semantic identifier is modified by the service, changed system:type to fishery and stocks. Other minor changes in resource names. Version is 1.4.0

git-svn-id: https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-catalogue/grsf-publisher-ws@153263 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>org.gcube.data-catalogue</groupId>
 	<artifactId>grsf-publisher-ws</artifactId>
-	<version>1.3.0-SNAPSHOT</version>
+	<version>1.4.0-SNAPSHOT</version>
 	<packaging>war</packaging>
 	<name>grsf-publisher-ws</name>
 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/record/FisheryRecord.java

@@ -115,7 +115,22 @@ public class FisheryRecord extends Common{
 	}
 
 	public void setFisheryId(String fisheryId) {
-		this.fisheryId = fisheryId;
+		String fisheryIdmodified = "";
+		if(fisheryId != null){
+			
+			String[] splitCodesValues = fisheryId.split("+");
+			for (int i = 0; i < splitCodesValues.length; i++) {
+				String prefixAndCode = splitCodesValues[i];
+				String prefix = prefixAndCode.split(":")[0];
+				String code = prefixAndCode.split(":")[1];
+				fisheryIdmodified += prefix.toLowerCase() + ":" + code.toUpperCase();
+				if(splitCodesValues.length > 1 && i < (splitCodesValues.length - 1))
+					fisheryIdmodified += "+";
+			}
+		}
+		
+		this.fisheryId = fisheryIdmodified;
+		
 	}
 
 	public List<String> getFishingArea() {

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/json/input/record/StockRecord.java

@@ -180,7 +180,22 @@ public class StockRecord extends Common{
 	}
 
 	public void setStockId(String stockId) {
-		this.stockId = stockId;
+		
+		String stockIdmodified = "";
+		if(stockId != null){
+			
+			String[] splitCodesValues = stockId.split("+");
+			for (int i = 0; i < splitCodesValues.length; i++) {
+				String prefixAndCode = splitCodesValues[i];
+				String prefix = prefixAndCode.split(":")[0];
+				String code = prefixAndCode.split(":")[1];
+				stockIdmodified += prefix.toLowerCase() + ":" + code.toUpperCase();
+				if(splitCodesValues.length > 1 && i < (splitCodesValues.length - 1))
+					stockIdmodified += "+";
+			}
+		}
+		
+		this.stockId = stockIdmodified;	
 	}
 
 	public List<String> getArea() {

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherFisheryService.java

@@ -29,7 +29,6 @@ import org.gcube.common.authorization.library.provider.AuthorizationProvider;
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.authorization.library.utils.Caller;
 import org.gcube.common.scope.api.ScopeProvider;
-import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.Common;
 import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.FisheryRecord;
 import org.gcube.data_catalogue.grsf_publish_ws.json.input.utils.DeleteProductBean;
 import org.gcube.data_catalogue.grsf_publish_ws.json.output.ResponseBean;
@@ -40,6 +39,7 @@ import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Product_Type;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Sources;
 import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogue;
 import org.gcube.datacatalogue.ckanutillibrary.shared.ResourceBean;
+import org.gcube.datacatalogue.ckanutillibrary.shared.RolesCkanGroupOrOrg;
 import org.slf4j.LoggerFactory;
 
 import eu.trentorise.opendata.jackan.model.CkanDataset;
@@ -109,13 +109,16 @@ public class GrsfPublisherFisheryService {
 				String apiKey = catalogue.getApiKeyFromUsername(username);
 				String organization =  HelperMethods.retrieveOrgNameFromScope(context); //"grsf_admin";
 				CommonServiceUtils.hasAdminRole(username, catalogue, apiKey, organization);
+				
+				// extend this role to the other organizations in this context
+				CommonServiceUtils.extendRoleToOtherOrganizations(username, catalogue, organization, RolesCkanGroupOrOrg.ADMIN);
 
 				// retrieve the user's email and fullname
 				String authorMail = HelperMethods.getUserEmail(context, token);
 				String authorFullname = HelperMethods.getUserFullname(context, token);
 
 				if(authorMail == null || authorFullname == null){
-					throw new Exception("Sorry but there was not possible to retrieve your fullname/email!");
+					throw new Exception("Sorry but it was not possible to retrieve your fullname/email!");
 				}
 
