git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-publishing/gCat-Feeder-Suite@179492 82a268e6-3cf1-43bd-a215-b396298e98cf

gCat-Controller/pom.xml

@@ -9,6 +9,18 @@
   <name>gCat Controller</name>
   <description>Controller implementation for GCat Service</description>
   
+  	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>org.gcube.distribution</groupId>
+				<artifactId>gcube-bom</artifactId>
+				<version>LATEST</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+
+		</dependencies>
+	</dependencyManagement>
   
   <dependencies>
   		<dependency>
@@ -32,6 +44,20 @@
     		<scope>test</scope>
   		</dependency>
   
+  
+  		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+			<scope>provided</scope>
+		</dependency>
+
+
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
+  
   </dependencies>
   
   <build>

gCat-Controller/src/main/java/org/gcube/data/publishing/gCataFeeder/catalogues/gCat/GCatController.java

@@ -63,7 +63,7 @@ public class GCatController implements CatalogueController{
 
 		try {
 			builder= factory.newDocumentBuilder();
-			expr= xpath.compile("string(/bookstore/book/title/@lang)");
+			expr= xpath.compile("string(//metadataformat/@type)");
 		} catch (ParserConfigurationException | XPathExpressionException e) {
 			throw new RuntimeException("Unable to initialize Controller");
 		}
@@ -141,7 +141,7 @@ public class GCatController implements CatalogueController{
 			}
 
 			log.debug("Publishing Item..");
-			String itemResp=createItem(itemNode.asText());
+			String itemResp=createItem(itemNode.toString(),itemNode.path("name").textValue());
 			String itemId = getId(itemResp);		
 			log.debug("Pubilshed Item with ID {} ",itemId);		
 
@@ -263,13 +263,17 @@ public class GCatController implements CatalogueController{
 	}
 
 
-	private String createItem(String toCreate) throws WrongObjectFormatException, PublicationException{
+	private String createItem(String toCreate,String name) throws WrongObjectFormatException, PublicationException{
 		Item item=null;
 		try{
 			if(isForcedUrl())
 				item = new Item(getForcedUrl());
 			else item=new Item();
-			return item.create(toCreate);
+			
+			if(existsItem(item,name))
+				return item.update(name, toCreate);
+			else return item.create(toCreate);
+			
 		}catch(WebApplicationException e) {
 			handleWebException(e);
 			return null;
@@ -280,7 +284,15 @@ public class GCatController implements CatalogueController{
 	}
 
 
-
+	private boolean existsItem(Item item,String name) {
+		try {
+			item.read(name);
+			return true;
+		}catch(WebApplicationException e) {
+			log.debug("Read Item returned error. Assuming it's missing ",e);
+			return false;
+		}
+	}
 
 
 
@@ -339,6 +351,7 @@ public class GCatController implements CatalogueController{
 	}
 
 
+
 	private static String getId(String publishResponse) {		
 		try {			
 			return mapper.readTree(publishResponse).path("result").path("id").asText();

gCat-Controller/src/test/resources/org/gcube/data/publishing/gCatFeeder/catalogues/gCat/full-algorithm.json

