Update 'pom.xml'

removed snapshot

.classpath

@@ -14,17 +14,20 @@
 	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="org.eclipse.jst.component.nondependency" value=""/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
 		<attributes>
 			<attribute name="optional" value="true"/>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
 		<attributes>
 			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
 	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">

.gitignore

@@ -0,0 +1 @@
+/target/

.project

@@ -5,11 +5,21 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.wst.common.project.facet.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.jdt.core.javabuilder</name>
 			<arguments>
 			</arguments>
 		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 		<buildCommand>
 			<name>org.eclipse.m2e.core.maven2Builder</name>
 			<arguments>
@@ -17,7 +27,10 @@
 		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>org.eclipse.jem.workbench.JavaEMFNature</nature>
+		<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
 	</natures>
 </projectDescription>

.settings/org.eclipse.jdt.core.prefs

@@ -7,6 +7,9 @@ org.eclipse.jdt.core.compiler.debug.lineNumber=generate
 org.eclipse.jdt.core.compiler.debug.localVariable=generate
 org.eclipse.jdt.core.compiler.debug.sourceFile=generate
 org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
 org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
 org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.release=disabled
 org.eclipse.jdt.core.compiler.source=1.8

.settings/org.eclipse.wst.common.component

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="dataminer">
+        <wb-resource deploy-path="/" source-path="/src/main/java"/>
+        <wb-resource deploy-path="/" source-path="/src/main/resources"/>
+    </wb-module>
+</project-modules>

.settings/org.eclipse.wst.common.project.facet.core.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <installed facet="java" version="1.8"/>
+  <installed facet="jst.utility" version="1.0"/>
+</faceted-project>

.settings/org.eclipse.wst.validation.prefs

@@ -0,0 +1,2 @@
+disabled=06target
+eclipse.preferences.version=1

CHANGELOG.md

@@ -0,0 +1,71 @@
+# Changelog
+
+
+## [v1.7.0] - 2020-11-20
+
+- import range modified to resolve old repositories invalid url
+
+## [v1.6.0] - 2020-05-12
+
+### Fixes
+
+- Added storagehub retry in InputsManager class, getLocalFile method [#19253]
+
+
+
+## [v1.5.9] - 2019-11-20
+
+### Fixes
+
+- Fixed Content-Type support for files in the results of computations [#18096]
+
+
+
+## [v1.5.8] - 2019-10-01
+
+### Fixes
+
+- Fixed https link for output parameter [#17659]
+
+
+
+## [v1.5.7] - 2019-03-01
+
+### Features
+
+- Updated https support [#13024]
+
+
+
+## [v1.5.2] - 2017-12-13
+
+### Fixes
+
+- added the right extension on output file
+- lock file created on execution
+
+
+
+## [v1.5.1] - 2017-09-14
+
+### Features
+
+- added accounting on algorithm execution
+
+
+
+## [v1.5.0] - 2017-07-31
+
+### Features
+
+- service interface classes moved to wps project
+
+
+
+## [v1.1.0] - 2016-10-03
+
+- First Release
+
+
+
+This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

FUNDING.md

@@ -0,0 +1,26 @@
+# Acknowledgments
+
+The projects leading to this software have received funding from a series of European Union programmes including:
+
+- the Sixth Framework Programme for Research and Technological Development
+    - [DILIGENT](https://cordis.europa.eu/project/id/004260) (grant no. 004260).
+- the Seventh Framework Programme for research, technological development and demonstration 
+    - [D4Science](https://cordis.europa.eu/project/id/212488) (grant no. 212488);
+    - [D4Science-II](https://cordis.europa.eu/project/id/239019) (grant no.239019);
+    - [ENVRI](https://cordis.europa.eu/project/id/283465) (grant no. 283465);
+    - [iMarine](https://cordis.europa.eu/project/id/283644) (grant no. 283644);
+    - [EUBrazilOpenBio](https://cordis.europa.eu/project/id/288754) (grant no. 288754).
+- the H2020 research and innovation programme 
+    - [SoBigData](https://cordis.europa.eu/project/id/654024) (grant no. 654024);
+    - [PARTHENOS](https://cordis.europa.eu/project/id/654119) (grant no. 654119);
+    - [EGI-Engage](https://cordis.europa.eu/project/id/654142) (grant no. 654142);
+    - [ENVRI PLUS](https://cordis.europa.eu/project/id/654182) (grant no. 654182);
+    - [BlueBRIDGE](https://cordis.europa.eu/project/id/675680) (grant no. 675680);
+    - [PerformFISH](https://cordis.europa.eu/project/id/727610) (grant no. 727610);
+    - [AGINFRA PLUS](https://cordis.europa.eu/project/id/731001) (grant no. 731001);
+    - [DESIRA](https://cordis.europa.eu/project/id/818194) (grant no. 818194);
+    - [ARIADNEplus](https://cordis.europa.eu/project/id/823914) (grant no. 823914);
+    - [RISIS 2](https://cordis.europa.eu/project/id/824091) (grant no. 824091);
+    - [EOSC-Pillar](https://cordis.europa.eu/project/id/857650) (grant no. 857650);
+    - [Blue Cloud](https://cordis.europa.eu/project/id/862409) (grant no. 862409);
+    - [SoBigData-PlusPlus](https://cordis.europa.eu/project/id/871042) (grant no. 871042);

LICENSE.md

@@ -0,0 +1,311 @@
+#European Union Public Licence V.1.1
+
+##*EUPL © the European Community 2007*
+
+
+This **European Union Public Licence** (the **“EUPL”**) applies to the Work or Software
+(as defined below) which is provided under the terms of this Licence. Any use of
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+
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+
+
+##14. Jurisdiction
+
+Any litigation resulting from the interpretation of this License, arising
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+
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+
+##15. Applicable Law
+
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+
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+
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+- Licensee; the Licensor, other than the European Commission, has no residence
+- or registered office inside a European Union country.
+
+
+---
+
+
+##Appendix
+
+
+**“Compatible Licences”** according to article 5 EUPL are:
+
+
+- GNU General Public License (GNU GPL) v. 2
+
+- Open Software License (OSL) v. 2.1, v. 3.0
+
+- Common Public License v. 1.0
+
+- Eclipse Public License v. 1.0
+
+- Cecill v. 2.0

README.md

@@ -0,0 +1,48 @@
+# DataMiner 
+
+DataMiner is a library for integrate WPS 52North in the D4Science Infrastructure.
+
+## Structure of the project
+
+* The source code is present in the src folder. 
+
+## Built With
+
+* [OpenJDK](https://openjdk.java.net/) - The JDK used
+* [Maven](https://maven.apache.org/) - Dependency Management
+
+## Documentation
+
+* Use of this library is described on [Wiki](https://wiki.gcube-system.org/gcube/DataMiner_Installation).
+
+## Change log
+
+See [Releases](https://code-repo.d4science.org/gCubeSystem/dataminer/releases).
+
+## Authors
+
+* **Gianpaolo Coro** ([ORCID]()) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
+* **Lucio Lelii** ([ORCID]()) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
+* **Giancarlo Panichi** ([ORCID](http://orcid.org/0000-0001-8375-6644)) - [ISTI-CNR Infrascience Group](http://nemis.isti.cnr.it/groups/infrascience)
+
+
+## License
+
+This project is licensed under the EUPL V.1.1 License - see the [LICENSE.md](LICENSE.md) file for details.
+
+
+## About the gCube Framework
+This software is part of the [gCubeFramework](https://www.gcube-system.org/ "gCubeFramework"): an
+open-source software toolkit used for building and operating Hybrid Data
+Infrastructures enabling the dynamic deployment of Virtual Research Environments
+by favouring the realisation of reuse oriented policies.
+ 
+The projects leading to this software have received funding from a series of European Union programmes including:
+
+- the Sixth Framework Programme for Research and Technological Development
+    - DILIGENT (grant no. 004260);
+- the Seventh Framework Programme for research, technological development and demonstration 
+    - D4Science (grant no. 212488), D4Science-II (grant no.239019), ENVRI (grant no. 283465), EUBrazilOpenBio (grant no. 288754), iMarine(grant no. 283644);
+- the H2020 research and innovation programme 
+    - BlueBRIDGE (grant no. 675680), EGIEngage (grant no. 654142), ENVRIplus (grant no. 654182), Parthenos (grant no. 654119), SoBigData (grant no. 654024),DESIRA (grant no. 818194), ARIADNEplus (grant no. 823914), RISIS2 (grant no. 824091), PerformFish (grant no. 727610), AGINFRAplus (grant no. 731001);
+    

