSON, for example, is the following one

/*TODO*/

the response obtained from the service is

/*TODO*/

Fishery Publication Example

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

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/fishery/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": [...],
   "uuid_knowledge_base" : ...,
   "traceability_flag": ...,
   "short_title": ...,
   "refers_to":[...],
   "data_owner": ...,
   "reporting_year": …,
   "type": ...,
   "fishery_name": ...,
   "fishery_id": ...,
   "scientific_name": ...,
   "fishing_area": [...],
   "exploited_stocks": [...],
   "management_entity": ...,
   "jurisdiction_area": ...,
   "production_system_type": ...,
   "flag_state": ...,
   "fishing_gear": ...,
   "status": ...,
   "environment”: ...
}

The response of the method is a JSON object of this kind

{
   "id": ... , // identifier of the created product in the catalogue
   "knowledge_base_id" : .... // identifier of the product in the knowledge base
   "product_url": ..., // url of the created product
   "error": ... // in case of error, check this field
}

In case of success the HTTP code is 201 (CREATED) and the response contains the url and the unique identifier assigned to the product. In case of errors (BAD_REQUEST, INTERNAL_SERVER_ERROR, FORBIDDEN ... ) the "error" message of the above object reports what was wrong.

Example

A valid JSON, for example, is the following one

/* TODO */

the response obtained from the service is

/* TODO */

Delete a published product

If for some reason you need to delete a published product, you can invoke the following delete http methods. For fishery it is

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/fishery/delete-product?gcube-token=YOUR_TOKEN

whereas for stock

[GRSF_PUBLISHER_WS_BASE_URL]/{...}/stock/delete-product?gcube-token=YOUR_TOKEN

You must provide the identifier (returned back at creation time) of the product, in a JSON that looks like

{"id": "product-to-delete-identifier"}

The response status of the service, in case of success is 200 (OK)

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 = [YOUR TOKEN]; //***********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 =
			   "{\"description\":\"This stock product was generated for testing purposes, to show how publication works. Please refer to https://wiki.gcube-system.org/gcube/GCube_Data_Catalogue_for_GRSF for more information\"," +
			   "\"license_id\":\"CC-BY-SA-4.0\"," +
			   "\"version\":1," +
			   "\"maintainer\":\"Francesco Mangiacrapa\","+
			   "\"maintainer_contact\":\"francesco.mangiacrapa@isti.cnr.it\","+
			   "\"catches_or_landings\":\"unknown\","+
			   "\"database_sources\":["+
			      "{\"name\":\"RAM\",\"url\":\"test url\"}" +
			      "]" +
			    ",\"source_of_information\":[{\"name\":\"the source of information\",\"url\":\"http://www.google.com\"}" +
			    "]," +
			   "\"data_owner\":\"IATTC\","+
			   "\"type\":\"Assessment Unit\","+
			   "\"stock_name\":\"Skipjack tuna - Western Pacific\","+ //YOU MUST CHANGE THE STOCK NAME FOR TESTING
			   "\"stock_id\":\"SKJ - EPO - TESTING\","+
			   "\"species_scientific_name\":\"SKJ\","+
			   "\"assessment_distribution_area\":\"Western Pacific\","+
			   "\"exploiting_fishery\":\"Tunas and billfishes fishery\","+
			   "\"management_entity\":\"DFO\","+
			   "\"assessment_methods\":\"Analytical assessment\","+
			   "\"state_of_marine_resource\":null,"+
			   "\"exploitation_rate\":\"High fishing mortality\","+
			   "\"abundance_level\":\"Intermediate abundance\","+
			   "\"narrative_state_and_trend\":\"Stock size and fishing pressure are considered to be close to their value at MSY.\","+
			   "\"scientific_advice\":\"The indices of abundance from two longline fleets available for this stock present divergent trends over the last few years, the differences observed in targeting are not fully explained.\","+
			   "\"reporting_entity\":\"GRP3\","+
			   "\"reporting_year\":2016,"+
			   "\"status\":\"pending\"}";

			String response = grsfP.publishProduct(PRODUCT_TYPE.stock, minimal_json_stock);
			logger.info("The Response: "+response);
		}catch (Exception e) {
			e.printStackTrace();
		}
	}

}

The response should look like:


call post to URI .... https://next.d4science.org/grsf-publisher-ws/rest/stock/publish-product?gcube-token=[YOUR TOKEN]
the body is...{"description":"This stock product was generated for testing purposes, to show how publication works. Please refer to https://wiki.gcube-system.org/gcube/GCube_Data_Catalogue_for_GRSF for more information","license_id":"CC-BY-SA-4.0","version":1,"maintainer":"Francesco Mangiacrapa","maintainer_contact":"francesco.mangiacrapa@isti.cnr.it","catches_or_landings":"unknown","database_sources":[{"name":"RAM","url":"test url"}],"source_of_information":[{"name":"the source of information","url":"http://www.google.com"}],"data_owner":"IATTC","type":"Assessment Unit","stock_name":"Skipjack tuna - Western Pacific Ocean 4","stock_id":"SKJ - EPO - TESTING","species_scientific_name":"SKJ","assessment_distribution_area":"Western Pacific Ocean 4","exploiting_fishery":"Tunas and billfishes fishery","management_entity":"DFO","assessment_methods":"Analytical assessment","state_of_marine_resource":null,"exploitation_rate":"High fishing mortality","abundance_level":"Intermediate abundance","narrative_state_and_trend":"Stock size and fishing pressure are considered to be close to their value at MSY.","scientific_advice":"The indices of abundance from two longline fleets available for this stock present divergent trends over the last few years, the differences observed in targeting are not fully explained.","reporting_entity":"GRP3","reporting_year":2016,"status":"pending"}
The Response: {"id":"8426bce9-15b9-4c4a-a526-e829882b91ec","dataset_url":"https://next.d4science.org/group/nextnext/data-catalogue?path=/dataset/skipjack_tuna_-_western_pacific_ocean_4","error":null}

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>

GRSF records - manage facility

GRSF records will be validated by experts, in order to check that they have been properly generated starting from source (i.e., FIRMS, RAM and FishSource) records. The GRSF Admin VRE is the environment dedicated to this activity. It will offer a manage facility to users having the GRSF Administrator role's rights.

By pushing on the "Manage Item" button when a GRSF record is selected, the manage panel shows up to report a summary of the item and currently allows to:

  • change the current status;
  • add an annotation message for the ongoing change.

The updates to the record will be notified to the Knowledge Base of GRSF records before any change is reflected to the catalogue.

Troubleshooting

Here are reported solutions to some of the errors may arise while you try to publish items. Generally, the error is specified in the message field of the returned JSON. In case it is empty but still the success field is set to false, then you should take in consideration the following:

  • Tags: they must have a length within the range [2, 100] characters

References

  1. Information System can be queried via ic-client read more