@@ -1,21 +1,39 @@
 {
-    "profile": "<metadataformat type=\"Algorithm\">\n    <metadatafield>\n        <fieldName>Input Parameter</fieldName>\n        <dataType>String</dataType>\n        <mandatory>false</mandatory>\n        <note>Input parameter expected for the execution of the algorithm</note>\n    </metadatafield>    \n</metadataformat>",
+    "profileID": "DataMiner Process",
+    "profile": "<metadataformat type=\"DataMiner Process\">\n\t<metadatafield>\n\t\t<fieldName>Input Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Input parameter expected for the execution of the process</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Output Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Output parameter expected from the execution of the process\n\t\t</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Process Author</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<maxOccurs>*</maxOccurs>\n\t\t<defaultValue />\n\t\t<note>The name of the author, with email and ORCID. The format should\n\t\t\tbe: family, given[, email][, ORCID]. Example: Smith, John,\n\t\t\tjs@acme.org, orcid.org/0000-0002-1825-0097</note>\n\t\t<validator>\n\t\t\t<regularExpression>^[a-zA-ZÀ-ÿ .'-]+, [a-zA-ZÀ-ÿ .'-]+[,\n\t\t\t\t]*([a-zA-Z0-9_!#$%’*+=?`{|}~^.-]+@[a-zA-Z0-9À-ÿ.-]+)?[,\n\t\t\t\t]*(orcid.org\\/0000-000(1-[5-9]|2-[0-9]|3-[0-4])\\d\\d\\d-\\d\\d\\d[\\dX])?$</regularExpression>\n\t\t</validator>\n\t</metadatafield>\n</metadataformat>",
     "item":
     {
-        "name": "step_4_vpa_iccat_bft_e_report_in_nextnext",
+        "name": "grid_cwp_to_coordinates_in_prevre",
-        "title": "Step 4 Vpa Iccat Bft E Report in NextNext",
+        "title": "Grid Cwp To Coordinates in preVRE",
-        "description": "ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD",
+        "description": "An algorithm that adds longitude, latitude and resolution columns analysing a column containing FAO Ocean Area codes (CWP format).",
         "version": null,
-        "visibility": null,
+        "license_id": "CC-BY-NC-SA-4.0",
-        "license": "CC-BY-NC-SA-4.0",
+        "author": null,
-        "author": "gianpaolo.coro",
+        "maintainer": null,
-        "maintainer": "gianpaolo.coro",
+        "tags": [
-        "tags": ["Iccat Eastern Bft Stock Assessment"],
+        {
+            "name": "Geo Processing"
+        },
+        {
+            "name": "preVRE"
+        },
+        {
+            "name": "WPS"
+        },
+        {
+            "name": "Analytics"
+        }],
         "extras": [
         {
-            "key": "system",
+            "key": "system:type",
-            "value": "Algorithm"
+            "value": "DataMiner Process"
-        }]
+        }],
+        "private": true
     },
-    "resources": []
+    "resources": [
+    {
+        "name": "Gateway Link",
+        "url": "https://pre.d4science.org/group/prevre/dataminer-manager?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GRID_CWP_TO_COORDINATES",
+        "description": "Link to the GUI designed to operate with DataMiner"
+    }]
 }

gCat-Controller/src/test/resources/org/gcube/data/publishing/gCatFeeder/catalogues/gCat/onlyItem.json

@@ -0,0 +1,101 @@
+{
+	"profile": null,
+	"item": {
+		"license_title": "Creative Commons Attribution Share-Alike 4.0",
+		"maintainer": null,
+		"searchable": "true",
+		"relationships_as_object": [],
+		"private": true,
+		"maintainer_email": null,
+		"num_tags": 2,
+		"metadata_created": "2019-03-19T15:03:28.482434",
+		"metadata_modified": "2019-03-19T15:03:30.676258",
+		"author": "luca_frosini",
+		"author_email": "luca.frosini@gcube.ckan.org",
+		"state": "active",
+		"version": null,
+		"creator_user_id": "287b2eec-4cd7-4e50-817f-e6dce19995c7",
+		"type": "dataset",
+		"tags": [
+			{
+				"vocabulary_id": null,
+				"state": "active",
+				"display_name": "Other",
+				"id": "8ca635e2-4f72-48ed-8460-6734e9070a00",
+				"name": "Other"
+			},
+			{
+				"vocabulary_id": null,
+				"state": "active",
+				"display_name": "REST",
+				"id": "3d481290-b3cd-466f-8142-51608c616e60",
+				"name": "REST"
+			}
+		],
+		"groups": [],
+		"license_id": "CC-BY-SA-4.0",
+		"extras": [
+			{
+				"key": "FSKX_model_parameters:Input Parameter",
+				"value": "standard desviation of Temperatures( sdTemp): 2.9 °c( Double)"
+			},
+			{
+				"key": "FSKX_model_parameters:Output Parameter",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Hazard",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Population",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Product",
+				"value": ""
+			},
+			{
+				"key": "Item URL",
+				"value": "http://data.d4science.org/ctlg/AGINFRAplusDev/my_first_restful_transaction_model"
+			},
+			{
+				"key": "Model Author",
+				"value": ""
+			},
+			{
+				"key": "Model Creator",
+				"value": ""
+			},
+			{
+				"key": "Model ID",
+				"value": ""
+			},
+			{
+				"key": "Model Language",
+				"value": "Other"
+			},
+			{
+				"key": "Population",
+				"value": "Italian"
+			},
+			{
+				"key": "ReadMe",
+				"value": ""
+			},
+			{
+				"key": "Reference Description",
+				"value": ""
+			},
+			{
+				"key": "Related Identifier",
+				"value": ""
+			},
+			{
+				"key": "system:type",
+				"value": "My Profile"
+			}
+		]
+	},
+	"resources": null
+} 

gCat-Controller/target/classes/META-INF/maven/org.gcube.data-publishing.gCat-Feeder/gCat-Controller/pom.properties