distro/LICENSE

@@ -1 +0,0 @@
-${gcube.license}

distro/README

@@ -1,69 +0,0 @@
-The gCube System - ${name}
---------------------------------------------------
- 
-${description}
- 
-
-${gcube.description}
- 
-${gcube.funding}
- 
- 
-Version
---------------------------------------------------
- 
-${version} (${buildDate})
- 
-Please see the file named "changelog.xml" in this directory for the release notes.
- 
- 
-Authors
---------------------------------------------------
-
-* Gianpaolo Coro (gianpaolo.coro-AT-isti.cnr.it), 
-		Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT
-
- 
-Maintainers
------------
- 
-* Gianpaolo Coro (gianpaolo.coro-AT-isti.cnr.it), 
-		Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" CNR, Pisa IT
-
- 
-Download information
---------------------------------------------------
- 
-Source code is available from SVN: 
-	${scm.url}
- 
-Binaries can be downloaded from the gCube website: 
-	${gcube.website}
- 
- 
-Installation
---------------------------------------------------
- 
-Installation documentation is available on-line in the gCube Wiki:
-	https://wiki.gcube-system.org/gcube/DataMiner_Installation
-  
- 
-Documentation 
---------------------------------------------------
- 
-Documentation is available on-line in the gCube Wiki:
-	https://wiki.gcube-system.org/gcube/DataMiner_Installation
-   
- 
-Support 
---------------------------------------------------
- 
-Bugs and support requests can be reported in the gCube issue tracking tool:
-	${gcube.issueTracking}
- 
- 
-Licensing
---------------------------------------------------
- 
-This software is licensed under the terms you may find in the file named "LICENSE" in this directory.
-

distro/changelog.xml

@@ -1,15 +0,0 @@
-<ReleaseNotes>
-    <Changeset component="${groupId}.${artifactId}.1-5-2" date="2017-12-13">
-		<Change>added the right extension on output file</Change>
-		<Change>lock file created on execution</Change>
-	</Changeset>
-	<Changeset component="${groupId}.${artifactId}.1-5-1" date="2017-09-14">
-		<Change>added accounting on algorithm execution</Change>
-	</Changeset>
-	<Changeset component="${groupId}.${artifactId}.1-5-0" date="2017-07-31">
-		<Change>service interface classes moved to wps project</Change>
-	</Changeset>
-	<Changeset component="${groupId}.${artifactId}.1-1-0" date="2016-10-03">
-		<Change>First Release</Change>
-	</Changeset>
-</ReleaseNotes>

distro/descriptor.xml

@@ -1,32 +0,0 @@
-<assembly
-	xmlns="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0"
-	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-	xsi:schemaLocation="http://maven.apache.org/plugins/maven-assembly-plugin/assembly/1.1.0 http://maven.apache.org/xsd/assembly-1.1.0.xsd">
-	<id>servicearchive</id>
-	<formats>
-		<format>tar.gz</format>
-	</formats>
-	<baseDirectory>/</baseDirectory>
-	<fileSets>
-		<fileSet>
-			<directory>${distroDirectory}</directory>
-			<outputDirectory>/</outputDirectory>
-			<useDefaultExcludes>true</useDefaultExcludes>
-			<includes>
-				<include>README</include>
-				<include>LICENSE</include>
-				<include>changelog.xml</include>
-				<include>profile.xml</include>
-			</includes>
-			<fileMode>755</fileMode>
-			<filtered>true</filtered>
-		</fileSet>
-	</fileSets>
-	<files>
-		<file>
-			<source>target/${build.finalName}.${project.packaging}</source>
-			<outputDirectory>/${artifactId}</outputDirectory>
-		</file>
-
-	</files>
-</assembly>

distro/profile.xml

@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<Resource>
-	<ID></ID>
-	<Type>Service</Type>
-	<Profile>
-		<Description>${project.description}</Description>
-		<Class>DataAnalysis</Class>
-		<Name>${project.name}</Name>
-		<Version>1.0.0</Version>
-		<Packages>
-			<Software>
-				<Name>${project.name}</Name>
-				<Description>${project.description}</Description>
-				<Version>${version}</Version>
-				<MavenCoordinates>
-					<groupId>${project.groupId}</groupId>
-					<artifactId>${project.artifactId}</artifactId>
-					<version>${project.version}</version>
-				</MavenCoordinates>
-				<Type>Service</Type>
-				<Files>
-					<File>${project.build.finalName}.${project.packaging}</File>	
-				</Files>
-			</Software>
-		</Packages>
-	</Profile>
-</Resource>
-
-
-

pom.xml

@@ -4,16 +4,19 @@
 	<parent>
 		<artifactId>maven-parent</artifactId>
 		<groupId>org.gcube.tools</groupId>
-		<version>1.0.0</version>
+		<version>1.1.0</version>
 		<relativePath />
 	</parent>
 	<groupId>org.gcube.dataanalysis</groupId>
 	<artifactId>dataminer</artifactId>
-	<version>1.5.3-SNAPSHOT</version>
+	<version>1.7.0</version>
 	<name>dataminer</name>
 	<description>An e-Infrastructure service providing state-of-the art DataMining algorithms and ecological modelling approaches under the Web Processing Service (WPS) standard.</description>
+	
 	<scm>
-		<url>https://svn.d4science.research-infrastructures.eu/gcube/trunk/data-analysis/DataMiner</url>
+		<connection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</connection>
+		<developerConnection>scm:git:https://code-repo.d4science.org/gCubeSystem/${project.artifactId}.git</developerConnection>
+		<url>https://code-repo.d4science.org/gCubeSystem/${project.artifactId}</url>
 	</scm>
 
 	<developers>
@@ -26,13 +29,40 @@
 				<role>developer</role>
 			</roles>
 		</developer>
+		<developer>
+			<name>Lucio Lelii</name>
+			<email>lucio.lelii@isti.cnr.it</email>
+			<organization>CNR Pisa, Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo"</organization>
+			<roles>
+				<role>architect</role>
+				<role>developer</role>
+			</roles>
+		</developer>
 	</developers>
+	
 	<properties>
 		<webappDirectory>${project.build.directory}/${project.build.finalName}</webappDirectory>
 		<distroDirectory>distro</distroDirectory>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
 	</properties>
+	
+	<dependencyManagement>
+		<!-- Old solution <dependencies> <dependency> <groupId>org.gcube.distribution</groupId> 
+			<artifactId>maven-smartgears-bom</artifactId> <version>2.1.0</version> <type>pom</type> 
+			<scope>import</scope> </dependency> </dependencies> -->
+		<dependencies>
+			<dependency>
+				<groupId>org.gcube.distribution</groupId>
+				<artifactId>gcube-bom</artifactId>
+				<version>2.0.0</version>
+				<type>pom</type>
+				<scope>import</scope>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+	
+	
 	<dependencies>
 		<!-- https://mvnrepository.com/artifact/org.reflections/reflections-maven -->
 		<dependency>
@@ -61,27 +91,22 @@
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>52n-wps-algorithm-gcube</artifactId>
-			<version>[3.6.1-SNAPSHOT,3.7.0-SNAPSHOT)</version>
+			<version>[3.6.1,3.7.0)</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>52n-wps-server-gcube</artifactId>
-			<version>[3.6.1-SNAPSHOT, 3.7.0-SNAPSHOT)</version>
+			<version>[3.6.1, 3.7.0)</version>
-		</dependency>
-		<dependency> 
-			<groupId>org.gcube.dataanalysis</groupId> 
-			<artifactId>ecological-engine</artifactId> 
-			<version>[1.8.5-SNAPSHOT,2.0.0-SNAPSHOT)</version> 
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine-wps-extension</artifactId>
-			<version>[1.0.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<version>[1.0.5,2.0.0-SNAPSHOT)</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine-geospatial-extensions</artifactId>
-			<version>[1.3.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<version>[1.5.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
 			<exclusions>
 				<exclusion>
 					<artifactId>log4j</artifactId>
@@ -92,12 +117,22 @@
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine-external-algorithms</artifactId>
-			<version>[1.1.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<version>[1.2.2-SNAPSHOT,2.0.0-SNAPSHOT)</version>
 		</dependency>
 		<dependency>
 			<groupId>org.gcube.dataanalysis</groupId>
 			<artifactId>ecological-engine-smart-executor</artifactId>
-			<version>[1.0.0-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<version>[1.6.5-SNAPSHOT,2.0.0-SNAPSHOT)</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.glassfish.jersey.core</groupId>
+					<artifactId>jersey-client</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.glassfish.jersey.media</groupId>
+					<artifactId>jersey-media-json-jackson</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>
@@ -116,24 +151,23 @@
 			<version>4.11</version>
 			<scope>test</scope>
 		</dependency>
-		<!-- <dependency> <groupId>org.gcube.common</groupId> <artifactId>common-authorization</artifactId> 
+
-			</dependency> <dependency> <groupId>org.gcube.core</groupId> <artifactId>common-scope</artifactId> 
-			</dependency> -->
 		<dependency>
 			<groupId>javassist</groupId>
 			<artifactId>javassist</artifactId>
 			<version>3.12.1.GA</version>
 		</dependency>
-		<dependency>
+
-			<groupId>org.gcube.common</groupId>
-			<artifactId>home-library-jcr</artifactId>
-			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
-		</dependency>
 