 				// The name of the product will be the uuid of the kb. The title will be the fishery's fishery_name. Fishery has also the constraint that
@@ -155,6 +158,8 @@ public class GrsfPublisherFisheryService {
 					throw new Exception("Failed to retrieve the namespaces for the key fields!");
 
 				customFields = HelperMethods.replaceFieldsKey(customFields, namespaces);
+				
+				String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
 
 				logger.info("Invoking create method..");
 
@@ -163,7 +168,7 @@ public class GrsfPublisherFisheryService {
 						apiKey, 
 						futureTitle, 
 						futureName,
-						organization, 
+						publishInOrganization, 
 						authorFullname, 
 						authorMail, 
 						record.getMaintainer() == null? authorFullname : record.getMaintainer(), 
@@ -241,10 +246,10 @@ public class GrsfPublisherFisheryService {
 			}
 
 			// check it is in the right source and it is a fishery
-			String grsfTypeValue = fisheryInCkan.getExtrasAsHashMap().get(Common.GRSF_DOMAIN_KEY);
+			String systemType = fisheryInCkan.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
-			String systemTypeValue = fisheryInCkan.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
 
-			if(systemTypeValue.equalsIgnoreCase(source) && Product_Type.FISHERY.getOrigName().equals(grsfTypeValue)){
+			if(fisheryInCkan.getOrganization().getName().equalsIgnoreCase(source) && 
+					CommonServiceUtils.SYSTEM_TYPE_FISHERY.equals(systemType)){
 
 				logger.debug("Ok, this is a fishery of the right source, removing it");
 				boolean deleted = catalogue.deleteProduct(fisheryInCkan.getId(), apiKey, true);
@@ -300,13 +305,13 @@ public class GrsfPublisherFisheryService {
 			if(sourceInPath.equals(Sources.GRSF))
 				datasetsIds = HelperMethods.getProductsInGroup(source + "-" + "fishery", catalogue);
 			else{
-				List<String> fullGroupListIds = HelperMethods.getProductsInGroup(source, catalogue);
+				List<String> fullGroupListIds = HelperMethods.getProductsInOrganization(source, catalogue);
 				String apiKey = catalogue.getApiKeyFromUsername(username);
 				for (String id : fullGroupListIds) {
 					CkanDataset dataset = catalogue.getDataset(id, apiKey);
 					if(dataset != null){
-						String grsfType = dataset.getExtrasAsHashMap().get(Common.GRSF_DOMAIN_KEY);
+						String type = dataset.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
-						if(grsfType.equals(Product_Type.FISHERY.getOrigName()))
+						if(CommonServiceUtils.SYSTEM_TYPE_FISHERY.equals(type))
 							datasetsIds.add(id);
 					}
 				}
@@ -476,6 +481,8 @@ public class GrsfPublisherFisheryService {
 
 				// replace fields
 				customFields = HelperMethods.replaceFieldsKey(customFields, namespaces);
+				
+				String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
 
 				logger.info("Invoking update method..");
 
@@ -484,7 +491,7 @@ public class GrsfPublisherFisheryService {
 						apiKey, 
 						catalogId, 
 						title, name, 
-						organization, 
+						publishInOrganization, 
 						authorFullname, 
 						authorMail, 
 						record.getMaintainer(), 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/services/GrsfPublisherStockService.java

@@ -29,7 +29,6 @@ import org.gcube.common.authorization.library.provider.AuthorizationProvider;
 import org.gcube.common.authorization.library.provider.SecurityTokenProvider;
 import org.gcube.common.authorization.library.utils.Caller;
 import org.gcube.common.scope.api.ScopeProvider;
-import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.Common;
 import org.gcube.data_catalogue.grsf_publish_ws.json.input.record.StockRecord;
 import org.gcube.data_catalogue.grsf_publish_ws.json.input.utils.DeleteProductBean;
 import org.gcube.data_catalogue.grsf_publish_ws.json.output.ResponseBean;
@@ -40,6 +39,7 @@ import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Product_Type;
 import org.gcube.data_catalogue.grsf_publish_ws.utils.groups.Sources;
 import org.gcube.datacatalogue.ckanutillibrary.server.DataCatalogue;
 import org.gcube.datacatalogue.ckanutillibrary.shared.ResourceBean;
+import org.gcube.datacatalogue.ckanutillibrary.shared.RolesCkanGroupOrOrg;
 import org.slf4j.LoggerFactory;
 
 import eu.trentorise.opendata.jackan.model.CkanDataset;
@@ -111,6 +111,9 @@ public class GrsfPublisherStockService {
 