@@ -1,5 +1,5 @@
 #Generated by Maven Integration for Eclipse
-#Wed May 08 18:18:34 CEST 2019
+#Mon May 20 17:18:44 CEST 2019
 version=1.0.0-SNAPSHOT
 groupId=org.gcube.data-publishing.gCat-Feeder
 m2e.projectName=gCat-Controller

gCat-Controller/target/classes/META-INF/maven/org.gcube.data-publishing.gCat-Feeder/gCat-Controller/pom.xml

@@ -9,6 +9,18 @@
   <name>gCat Controller</name>
   <description>Controller implementation for GCat Service</description>
   
+  	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>org.gcube.distribution</groupId>
+				<artifactId>gcube-bom</artifactId>
+				<version>LATEST</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+
+		</dependencies>
+	</dependencyManagement>
   
   <dependencies>
   		<dependency>
@@ -32,6 +44,20 @@
     		<scope>test</scope>
   		</dependency>
   
+  
+  		<dependency>
+			<groupId>com.fasterxml.jackson.core</groupId>
+			<artifactId>jackson-databind</artifactId>
+			<scope>provided</scope>
+		</dependency>
+
+
+		<dependency>
+			<groupId>org.slf4j</groupId>
+			<artifactId>slf4j-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
+  
   </dependencies>
   
   <build>

gCat-Controller/target/test-classes/org/gcube/data/publishing/gCatFeeder/catalogues/gCat/full-algorithm.json

@@ -1,21 +1,39 @@
 {
-    "profile": "<metadataformat type=\"Algorithm\">\n    <metadatafield>\n        <fieldName>Input Parameter</fieldName>\n        <dataType>String</dataType>\n        <mandatory>false</mandatory>\n        <note>Input parameter expected for the execution of the algorithm</note>\n    </metadatafield>    \n</metadataformat>",
+    "profileID": "DataMiner Process",
+    "profile": "<metadataformat type=\"DataMiner Process\">\n\t<metadatafield>\n\t\t<fieldName>Input Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Input parameter expected for the execution of the process</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Output Parameter</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<note>Output parameter expected from the execution of the process\n\t\t</note>\n\t</metadatafield>\n\t<metadatafield>\n\t\t<fieldName>Process Author</fieldName>\n\t\t<mandatory>false</mandatory>\n\t\t<dataType>String</dataType>\n\t\t<maxOccurs>*</maxOccurs>\n\t\t<defaultValue />\n\t\t<note>The name of the author, with email and ORCID. The format should\n\t\t\tbe: family, given[, email][, ORCID]. Example: Smith, John,\n\t\t\tjs@acme.org, orcid.org/0000-0002-1825-0097</note>\n\t\t<validator>\n\t\t\t<regularExpression>^[a-zA-ZÀ-ÿ .'-]+, [a-zA-ZÀ-ÿ .'-]+[,\n\t\t\t\t]*([a-zA-Z0-9_!#$%’*+=?`{|}~^.-]+@[a-zA-Z0-9À-ÿ.-]+)?[,\n\t\t\t\t]*(orcid.org\\/0000-000(1-[5-9]|2-[0-9]|3-[0-4])\\d\\d\\d-\\d\\d\\d[\\dX])?$</regularExpression>\n\t\t</validator>\n\t</metadatafield>\n</metadataformat>",
     "item":
     {
-        "name": "step_4_vpa_iccat_bft_e_report_in_nextnext",
+        "name": "grid_cwp_to_coordinates_in_prevre",
-        "title": "Step 4 Vpa Iccat Bft E Report in NextNext",
+        "title": "Grid Cwp To Coordinates in preVRE",
-        "description": "ICCAT (Eastern) Bluefin Tuna Stock Assessment. This set of R and Fortran code have been provided by ICCAT and IFremer to execute the whole Stock assessment workflow online integration has been done with the help (mediation) of CNR and IRD",
+        "description": "An algorithm that adds longitude, latitude and resolution columns analysing a column containing FAO Ocean Area codes (CWP format).",
         "version": null,
-        "visibility": null,
+        "license_id": "CC-BY-NC-SA-4.0",
-        "license": "CC-BY-NC-SA-4.0",
+        "author": null,
-        "author": "gianpaolo.coro",
+        "maintainer": null,
-        "maintainer": "gianpaolo.coro",
+        "tags": [
-        "tags": ["Iccat Eastern Bft Stock Assessment"],
+        {
+            "name": "Geo Processing"
+        },
+        {
+            "name": "preVRE"
+        },
+        {
+            "name": "WPS"
+        },
+        {
+            "name": "Analytics"
+        }],
         "extras": [
         {
-            "key": "system",
+            "key": "system:type",
-            "value": "Algorithm"
+            "value": "DataMiner Process"
-        }]
+        }],
+        "private": true
     },
-    "resources": []
+    "resources": [
+    {
+        "name": "Gateway Link",
+        "url": "https://pre.d4science.org/group/prevre/dataminer-manager?OperatorId=org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mappedclasses.transducerers.GRID_CWP_TO_COORDINATES",
+        "description": "Link to the GUI designed to operate with DataMiner"
+    }]
 }