 		<dependency>
 			<groupId>org.gcube.common</groupId>
-			<artifactId>home-library</artifactId>
+			<artifactId>storagehub-client-library</artifactId>
-			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
+			<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
+		</dependency>
+		<dependency>
+			<groupId>org.gcube.common</groupId>
+			<artifactId>storagehub-model</artifactId>
+			<version>[1.0.0, 2.0.0-SNAPSHOT)</version>
 		</dependency>
 
 		<dependency>
@@ -145,7 +179,6 @@
 		<dependency>
 			<groupId>org.gcube.accounting</groupId>
 			<artifactId>accounting-lib</artifactId>
-			<version>[3.0.0-SNAPSHOT,4.0.0-SNAPSHOT)</version>
 			<scope>provided</scope>
 		</dependency>
 
@@ -154,44 +187,14 @@
 	<build>
 		<plugins>
 
-
-			<plugin>
-				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.1</version>
-				<configuration>
-					<source>1.8</source>
-					<target>1.8</target>
-				</configuration>
-			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-surefire-plugin</artifactId>
-				<version>2.18.1</version>
 				<configuration>
 					<skipTests>true</skipTests>
 				</configuration>
 			</plugin>
 
-
-
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-assembly-plugin</artifactId>
-				<configuration>
-					<descriptors>
-						<descriptor>${distroDirectory}/descriptor.xml</descriptor>
-					</descriptors>
-				</configuration>
-				<executions>
-					<execution>
-						<id>servicearchive</id>
-						<phase>install</phase>
-						<goals>
-							<goal>single</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
 		</plugins>
 	</build>
 	<repositories>

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/infrastructure/InfrastructureDialoguer.java

@@ -30,7 +30,7 @@ public class InfrastructureDialoguer {
 	public DatabaseInfo getDatabaseInfo(String resourceName) throws Exception{
 		DatabaseInfo dbi = new DatabaseInfo();
 
-		LOGGER.debug("Searching for Database "+resourceName+" in scope "+scope);
+		LOGGER.debug("Searching for Database {} in scope {}", resourceName, scope);
 		SimpleQuery query = queryFor(ServiceEndpoint.class);
 		//		 query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq 'StatisticalManagerDataBase' ");
 		//		query.addCondition("$resource/Profile/Category/text() eq 'Database' and $resource/Profile/Name eq '"+resourceName+"' ");
@@ -51,7 +51,7 @@ public class InfrastructureDialoguer {
 					dbi.driver = property.value(); 
 			}
 
-			LOGGER.debug("Found Database : "+dbi);
+			LOGGER.debug("Found Database : {}",dbi);
 		}
 
 		if (dbi.url == null)

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/AbstractEcologicalEngineMapper.java

@@ -62,6 +62,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 	
 	private TokenManager tokenm = null;
 	
+	private EnvironmentVariableManager env = null;
+	
 	// inputs and outputs
 	public LinkedHashMap<String, Object> inputs = new LinkedHashMap<String, Object>();
 	public LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
@@ -246,14 +248,14 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 
 	float previousStatus = -3;
 	String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
-	public void updateStatus(float status) {
+	public void updateStatus(float status, boolean canWrite) {
 		if (agent != null) {
 			if (status != previousStatus) {
 				LOGGER.debug("STATUS update to: {} ", status );
 				previousStatus = status;
 				super.update(new Integer((int) status));
 				try {
-					updateComputationOnWS(status, null);
+					if (canWrite) updateComputationOnWS(status, null);
 				} catch (Exception e) {
 					LOGGER.warn("error updating compution on WS");
 				}
@@ -262,6 +264,10 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 
 	}
 
+	public void setEnvironmentVariableManager(EnvironmentVariableManager env) {
+		this.env = env;
+	}
+	
 	public void updateComputationOnWS(float status, String exception) {
 		updateComputationOnWS(status, exception, null, null);
 	}
@@ -290,7 +296,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 			currentComputation.setStatus("" + status);
 			if (exception != null && exception.length() > 0)
 				currentComputation.setException(exception);
-
+			LOGGER.debug("RunDataspaceManager: [inputData="+inputData+", generatedData="+generatedData+"]");
 			RunDataspaceManager rundm = new RunDataspaceManager(inputData,generatedData);
 			rundm.run();
 
@@ -301,6 +307,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 		}
 	}
 
+	
+	
 	@Execute
 	public void run() throws Exception {
 		if (observer!=null)
@@ -324,8 +332,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 		} else
 			LOGGER.info("Wps External ID not set");
 		InputsManager inputsManager = null;
-		ConfigurationManager configManager = new ConfigurationManager(); // initializes parameters from file
+		ConfigurationManager configManager = new ConfigurationManager(this.env); // initializes parameters from web.xml
 		manageUserToken();
+		
+		boolean canWriteOnShub = checkWriteAuthorization(tokenm.getUserName());
+		
 		Path dir = Paths.get(System.getProperty("java.io.tmpdir"), "dmlocks");
 		if (!Files.exists(dir))
 			dir = Files.createDirectory(dir);
@@ -380,7 +391,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 			time("Ecological Engine Algorithm selection");
 			// adding service parameters to the configuration
 			LOGGER.info("5 - Adding Service parameters to the configuration");
-			inputsManager.addInputServiceParameters(getInputParameters(algorithm), infrastructureDialoguer);
+			List<StatisticalType> dataminerInputParameters = getInputParameters(algorithm);
+			LOGGER.debug("Dataminer Algo Default InputParameters: "+dataminerInputParameters);
+			inputsManager.addInputServiceParameters(dataminerInputParameters, infrastructureDialoguer);
 			time("Service parameters added to the algorithm");
 			// merging wps with ecological engine parameters - modifies the
 			// config
@@ -388,7 +401,7 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 			LOGGER.debug("Operator class is " + this.getClass().getCanonicalName());
 			// build computation Data
 			currentComputation = new ComputationData(config.getTaskID(), config.getAgent(), "", "", startTime, "-", "0", config.getTaskID(), configManager.getUsername(), config.getGcubeScope(), this.getClass().getCanonicalName());
-			inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo);
+			inputsManager.mergeWpsAndEcologicalInputs(supportDatabaseInfo, dataminerInputParameters);
 			generatedInputTables = inputsManager.getGeneratedTables();
 			generatedFiles = inputsManager.getGeneratedInputFiles();
 			time("Setup and download of input parameters with tables creation");
@@ -412,11 +425,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 			LOGGER.info("9 - Running the computation and updater");
 