 				// check it has admin role or throw exception
 				CommonServiceUtils.hasAdminRole(username, catalogue, apiKey, organization);
+				
+				// extend this role to the other organizations in this context
+				CommonServiceUtils.extendRoleToOtherOrganizations(username, catalogue, organization, RolesCkanGroupOrOrg.ADMIN);
 
 				// retrieve the user's email and fullname
 				String authorMail = HelperMethods.getUserEmail(context, token);
@@ -170,6 +173,8 @@ public class GrsfPublisherStockService {
 					throw new Exception("Failed to retrieve the namespaces for the key fields!");
 
 				customFields = HelperMethods.replaceFieldsKey(customFields, namespaces);
+				
+				String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
 
 				logger.info("Invoking create method..");
 
@@ -178,7 +183,7 @@ public class GrsfPublisherStockService {
 						apiKey, 
 						futureTitle, 
 						futureName,
-						organization,
+						publishInOrganization,
 						authorFullname, 
 						authorMail, 
 						record.getMaintainer() == null? authorFullname : record.getMaintainer(), 
@@ -256,10 +261,10 @@ public class GrsfPublisherStockService {
 			}
 
 			// check it is in the right source and it is a stock
-			String grsfTypeValue = stockInCkan.getExtrasAsHashMap().get(Common.GRSF_DOMAIN_KEY);
+			String systemType = stockInCkan.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
-			String systemTypeValue = stockInCkan.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
 
-			if(systemTypeValue.equalsIgnoreCase(source) && Product_Type.STOCK.getOrigName().equals(grsfTypeValue)){
+			if(stockInCkan.getOrganization().getName().equalsIgnoreCase(source) && 
+					CommonServiceUtils.SYSTEM_TYPE_STOCK.equals(systemType)){
 
 				logger.debug("Ok, this is a stock of the right type, removing it");
 				boolean deleted = catalogue.deleteProduct(stockInCkan.getId(), apiKey, true);
@@ -314,12 +319,12 @@ public class GrsfPublisherStockService {
 			if(sourceInPath.equals(Sources.GRSF))
 				datasetsIds = HelperMethods.getProductsInGroup(source + "-" + "stock", catalogue);
 			else{
-				List<String> fullGroupListIds = HelperMethods.getProductsInGroup(source, catalogue);
+				List<String> fullGroupListIds = HelperMethods.getProductsInOrganization(source, catalogue);
 				for (String id : fullGroupListIds) {
 					CkanDataset dataset = catalogue.getDataset(id, catalogue.getApiKeyFromUsername(username));
 					if(dataset != null){
-						String grsfType = dataset.getExtrasAsHashMap().get(Common.GRSF_DOMAIN_KEY);
+						String type = dataset.getExtrasAsHashMap().get(CommonServiceUtils.SYSTEM_TYPE);
-						if(grsfType.equals(Product_Type.STOCK.getOrigName()))
+						if(CommonServiceUtils.SYSTEM_TYPE_STOCK.equals(type))
 							datasetsIds.add(id);
 					}
 				}
@@ -484,6 +489,8 @@ public class GrsfPublisherStockService {
 
 				// replace fields
 				customFields = HelperMethods.replaceFieldsKey(customFields, namespaces);
+				
+				String publishInOrganization = CommonServiceUtils.evaluateOrganization(organization, sourceInPath);
 
 				logger.info("Invoking update method..");
 
@@ -492,7 +499,7 @@ public class GrsfPublisherStockService {
 						apiKey, 
 						catalogId, 
 						title, name, 
-						organization, 
+						publishInOrganization, 
 						authorFullname, 
 						authorMail, 
 						record.getMaintainer(), 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/CSVUtils.java