gCat-Controller/target/test-classes/org/gcube/data/publishing/gCatFeeder/catalogues/gCat/onlyItem.json

@@ -0,0 +1,101 @@
+{
+	"profile": null,
+	"item": {
+		"license_title": "Creative Commons Attribution Share-Alike 4.0",
+		"maintainer": null,
+		"searchable": "true",
+		"relationships_as_object": [],
+		"private": true,
+		"maintainer_email": null,
+		"num_tags": 2,
+		"metadata_created": "2019-03-19T15:03:28.482434",
+		"metadata_modified": "2019-03-19T15:03:30.676258",
+		"author": "luca_frosini",
+		"author_email": "luca.frosini@gcube.ckan.org",
+		"state": "active",
+		"version": null,
+		"creator_user_id": "287b2eec-4cd7-4e50-817f-e6dce19995c7",
+		"type": "dataset",
+		"tags": [
+			{
+				"vocabulary_id": null,
+				"state": "active",
+				"display_name": "Other",
+				"id": "8ca635e2-4f72-48ed-8460-6734e9070a00",
+				"name": "Other"
+			},
+			{
+				"vocabulary_id": null,
+				"state": "active",
+				"display_name": "REST",
+				"id": "3d481290-b3cd-466f-8142-51608c616e60",
+				"name": "REST"
+			}
+		],
+		"groups": [],
+		"license_id": "CC-BY-SA-4.0",
+		"extras": [
+			{
+				"key": "FSKX_model_parameters:Input Parameter",
+				"value": "standard desviation of Temperatures( sdTemp): 2.9 °c( Double)"
+			},
+			{
+				"key": "FSKX_model_parameters:Output Parameter",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Hazard",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Population",
+				"value": ""
+			},
+			{
+				"key": "FSKX_model_scope:Product",
+				"value": ""
+			},
+			{
+				"key": "Item URL",
+				"value": "http://data.d4science.org/ctlg/AGINFRAplusDev/my_first_restful_transaction_model"
+			},
+			{
+				"key": "Model Author",
+				"value": ""
+			},
+			{
+				"key": "Model Creator",
+				"value": ""
+			},
+			{
+				"key": "Model ID",
+				"value": ""
+			},
+			{
+				"key": "Model Language",
+				"value": "Other"
+			},
+			{
+				"key": "Population",
+				"value": "Italian"
+			},
+			{
+				"key": "ReadMe",
+				"value": ""
+			},
+			{
+				"key": "Reference Description",
+				"value": ""
+			},
+			{
+				"key": "Related Identifier",
+				"value": ""
+			},
+			{
+				"key": "system:type",
+				"value": "My Profile"
+			}
+		]
+	},
+	"resources": null
+} 