 			LOGGER.info("Initializing the WPS status of the computation");
-			updateStatus(0);
+			updateStatus(0, canWriteOnShub);
 			LOGGER.info("Initializing the computation");
 			agent.init();
 			LOGGER.info("Updating status");
-			runStatusUpdater();
+			runStatusUpdater(canWriteOnShub);
 			LOGGER.info("Running the computation");
 			agent.compute();
 			LOGGER.info("The computation has finished. Retrieving output");
@@ -440,13 +453,13 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 
 			outputmanager.shutdown();
 			
-			// delete all temporary tables
+			LOGGER.debug("12 - Final Computation Output");
-			LOGGER.info("12 - Deleting possible generated temporary tables");
+			LOGGER.debug("Outputs: "+ outputs);
-			LOGGER.debug("Final Computation Output: " + outputs);
 
 			endTime = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
 			if (!isCancelled()) {
-				saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
+				LOGGER.debug("Save Computation Data");
+				if (canWriteOnShub) saveComputationOnWS(inputsManager.getProvenanceData(), outputmanager.getProvenanceData(), agent, generatedFiles);
 			} else {
 				LOGGER.debug("Computation interrupted - no update");
 				throw new Exception("Computation cancelled");
@@ -461,9 +474,9 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 				exitstatus = -1;
 
 			if (inputsManager != null)
-				updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
+				if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage(), inputsManager.getProvenanceData(), generatedFiles);
 			else
-				updateComputationOnWS(exitstatus, e.getMessage());
+				if (canWriteOnShub) updateComputationOnWS(exitstatus, e.getMessage());
 			if (isCancelled())
 				throw new Exception("Computation cancelled");
 			else
@@ -490,6 +503,18 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 
 	}
 
+	private boolean checkWriteAuthorization(String username) {
+		if (env!=null && env.getShubUsersExcluded()!=null) {
+			if (env.getShubUsersExcluded().isEmpty()) {
+				return false;
+			}
+			if (env.getShubUsersExcluded().contains(username)) {
+				return false;
+			}
+		}
+		return true;
+	}
+
 	private void accountAlgorithmExecution(long start, long end, OperationResult result) {
 		try{
 			JobUsageRecord jobUsageRecord = new JobUsageRecord();
@@ -513,11 +538,17 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 
 	public class StatusUpdater implements Runnable {
 		
+		private boolean canWrite = true;
+		
+		public StatusUpdater(boolean canWrite) {
+			this.canWrite = canWrite;
+		}
+		
 		@Override
 		public void run() {
 			while (agent != null && !isCancelled() && agent.getStatus() < 100) {
 				try {
-					updateStatus(agent.getStatus());
+					updateStatus(agent.getStatus(), canWrite);
 					Thread.sleep(10000);
 				} catch (InterruptedException e) {}
 			}
@@ -525,8 +556,8 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 		}
 	}
 
-	private void runStatusUpdater() {
+	private void runStatusUpdater(boolean canWrite) {
-		StatusUpdater updater = new StatusUpdater();
+		StatusUpdater updater = new StatusUpdater(canWrite);
 
 		Thread t = new Thread(updater);
 		t.start();
@@ -534,6 +565,11 @@ public class AbstractEcologicalEngineMapper extends AbstractAnnotatedAlgorithm i
 	}
 
 	private void saveComputationOnWS(List<StoredData> inputData, List<StoredData> outputData, ComputationalAgent agent, List<File> generatedFiles) {
+		LOGGER.debug("Save Computation On WS");
+		LOGGER.debug("InputData: "+inputData);
+		LOGGER.debug("OutputData: "+outputData);
+		LOGGER.debug("Agent: "+agent);
+		LOGGER.debug("Generated files: "+generatedFiles);
 		LOGGER.debug("Provenance manager started for operator " + this.getClass().getCanonicalName());
 		
 		ComputationData computation = new ComputationData(config.getTaskID(), config.getAgent(), agent.getDescription(), agent.getInfrastructure().name(), startTime, endTime, "100", config.getTaskID(), config.getParam(ConfigurationManager.serviceUserNameParameterVariable), config.getGcubeScope(), this.getClass().getCanonicalName());

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/ConfigurationManager.java

@@ -29,6 +29,9 @@ public class ConfigurationManager {
 	private static Boolean useStorage = null;
 	static boolean simulationMode = false;
 
+
+	EnvironmentVariableManager env = null;
+
 	public static synchronized Integer getMaxComputations(){
 		return maxComputations;
 	}
@@ -41,7 +44,12 @@ public class ConfigurationManager {
 		return simulationMode;
 	}
 
+	@Deprecated
 	public void getInitializationProperties() {
+
+	}
+
+	private void inizializePropertiesUsingTemplateFile() {
 		try {
 			if (maxComputations == null) {
 				Properties options = new Properties();
@@ -49,6 +57,7 @@ public class ConfigurationManager {
 				options.load(is);
 				is.close();
 				maxComputations = Integer.parseInt(options.getProperty("maxcomputations"));
+				logger.info("setting max computation to {}",maxComputations);
 				useStorage = Boolean.parseBoolean(options.getProperty("saveond4sstorage"));
 				simulationMode=Boolean.parseBoolean(options.getProperty("simulationMode"));
 			}
@@ -70,8 +79,13 @@ public class ConfigurationManager {
 		return username;
 	}
 
-	public ConfigurationManager() {
+	public ConfigurationManager(EnvironmentVariableManager env) {
-		getInitializationProperties();
+		if (env == null) inizializePropertiesUsingTemplateFile();
+		else {
+			maxComputations = env.getMaxComputation();
+			useStorage = env.isSaveOnStorage();
+			simulationMode = env.isSimulationMode();
+		}
 	}
 
 	public AlgorithmConfiguration getConfig() {
@@ -88,35 +102,33 @@ public class ConfigurationManager {
 		config.setAlgorithmClassLoader(Thread.currentThread().getContextClassLoader());
 		String webperspath = WPSConfig.getConfigDir() + "../persistence/";
 		// selecting persistence path
-//		String persistencePath = File.createTempFile("wpsstatcheck", ".sm").getParent() + "/../cfg/";
-	
-		//TODO: REMOVE this shit (the persistence must be the persistence dir of the webapp)
 		String persistencePath = WPSConfig.getConfigDir() + "../ecocfg/";
 		String configPath = persistencePath;
 		if (!new File(configPath).isDirectory()) {
 			configPath = "./cfg/";
 			persistencePath = "./";
 		}
-		logger.debug("Taking configuration from " + (new File(configPath).getAbsolutePath()) + " and persistence in " + persistencePath);
+		logger.debug("Taking configuration from  {}", configPath); 
+		//+ " and persistence in " + persistencePath);
 		// setting configuration and logger
-		config.setPersistencePath(persistencePath);
+		config.setPersistencePath(configPath);
 		config.setConfigPath(configPath);
 		config.setNumberOfResources(1);
 		// setting application paths
 		String webapp = WPSConfig.getInstance().getWPSConfig().getServer().getWebappPath();
 		String host = WPSConfig.getInstance().getWPSConfig().getServer().getHostname();
 		String port = WPSConfig.getInstance().getWPSConfig().getServer().getHostport();
-		logger.debug("Host: " + host + " Port: " + port + " Webapp: " + webapp + " ");
+		logger.debug("Host: {}  Port: {} Webapp: {} ", host, port, webapp );
-		logger.debug("Web persistence path: " + webperspath);
+		logger.debug("Web persistence path:{} ", webperspath);
 
 		String webPath = "http://" + host + ":" + port + "/" + webapp + "/persistence/";
 
 		// logger.debug("Env Vars: \n"+System.getenv());
-		logger.debug("Web app path: " + webPath);
+		logger.debug("Web app path: {} ",  webPath);
 
 		// retrieving scope
 		scope = (String) inputs.get(scopeParameter);
-		logger.debug("Retrieved scope: " + scope);
+		logger.debug("Retrieved scope: {} ",  scope);
 		if (scope == null)
 			throw new Exception("Error: scope parameter (scope) not set! This violates e-Infrastructure security policies");
 		if (!scope.startsWith("/"))
@@ -125,8 +137,8 @@ public class ConfigurationManager {
 		username = (String) inputs.get(usernameParameter);
 		token = (String) inputs.get(tokenParameter);
 