@@ -4,7 +4,9 @@ import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.OutputStreamWriter;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.gcube.data_catalogue.grsf_publish_ws.json.input.utils.TimeSeriesBean;
 import org.slf4j.LoggerFactory;
@@ -26,10 +28,11 @@ public class CSVUtils {
 	 * Write a time series to a csv file, and returns the file reference.<br>
 	 * Please give the timeSeries already sorted per year
 	 * @param timeSeries
+	 * @param relevantSources 
 	 * @param <T>
 	 * @param <T1>
 	 */
-	public static <T, T1> File listToCSV(List<TimeSeriesBean<T, T1>> timeSeries){
+	public static <T, T1> File listToCSV(List<TimeSeriesBean<T, T1>> timeSeries, String[] relevantSources){
 
 		if(timeSeries == null || timeSeries.isEmpty()){
 			logger.warn("The time series provided is null or empty ... " + timeSeries );
@@ -44,12 +47,14 @@ public class CSVUtils {
 				FileOutputStream fo = new FileOutputStream(file);
 				BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fo, "UTF-8"));
 
+				Set<String> sources = new HashSet<String>(3);
+
 				// discover how the header will look like 
 				boolean isUnitPresent = false;
 				boolean isValuePresent = false;
 				boolean isSourcePresent = false;
 				boolean isAssessmentPresent = false;
-				
+
 				for (TimeSeriesBean<T, T1> timeSeriesBean : timeSeries) {
 					if(timeSeriesBean.isSourcePresent())
 						isSourcePresent = true;
@@ -78,7 +83,7 @@ public class CSVUtils {
 					headerLine.append(CSV_SEPARATOR);
 					headerLine.append(TimeSeriesBean.SOURCE_FIELD);
 				}
-				
+
 				if(isAssessmentPresent){
 					headerLine.append(CSV_SEPARATOR);
 					headerLine.append(TimeSeriesBean.ASSESSMENT_FIELD);
@@ -107,8 +112,10 @@ public class CSVUtils {
 					if(isSourcePresent){
 						oneLine.append(CSV_SEPARATOR);
 						oneLine.append(bean.getSource() != null? bean.getSource() : "");
+						if(bean.getSource() != null && !bean.getSource().isEmpty())
+							sources.add(bean.getSource());
 					}
-					
+
 					if(isAssessmentPresent){
 						oneLine.append(CSV_SEPARATOR);
 						oneLine.append(bean.getAssessment() != null? bean.getAssessment() : "");
@@ -123,7 +130,12 @@ public class CSVUtils {
 
 				// file created
 				logger.debug("CSV file created correctly on this machine!");
-
+				
+				for (String source : sources) {
+					relevantSources[0] += source + "_";
+				}
+				relevantSources[0] = relevantSources[0].substring(0, relevantSources[0].length() - 1);
+				
 				// on exit delete it...
 				file.deleteOnExit();
 				return file;
@@ -133,6 +145,6 @@ public class CSVUtils {
 			return null;
 		}
 	}
-	
+
 
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/CommonServiceUtils.java

@@ -52,9 +52,12 @@ public class CommonServiceUtils {
 	private static final int TIME_SERIES_TAKE_LAST_VALUES = 5;
 	private static final String REGEX_TAGS = "[^\\s\\w-_.]";
 	public static final String SYSTEM_TYPE = "system:type";
+	public static final String SYSTEM_TYPE_STOCK = "GRSF Stock";
+	public static final String SYSTEM_TYPE_FISHERY = "GRSF Fishery";
 
 	// item url property
 	public static final String ITEM_URL_FIELD = "GRSF Record URL";
+	private static final String GRSF_ADMIN_ORGANIZATION_NAME = "grsf_admin";
 
 	/**
 	 * Retrieve the list of licenses for stocks and fisheries
@@ -450,7 +453,7 @@ public class CommonServiceUtils {
 		CommonServiceUtils.getTagsGroupsResourcesExtrasByRecord(tags, skipTags, groups, false, resources, false, customFields, record, username, sourceInPath);
 
 		// add the SYSTEM_TYPE
-		customFields.put(CommonServiceUtils.SYSTEM_TYPE, Arrays.asList(sourceInPath.getOrigName()));
+		customFields.put(CommonServiceUtils.SYSTEM_TYPE, productType.equals(Product_Type.STOCK)? Arrays.asList(SYSTEM_TYPE_STOCK) : Arrays.asList(SYSTEM_TYPE_FISHERY));
 	}
 