gCat-Feeder/.settings/org.eclipse.wst.common.component

@@ -4,15 +4,6 @@
         <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
         <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/resources"/>
-        <dependent-module archiveName="collectors-plugin-framework-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/collectors-plugin-framework/collectors-plugin-framework">
-            <dependency-type>uses</dependency-type>
-        </dependent-module>
-        <dependent-module archiveName="commons-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/commons/commons">
-            <dependency-type>uses</dependency-type>
-        </dependent-module>
-        <dependent-module archiveName="catalogue-plugin-framework-1.0.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/catalogue-plugin-framework/catalogue-plugin-framework">
-            <dependency-type>uses</dependency-type>
-        </dependent-module>
         <property name="context-root" value="gCat-Feeder"/>
         <property name="java-output-path" value="/gCat-Feeder/target/classes"/>
     </wb-module>

gCat-Feeder/src/main/java/org/gcube/data/publishing/gCatFeeder/service/engine/LocalConfiguration.java

@@ -7,8 +7,8 @@ public interface LocalConfiguration {
 	public static final String POOL_MIN_IDLE="db.pools.min_total";
 	
 	
-	public static final String MAPPING_DB_ENDPOINT_NAME="db.ep.name";
+	public static final String DB_ENDPOINT_NAME="db.ep.name";
-	public static final String MAPPING_DB_ENDPOINT_CATEGORY="db.ep.category";
+	public static final String DB_ENDPOINT_CATEGORY="db.ep.category";
 	
 	
 	

gCat-Feeder/src/main/java/org/gcube/data/publishing/gCatFeeder/service/engine/impl/persistence/ConnectionManagerImpl.java

@@ -59,16 +59,17 @@ public class ConnectionManagerImpl implements ConnectionManager {
 	@Inject
 	private LocalConfiguration configuration;
 	
-	private synchronized DatabaseConnectionDescriptor getDB() throws InternalError {
+	private synchronized DatabaseConnectionDescriptor getDB() throws InternalError {		
 		if(!databases.containsKey(infrastructure.getCurrentContext()))
 			databases.put(infrastructure.getCurrentContext(), infrastructure.queryForDatabase(
-					configuration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_CATEGORY),
+					configuration.getProperty(LocalConfiguration.DB_ENDPOINT_CATEGORY),
-					configuration.getProperty(LocalConfiguration.MAPPING_DB_ENDPOINT_NAME)));
+					configuration.getProperty(LocalConfiguration.DB_ENDPOINT_NAME)));
 		return databases.get(infrastructure.getCurrentContext());
 	}
 	
 	@Override
 	public Connection getConnection() throws SQLException, InternalError {
+		log.debug("Getting DB connection in {} ",infrastructure.getCurrentContext());
 		DataSource ds=getDataSource();		
 		Connection conn=ds.getConnection();
 		conn.setAutoCommit(false);		
@@ -119,8 +120,8 @@ public class ConnectionManagerImpl implements ConnectionManager {
 	        Connection conn=null;
 	        try{
 	        	conn=dataSource.getConnection();
-	        	conn.createStatement().executeUpdate(Queries.getInitDB(db.getFlavor()));
+	        	conn.setAutoCommit(true);
-	        	conn.commit();
+	        	conn.createStatement().executeUpdate(Queries.getInitDB(db.getFlavor()));	        	
 	        }catch(SQLException e) {
 	        	throw new InternalError("Unable to Init database "+db,e);
 	        }finally {

gCat-Feeder/src/main/java/org/gcube/data/publishing/gCatFeeder/service/engine/impl/persistence/PersistenceManagerImpl.java

@@ -106,7 +106,7 @@ public class PersistenceManagerImpl implements PersistenceManager {
 			throws PersistenceError, InvalidRequest {
 		Connection conn=null;
 		try {
-			log.debug("Looking for execution according to filter {} ",filter);
+			log.debug("Looking for execution according to filter {}",filter);
 			conn=connections.getConnection();
 			ArrayList<ExecutionDescriptor> toReturn=new ArrayList<>();			
 			PreparedStatement psGet=Queries.GET_ALL.get(conn, filter);

gCat-Feeder/src/main/resources/gcat-feeder-config.properties

@@ -2,5 +2,5 @@ db.pools.max_idle=5
 db.pools.max_total=50
 db.pools.min_total=3
 
-mapping-db.ep.name=Feeder_DB
+db.ep.name=Feeder_DB
-mapping-db.ep.category=Database
+db.ep.category=Database