-		logger.debug("User name used by the client: " + username);
+		logger.debug("User name used by the client:{} ", username);
-		logger.debug("User token used by the client: " + token);
+		logger.debug("User token used by the client:{} ", token);
 
 		if (username == null || username.trim().length() == 0)
 			throw new Exception("Error: user name parameter (user.name) not set! This violates e-Infrastructure security policies");
@@ -139,7 +151,7 @@ public class ConfigurationManager {
 		config.setGcubeToken(token);
 		// DONE get username from request
 		config.setParam(serviceUserNameParameterVariable, username);
-		config.setParam(processingSessionVariable, "" + UUID.randomUUID());
+		config.setParam(processingSessionVariable, UUID.randomUUID().toString());
 		config.setParam(webpathVariable, webPath);
 		config.setParam(webPersistencePathVariable, webperspath);
 

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/EnvironmentVariableManager.java

@@ -0,0 +1,38 @@
+package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping;
+
+import java.util.List;
+
+public class EnvironmentVariableManager {
+	
+	public EnvironmentVariableManager(int maxComputation, boolean saveOnStorage, boolean simulationMode, List<String> shubUsersExcluded) {
+		super();
+		this.maxComputation = maxComputation;
+		this.saveOnStorage = saveOnStorage;
+		this.simulationMode = simulationMode;
+		this.shubUsersExcluded = shubUsersExcluded;
+	}
+	
+	private int maxComputation;
+	private boolean saveOnStorage;
+	private boolean  simulationMode;
+	
+	//null: all users will write on SHub
+	//empty: no one will write on Shub
+	//filled: users reported will not write on Shub
+	private List<String> shubUsersExcluded;
+	
+	public int getMaxComputation() {
+		return maxComputation;
+	}
+	public boolean isSaveOnStorage() {
+		return saveOnStorage;
+	}
+	public boolean isSimulationMode() {
+		return simulationMode;
+	}
+	
+	public List<String> getShubUsersExcluded() {
+		return shubUsersExcluded;
+	}
+
+}

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/InputsManager.java

@@ -5,6 +5,7 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.FileReader;
+import java.io.IOException;
 import java.io.InputStream;
 import java.net.HttpURLConnection;
 import java.net.URL;
@@ -43,6 +44,8 @@ public class InputsManager {
 
 	private static final Logger LOGGER = LoggerFactory.getLogger(InputsManager.class);
 
+	private static final long SHUB_RETRY_MILLIS = 2000;
+
 	LinkedHashMap<String, Object> inputs;
 	List<String> generatedTables;
 	List<File> generatedFiles;
@@ -51,11 +54,11 @@ public class InputsManager {
 	String computationId;
 
 	List<StoredData> provenanceData = new ArrayList<StoredData>();
+
 	public List<StoredData> getProvenanceData() {
 		return provenanceData;
 	}
 
-
 	public static String inputsSeparator = "\\|";
 
 	public AlgorithmConfiguration getConfig() {
@@ -92,30 +95,35 @@ public class InputsManager {
 		config.setParam("DatabaseURL", supportDatabaseInfo.url);
 	}
 
-	public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo) throws Exception {
+	public void mergeWpsAndEcologicalInputs(DatabaseInfo supportDatabaseInfo,
+			List<StatisticalType> dataminerInputParameters) throws Exception {
+		LOGGER.debug("Merge WPS And Ecological Inputs");
 		// browse input parameters from WPS
 		for (String inputName : inputs.keySet()) {
 			Object input = inputs.get(inputName);
-			LOGGER.debug("Managing Input Parameter with Name "+ inputName);
+			LOGGER.debug("Managing Input Parameter with Name " + inputName);
 			// case of simple input
 			if (input instanceof String) {
-				LOGGER.debug("Simple Input: "+ input);
+				LOGGER.debug("Simple Input: " + input);
 				// manage lists
 				String inputAlgoOrig = ((String) input).trim();
-				String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator, AlgorithmConfiguration.listSeparator);
+				String inputAlgo = ((String) input).trim().replaceAll(inputsSeparator,
+						AlgorithmConfiguration.listSeparator);
 				LOGGER.debug("Simple Input Transformed: " + inputAlgo);
 				config.setParam(inputName, inputAlgo);
 
-				saveInputData(inputName,inputName,inputAlgoOrig);
+				saveInputData(inputName, inputName, inputAlgoOrig);
 			}
 			// case of Complex Input
 			else if (input instanceof GenericFileData) {
 
-				LOGGER.debug("Complex Input: " + input);
+				LOGGER.debug("Complex Input");
 				// retrieve payload
 				GenericFileData files = ((GenericFileData) input);
+				LOGGER.debug("GenericFileData: [fileExtension=" + files.getFileExtension() + ", mimeType="
+						+ files.getMimeType() + "]");
 
-				List<File> localfiles = getLocalFiles(files,inputName);
+				List<File> localfiles = getLocalFiles(files, inputName, dataminerInputParameters);
 				String inputtables = "";
 				int nfiles = localfiles.size();
 				StringBuffer sb = new StringBuffer();
@@ -128,10 +136,11 @@ public class InputsManager {
 
 					if (inputTableTemplates.get(inputName) != null) {
 						LOGGER.debug("Creating table: " + tableName);
-						createTable(tableName, tableFile, config, supportDatabaseInfo, inputTableTemplates.get(inputName));
+						createTable(tableName, tableFile, config, supportDatabaseInfo,
+								inputTableTemplates.get(inputName));
 						generatedTables.add(tableName);
 					}
-					//case of non-table input file, e.g. FFANN
+					// case of non-table input file, e.g. FFANN
 					else
 						tableName = tableFile.getAbsolutePath();
 					if (i > 0)
@@ -140,13 +149,13 @@ public class InputsManager {
 					inputtables += tableName;
 
 					saveInputData(tableFile.getName(), inputName, tableFile.getAbsolutePath());
-					if (i>0)
+					if (i > 0)
 						sb.append("|");
 
 					sb.append(tableFile.getName());
 				}
 				sb.append("|");
-				if (nfiles>0)
+				if (nfiles > 0)
 					saveInputData(inputName, inputName, sb.toString());
 
 				// the only possible complex input is a table - check the WPS
@@ -157,7 +166,7 @@ public class InputsManager {
 
 	}
 
-	public boolean isXML(String fileContent){
+	public boolean isXML(String fileContent) {
 
 		if (fileContent.startsWith("&lt;"))
 			return true;
@@ -165,7 +174,7 @@ public class InputsManager {
 			return false;
 	}
 
-	public String readOneLine(String filename){
+	public String readOneLine(String filename) {
 
 		try {
 			BufferedReader in = new BufferedReader(new FileReader(new File(filename)));
@@ -173,7 +182,7 @@ public class InputsManager {
 			String vud = "";
 
 			while ((line = in.readLine()) != null) {
-				if (line.trim().length()>0){
+				if (line.trim().length() > 0) {
 					vud = line.trim();
 					break;
 				}
@@ -186,61 +195,82 @@ public class InputsManager {
 		}
 	}
 
-	public String inputNameFromHttpHeader(String url) throws Exception{
+	public String inputNameFromHttpHeader(String url) throws Exception {
+		LOGGER.debug("Search filename in http header from: " + url);
 		URL obj = new URL(url);
 		URLConnection conn = obj.openConnection();
-		String filename=null;
+		String filename = null;
 		// get all headers
 		Map<String, List<String>> map = conn.getHeaderFields();
-		LOGGER.debug("Getting file name from http header");
 		for (Map.Entry<String, List<String>> entry : map.entrySet()) {
 			String value = entry.getValue().toString();
-			if (value.toLowerCase().contains("filename=")){
+			LOGGER.debug("Header value: " + value);
-				LOGGER.debug("Searching in http header: found file name in header value "+value);
+			if (value.toLowerCase().contains("filename")) {
-				filename=value.substring(value.indexOf("=")+1);
+				LOGGER.debug("Searching in http header: found file name in header value {}", value);
-				filename=filename.replace("\"", "").replace("]", "");
+				filename = value.substring(value.indexOf("=") + 1);
-				LOGGER.debug("Searching in http header: retrieved file name "+filename);
+				filename = filename.replace("\"", "").replace("]", "");
+				LOGGER.debug("Searching in http header: retrieved file name {}", filename);
 				break;
 			}
 		}
+		LOGGER.debug("Filename retrieved from http header: " + filename);
 		return filename;
 	}
 