 	/**
@@ -568,4 +571,33 @@ public class CommonServiceUtils {
 			}
 		}).start();
 	}
+
+	/**
+	 * Extend roles to other organization
+	 * @param username
+	 * @param catalogue
+	 * @param organization
+	 * @param admin
+	 */
+	public static void extendRoleToOtherOrganizations(String username,
+			DataCatalogue catalogue, String organization,
+			RolesCkanGroupOrOrg admin) {
+
+		logger.debug("Checking if role extension is needed here");
+		catalogue.assignRolesOtherOrganization(username, organization, admin);
+
+	}
+
+	/**
+	 * Evaluate in which organization a record has to be published. The only expcetion is when grsf_admin is involved.
+	 * @param organization
+	 * @param sourceInPath
+	 * @return
+	 */
+	public static String evaluateOrganization(String organization, Sources sourceInPath) {
+		if(sourceInPath.equals(Sources.GRSF) && organization.equals(GRSF_ADMIN_ORGANIZATION_NAME))
+			return GRSF_ADMIN_ORGANIZATION_NAME;
+		else
+			return sourceInPath.getOrigName().toLowerCase();
+	}
 }

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/HelperMethods.java

@@ -493,6 +493,21 @@ public abstract class HelperMethods {
 	 * @throws SQLException 
 	 * @throws ClassNotFoundException 
 	 */
+	public static List<String> getProductsInOrganization(String groupName,
+			DataCatalogue catalogue) throws ClassNotFoundException, SQLException {
+
+		return catalogue.getProductsIdsInGroupOrOrg(groupName, true, 0, Integer.MAX_VALUE);
+
+	}
+	
+	/**
+	 * Retrieve the identifiers of the products in a given organization. It doesn't use CKAN API because they would return at most 1000 ids.
+	 * @param string
+	 * @param catalogue
+	 * @return
+	 * @throws SQLException 
+	 * @throws ClassNotFoundException 
+	 */
 	public static List<String> getProductsInGroup(String groupName,
 			DataCatalogue catalogue) throws ClassNotFoundException, SQLException {
 

src/main/java/org/gcube/data_catalogue/grsf_publish_ws/utils/threads/ManageTimeSeriesThread.java

@@ -194,7 +194,8 @@ public class ManageTimeSeriesThread extends Thread{
 
 									CkanResourceBase ckanResource = null;
 									ExternalFile createdFileOnWorkspace = null;
-									File csvFile = CSVUtils.listToCSV(asList);
+									String[] relevantSources = new String[1];
+  									File csvFile = CSVUtils.listToCSV(asList, relevantSources);
 									if(csvFile != null){
 
 										for (int i = 0; i < CHANCES; i++) {
@@ -207,7 +208,8 @@ public class ManageTimeSeriesThread extends Thread{
 											if(ckanResource != null){
 
 												if(createdFileOnWorkspace == null)
-													createdFileOnWorkspace = HelperMethods.uploadExternalFile(csvFolder, csvFileName + "_"  + customAnnotation.key() + CSVUtils.CSV_EXTENSION, resourceToAttachOnCkanDescription, csvFile);
+													createdFileOnWorkspace = HelperMethods.uploadExternalFile(csvFolder, csvFileName + "_" + (relevantSources[0] != null ? relevantSources[0] + "_" : "")  
+															+ customAnnotation.key() + CSVUtils.CSV_EXTENSION, resourceToAttachOnCkanDescription, csvFile);
 
 												if(createdFileOnWorkspace != null){
 													String publicUrlToSetOnCkan = createdFileOnWorkspace.getPublicLink(true);

src/test/java/org/gcube/data_catalogue/grsf_publish_ws/JTests.java

@@ -233,7 +233,7 @@ public class JTests {
 
 		Collections.sort(timeSeries);
 
-		File csvFile = CSVUtils.listToCSV(timeSeries);
+		File csvFile = CSVUtils.listToCSV(timeSeries, null);
 
 		// send file
 		instance.uploadResourceFile(csvFile, datasetName, instance.getApiKeyFromUsername("costantino.perciante"), "random_name.csv", null, null, null);