-	public List<File> getLocalFiles(GenericFileData files,String inputName) throws Exception {
+	public List<File> getLocalFiles(GenericFileData files, String inputName,
-
+			List<StatisticalType> dataminerInputParameters) throws Exception {
+		LOGGER.debug("GetLocalFiles: [files: " + files + ", inputName: " + inputName + "]");
 		// download input
 		List<File> filesList = new ArrayList<File>();
 		File f = files.getBaseFile(false);
-		LOGGER.debug("Retrieving file content as a URL link: " + f.getAbsolutePath());
+		LOGGER.debug("Retrieving local files: " + f.getAbsolutePath());
-		//TODO DO NOT READ FILE INTO MEMORY
+		// TODO DO NOT READ FILE INTO MEMORY
 		// read file content
 		String fileLink = readOneLine(f.getAbsolutePath());
-		LOGGER.debug("File link: " + fileLink.substring(0,Math.min(fileLink.length(),10)) + "...");
+		LOGGER.debug("Check File is link: {} ...", fileLink.substring(0, Math.min(fileLink.length(), 10)));
 		String fileName = "";
 		// case of a http link
-		if (fileLink!=null && fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:")) {
+		if (fileLink != null
+				&& (fileLink.toLowerCase().startsWith("http:") || fileLink.toLowerCase().startsWith("https:"))) {
 			// manage the case of multiple files
+			LOGGER.debug("Complex Input payload is link");
+
+			LOGGER.debug("Retrieving files from url: " + fileLink);
 			String[] remotefiles = fileLink.split(inputsSeparator);
 			for (String subfilelink : remotefiles) {
 				subfilelink = subfilelink.trim();
-				LOGGER.debug("Managing link: " + subfilelink);
+				LOGGER.debug("Managing link: {}", subfilelink);
 				if (subfilelink.length() == 0)
 					continue;
 				InputStream is = null;
 				HttpURLConnection urlConnection = null;
 				URL url = new URL(subfilelink);
-				urlConnection = (HttpURLConnection) url.openConnection();
+				try {
-				is = new BufferedInputStream(urlConnection.getInputStream());
+					urlConnection = (HttpURLConnection) url.openConnection();
+					is = new BufferedInputStream(urlConnection.getInputStream());
+				}catch(IOException e) {
+					LOGGER.warn("download from storagehub failed. Retry ongoing...");
+					LOGGER.debug("waiting "+SHUB_RETRY_MILLIS+" millis ");
+					Thread.sleep(SHUB_RETRY_MILLIS);					
+					urlConnection = (HttpURLConnection) url.openConnection();
+					is = new BufferedInputStream(urlConnection.getInputStream());
+					LOGGER.debug(" retry success ");
+				}				
 				// retrieve payload: for test purpose only
 				String fileNameTemp = inputNameFromHttpHeader(subfilelink);
 
-				if (fileNameTemp==null)
+				LOGGER.debug("the fileNameTemp is {}", fileNameTemp);
-					fileName = inputName+"_[" + computationId + "]";
+
-				else
+				if (fileNameTemp != null && !fileNameTemp.isEmpty()) {
-					fileName = fileNameTemp+ "_[" + computationId + "]."+FilenameUtils.getExtension(fileNameTemp);
+					fileName = String.format("%s_(%s).%s", inputName, computationId,
+							FilenameUtils.getExtension(fileNameTemp));
+				} else {
+					fileName = String.format("%s_(%s).%s", inputName, computationId,
+							FilenameUtils.getExtension(inputName));
+
+				}
+				LOGGER.debug("the name of the generated file is {}", fileName);
 
-				LOGGER.debug("Retrieving remote input in file: " + fileName);
-				LOGGER.debug("Creating local temp file: " + fileName);
 				File of = new File(config.getPersistencePath(), fileName);
 				FileOutputStream fos = new FileOutputStream(of);
 				IOUtils.copy(is, fos);
@@ -249,32 +279,57 @@ public class InputsManager {
 				fos.close();
 				urlConnection.disconnect();
 				filesList.add(of);
-				LOGGER.debug("Created local file: " + of.getAbsolutePath());
+				LOGGER.debug("Created local file: {}", of.getAbsolutePath());
 			}
 		} else {
-			LOGGER.debug("Complex Input payload is the filelink");
+			LOGGER.debug("Complex Input payload is file");
 			fileName = f.getName();
-			LOGGER.debug("Retriving local input from file: " + fileName);
 
-			if (isXML(fileLink))
+			LOGGER.debug("Retrieving local input from file: {}", fileName);
-			{
+
+			String fileExt = null;
+
+			if (isXML(fileLink)) {
 				String xmlFile = f.getAbsolutePath();
-				String csvFile = xmlFile+".csv";
+				String csvFile = xmlFile + ".csv";
-				LOGGER.debug("Transforming XML file into a csv: " +  csvFile);
+				LOGGER.debug("Transforming XML file into a csv: {} ", csvFile);
 				GML2CSV.parseGML(xmlFile, csvFile);
-				LOGGER.debug("GML Parsed: " + readOneLine(csvFile)+"[..]");
+				LOGGER.debug("GML Parsed: {} [..]", readOneLine(csvFile));
 				f = new File(csvFile);
+				fileExt = "csv";
+			} else {
+				LOGGER.debug("The file is a csv: {}", f.getAbsolutePath());
+				fileExt = FilenameUtils.getExtension(fileName);
 			}
-			else{
+
-				LOGGER.debug("The file is a csv: " + f.getAbsolutePath());
+			LOGGER.debug("Retrieve default extension");
+			String fileDefaultValue = null;
+			for (StatisticalType defaultInputParameter : dataminerInputParameters) {
+				if (defaultInputParameter.getName().compareTo(inputName) == 0) {
+					fileDefaultValue = defaultInputParameter.getDefaultValue();
+					break;
+				}
 			}
-			String absFile = new File(f.getParent(),inputName+ "_[" + computationId + "].csv").getAbsolutePath();
+			LOGGER.debug("Parameter default value retrieved: " + fileDefaultValue);
-			LOGGER.debug("Renaming to: "+absFile);
+
+			if (fileDefaultValue != null && !fileDefaultValue.isEmpty()) {
+				int lastPointIndex = fileDefaultValue.lastIndexOf(".");
+				if (lastPointIndex > -1 && lastPointIndex < (fileDefaultValue.length() - 1)) {
+					fileExt = fileDefaultValue.substring(lastPointIndex + 1);
+					LOGGER.debug("Default Extension retrieved: " + fileExt);
+				}
+			}
+
+			LOGGER.debug("Use extension: " + fileExt);
+
+			String absFile = new File(f.getParent(), String.format("%s_(%s).%s", inputName, computationId, fileExt))
+					.getAbsolutePath();
+			LOGGER.debug("Renaming to: " + absFile);
 			System.gc();
 			boolean renamed = f.renameTo(new File(absFile));
 			if (renamed)
 				f = new File(absFile);
-			LOGGER.debug("The file has been renamed as : " + f.getAbsolutePath()+" - "+renamed);
+			LOGGER.debug("The file has been renamed as : {} - {}", f.getAbsolutePath(), renamed);
 			filesList.add(f);
 
 		}
@@ -282,7 +337,8 @@ public class InputsManager {
 		return filesList;
 	}
 
-	public void createTable(String tableName, File tableFile, AlgorithmConfiguration config, DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception {
+	public void createTable(String tableName, File tableFile, AlgorithmConfiguration config,
+			DatabaseInfo supportDatabaseInfo, String inputTableTemplate) throws Exception {
 
 		// creating table
 		LOGGER.debug("Complex Input size after download: " + tableFile.length());
@@ -308,11 +364,13 @@ public class InputsManager {
 			TableTemplatesMapper mapper = new TableTemplatesMapper();
 			String createstatement = mapper.generateCreateStatement(tableName, templatename, tableStructure);
 			LOGGER.debug("Creating table: " + tableName);
-			DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
+			DatabaseUtils.createBigTable(true, tableName, supportDatabaseInfo.driver, supportDatabaseInfo.username,
-			DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true, supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
+					supportDatabaseInfo.password, supportDatabaseInfo.url, createstatement, dbConnection);
+			DatabaseUtils.createRemoteTableFromFile(tableFile.getAbsolutePath(), tableName, ",", true,
+					supportDatabaseInfo.username, supportDatabaseInfo.password, supportDatabaseInfo.url);
 
 		} catch (Exception e) {
-			LOGGER.error("Error in database transaction " ,e);
+			LOGGER.error("Error in database transaction ", e);
 			throw new Exception("Error in creating the table for " + tableName + ": " + e.getLocalizedMessage());
 		} finally {
 			DatabaseUtils.closeDBConnection(dbConnection);
@@ -368,7 +426,8 @@ public class InputsManager {
 		return structure.toString();
 	}
 
-	public void addInputServiceParameters(List<StatisticalType> agentInputs, InfrastructureDialoguer infrastructureDialoguer) throws Exception {
+	public void addInputServiceParameters(List<StatisticalType> agentInputs,
+			InfrastructureDialoguer infrastructureDialoguer) throws Exception {
 
 		// check and fullfil additional parameters
 		DatabaseInfo dbinfo = null;
@@ -376,10 +435,10 @@ public class InputsManager {
 
 		for (StatisticalType type : agentInputs) {
 			if (type instanceof PrimitiveType) {
-				if (((PrimitiveType) type).getType()==PrimitiveTypes.CONSTANT){
+				if (((PrimitiveType) type).getType() == PrimitiveTypes.CONSTANT) {
-					String constant = ""+((PrimitiveType) type).getDefaultValue();
+					String constant = "" + ((PrimitiveType) type).getDefaultValue();
 					config.setParam(type.getName(), constant);
-					LOGGER.debug("Constant parameter: "+constant);
+					LOGGER.debug("Constant parameter: " + constant);
 				}
 			}
 			if (type instanceof ServiceType) {
@@ -392,10 +451,10 @@ public class InputsManager {
 				String value = "";
 				if (sp == ServiceParameters.RANDOMSTRING)
 					value = "stat" + UUID.randomUUID().toString().replace("-", "");
-				else if (sp == ServiceParameters.USERNAME){
+				else if (sp == ServiceParameters.USERNAME) {
 					value = (String) inputs.get(ConfigurationManager.usernameParameter);
 
-					LOGGER.debug("User name used by the client: "+value);
+					LOGGER.debug("User name used by the client: " + value);
 				}
 				LOGGER.debug("ServiceType Adding: (" + name + "," + value + ")");
 				config.setParam(name, value);
@@ -436,8 +495,8 @@ public class InputsManager {
 
 	}
 
-
+	private void saveInputData(String name, String description, String payload) {
-	private void saveInputData(String name, String description, String payload){
+		LOGGER.debug("SaveInputData [name="+name+", description="+description+", payload="+payload+"]");
 		String id = name;
 		DataProvenance provenance = DataProvenance.IMPORTED;
 		String creationDate = new java.text.SimpleDateFormat("dd/MM/yyyy HH:mm:ss").format(System.currentTimeMillis());
@@ -445,18 +504,17 @@ public class InputsManager {
 
 		String type = "text/plain";
 
-		if (payload != null && (new File (payload).exists())) {
+		if (payload != null && (new File(payload).exists())) {
 			if (payload.toLowerCase().endsWith(".csv") || payload.toLowerCase().endsWith(".txt")) {
 				type = "text/csv";
 			} else
 				type = "application/d4science";
 		}
 
-		StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope());
+		StoredData data = new StoredData(name, description, id, provenance, creationDate, operator, computationId, type,
+				payload, config.getGcubeScope());
 
 		provenanceData.add(data);
 	}
 
-
-
 }

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/OutputsManager.java

@@ -46,12 +46,13 @@ public class OutputsManager {
 		return generatedTables;
 	}
 
-	public OutputsManager(AlgorithmConfiguration config,String computationsession) {
+	public OutputsManager(AlgorithmConfiguration config, String computationsession) {
 		this.config = config;
-		this.computationsession=computationsession;
+		this.computationsession = computationsession;
 	}
 
-	public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput) throws Exception {
+	public LinkedHashMap<String, Object> createOutput(StatisticalType prioroutput, StatisticalType posterioroutput)
+			throws Exception {
 
 		LinkedHashMap<String, Object> outputs = new LinkedHashMap<String, Object>();
 
@@ -66,9 +67,9 @@ public class OutputsManager {
 		StatisticalTypeToWPSType postconverter = new StatisticalTypeToWPSType();
 		postconverter.convert2WPSType(posterioroutput, false, config);
 		generatedFiles.addAll(postconverter.getGeneratedFiles());
-		LOGGER.debug("Generated Files "+generatedFiles);
+		LOGGER.debug("Generated Files " + generatedFiles);
 		generatedTables.addAll(postconverter.getGeneratedTables());
-		LOGGER.debug("Generated Tables "+generatedFiles);
+		LOGGER.debug("Generated Tables " + generatedFiles);
 
 		LinkedHashMap<String, IOWPSInformation> postOutput = postconverter.outputSet;
 
@@ -102,21 +103,23 @@ public class OutputsManager {
 				if (ConfigurationManager.useStorage()) {
 					if (postInfo.getLocalMachineContent() != null) {
 						// return the url from storage manager
-						String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(), postInfo.getMimetype());
+						String storageurl = uploadFileOnStorage(postInfo.getLocalMachineContent(),
+								postInfo.getMimetype());
 						postInfo.setContent(storageurl);
 					}
 				}
 				/*
-				else if (postInfo.getLocalMachineContent() != null) {
+				 * else if (postInfo.getLocalMachineContent() != null) { String
-					String url = "<wps:Reference mimeType=\""+postInfo.getMimetype()+"\" xlink:href=\""+postInfo.getContent()+"\" method=\"GET\"/>";					
+				 * url = "<wps:Reference mimeType=\""+postInfo.getMimetype()
-					LOGGER.debug("Reference URL: " + url);
+				 * +"\" xlink:href=\""+postInfo.getContent()
-					outputs.put(okey, url);
+				 * +"\" method=\"GET\"/>"; LOGGER.debug("Reference URL: " +
-				}
+				 * url); outputs.put(okey, url); } else
-				else*/ 
+				 */
 				if (info != null) {
 					LOGGER.debug("Found a corresponding output: " + okey);
 					outputs.put(okey, postInfo.getContent());
-					//add link to the file also among the non deterministic output
+					// add link to the file also among the non deterministic
+					// output
 					if (postInfo.getLocalMachineContent() != null) {
 						ndoutput.put(okey, postInfo);
 					}
@@ -133,19 +136,19 @@ public class OutputsManager {
 		XmlObject ndxml = generateNonDeterministicOutput(ndoutput);
 		outputs.put("non_deterministic_output", ndxml);
 
-		//safety check for declared output, i.e. a priori output
+		// safety check for declared output, i.e. a priori output
-		for (String pkey:priorOutput.keySet()){
+		for (String pkey : priorOutput.keySet()) {
-			if (outputs.get(pkey)==null){
+			if (outputs.get(pkey) == null) {
-				LOGGER.debug("Safety check: adding empty string for " + pkey+ " of type "+priorOutput.get(pkey).getClassname());
+				LOGGER.debug("Safety check: adding empty string for " + pkey + " of type "
+						+ priorOutput.get(pkey).getClassname());
 				outputs.put(pkey, "");
 			}
 		}
-		
+		LOGGER.debug("OutputsManager outputs " + outputs);
 		return outputs;
 	}
 
-	
+	private void saveProvenanceData(IOWPSInformation info) {
-	private void saveProvenanceData(IOWPSInformation info){
 		String name = info.getName();
 		String id = info.getName();
 		DataProvenance provenance = DataProvenance.COMPUTED;
@@ -153,59 +156,97 @@ public class OutputsManager {
 		String operator = config.getAgent();
 		String computationId = computationsession;
 		String type = info.getMimetype();
-/*		if (info.getLocalMachineContent() != null) {
+		/*
-			type = StoredType.DATA;
+		 * if (info.getLocalMachineContent() != null) { type = StoredType.DATA;
-		}
+		 * }
-		*/
+		 */
 		String payload = info.getContent();
 
-		StoredData data = new StoredData(name, info.getAbstractStr(),id, provenance, creationDate, operator, computationId, type,payload,config.getGcubeScope());
+		StoredData data = new StoredData(name, info.getAbstractStr(), id, provenance, creationDate, operator,
+				computationId, type, payload, config.getGcubeScope());
 
 		provenanceData.add(data);
 	}
 
 	private void prepareForStoring() {
 		LOGGER.debug("Preparing storage client");
-		//String scope = config.getGcubeScope();
+		// String scope = config.getGcubeScope();
-		//ScopeProvider.instance.set(scope);
+		// ScopeProvider.instance.set(scope);
 		String serviceClass = "WPS";
 		String serviceName = "wps.synch";
 		String owner = config.getParam(ConfigurationManager.serviceUserNameParameterVariable);
-		storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE).getClient();
+		storageclient = new StorageClient(serviceClass, serviceName, owner, AccessType.SHARED, MemoryType.VOLATILE)
+				.getClient();
 		LOGGER.debug("Storage client ready");
 	}
 
-	
 	private String uploadFileOnStorage(String localfile, String mimetype) throws Exception {
 		LOGGER.debug("Storing->Start uploading on storage the following file: " + localfile);
 		File localFile = new File(localfile);
-		String remotef = "/wps_synch_output/" +config.getAgent()+"/"+computationsession+"/"+ localFile.getName();
+		String remotef = "/wps_synch_output/" + config.getAgent() + "/" + computationsession + "/"
-		storageclient.put(true).LFile(localfile).RFile(remotef);
+				+ localFile.getName();
-		
+		String contentType=retrieveContentType(localfile);
-		String url = storageclient.getHttpUrl().RFile(remotef);
+		LOGGER.debug("Retrieved Content-Type: "+contentType);
+		if(contentType==null||contentType.isEmpty()){
+			storageclient.put(true).LFile(localfile).RFile(remotef);
+		} else {
+			storageclient.put(true,contentType).LFile(localfile).RFile(remotef);
+		}
+		String url = storageclient.getHttpsUrl().RFile(remotef);
 
 		/*
-		if (config.getGcubeScope().startsWith("/gcube"))
+		 * if (config.getGcubeScope().startsWith("/gcube")) url =
-			url = "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url + "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
+		 * "http://data-d.d4science.org/uri-resolver/smp?smp-uri=" + url +
-		else
+		 * "&fileName=" + localFile.getName() + "&contentType=" + mimetype; else
-			url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+ "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
+		 * url = "http://data.d4science.org/uri-resolver/smp?smp-uri=" + url+
-			*/
+		 * "&fileName=" + localFile.getName() + "&contentType=" + mimetype;
+		 */
 		LOGGER.info("Storing->Uploading finished - URL: " + url);
 		return url;
 
 	}
 
+	private String retrieveContentType(String fileName) {
+		String contentType=null;
+		if (fileName != null && !fileName.isEmpty()) {
+			String fileNameLowerCase = fileName.toLowerCase();
+			if (fileNameLowerCase.endsWith(".html") || fileNameLowerCase.endsWith(".htm")) {
+				contentType="text/html";
+			} else {
+				if (fileNameLowerCase.endsWith(".pdf")) {
+					contentType="application/pdf";
+				} else {
+					if (fileNameLowerCase.endsWith(".log") || fileNameLowerCase.endsWith(".txt")) {
+						contentType="text/plain";
+					} else {
+						if (fileNameLowerCase.endsWith(".json")) {
+							contentType="application/json";
+						} else {
+						}
+					}
+				}
+			}
+		}
+		return contentType;
+	}
+
 	public String cleanTagString(String tag) {
 		return tag.replace(" ", "_").replaceAll("[\\]\\[!\"#$%&'()*+,\\./:;<=>?@\\^`{|}~-]", "");
 	}
 
-	public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
+	public XmlObject generateNonDeterministicOutputPlain(LinkedHashMap<String, IOWPSInformation> ndoutput)
-		String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n" + "	<d4science:output fid=\"outputcollection\">\n";
+			throws Exception {
+		String XMLString = "<gml:featureMember xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">\n"
+				+ "	<d4science:output fid=\"outputcollection\">\n";
 		for (String key : ndoutput.keySet()) {
 			IOWPSInformation info = ndoutput.get(key);
 			String payload = info.getContent();
 			String mimetype = info.getMimetype();
-			XMLString += "		<d4science:k_" + cleanTagString(key) + ">" + "			<d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</d4science:k_" + cleanTagString(key) + ">\n";
+			XMLString += "		<d4science:k_" + cleanTagString(key) + ">" + "			<d4science:Data><![CDATA["
+					+ payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA["
+					+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
+					+ "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</d4science:k_"
+					+ cleanTagString(key) + ">\n";
 		}
 		XMLString += "	</d4science:output>\n" + "</gml:featureMember>\n";
 
@@ -219,16 +260,21 @@ public class OutputsManager {
 		return xmlData;
 	}
 
-	public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
+	public XmlObject generateNonDeterministicOutputCollection(LinkedHashMap<String, IOWPSInformation> ndoutput)
-		String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" +
+			throws Exception {
-				"\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n" +
+		String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
-						"	<d4science:output fid=\"outputcollection\">\n";
+				+ "\n<gml:featureMember>\n" + " <ogr:Result fid=\"F0\">\n"
+				+ "	<d4science:output fid=\"outputcollection\">\n";
 
 		for (String key : ndoutput.keySet()) {
 			IOWPSInformation info = ndoutput.get(key);
 			String payload = info.getContent();
 			String mimetype = info.getMimetype();
-			XMLString += "		<d4science:k_" + cleanTagString(key) + ">" + "			<d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</d4science:k_" + cleanTagString(key) + ">\n";
+			XMLString += "		<d4science:k_" + cleanTagString(key) + ">" + "			<d4science:Data><![CDATA["
+					+ payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA["
+					+ (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n"
+					+ "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</d4science:k_"
+					+ cleanTagString(key) + ">\n";
 		}
 		XMLString += "	</d4science:output>\n" + "  </ogr:Result>\n</gml:featureMember>\n</ogr:FeatureCollection>";
 
@@ -244,11 +290,11 @@ public class OutputsManager {
 
 	public XmlObject generateNonDeterministicOutput(LinkedHashMap<String, IOWPSInformation> ndoutput) throws Exception {
 
-		if (ndoutput.size()==0)
+		if (ndoutput.size() == 0)
 			return null;
 
-		String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">" +
+		String XMLString = "<ogr:FeatureCollection xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://ogr.maptools.org/ result_8751.xsd\" xmlns:ogr=\"http://ogr.maptools.org/\" xmlns:gml=\"http://www.opengis.net/gml\" xmlns:d4science=\"http://www.d4science.org\">"
-				"\n<gml:featureMember>\n";
+				+ "\n<gml:featureMember>\n";
 		int count = 0;
 		for (String key : ndoutput.keySet()) {
 			IOWPSInformation info = ndoutput.get(key);
@@ -256,25 +302,31 @@ public class OutputsManager {
 			String mimetype = info.getMimetype();
 			String abstractStr = info.getAbstractStr();
 
-			LOGGER.debug("IOWPS Information: " + "name "+info.getName()+","
+			LOGGER.debug("IOWPS Information [name=" + info.getName() + ", abstr=" + info.getAbstractStr() + ", content="
-					+"abstr "+info.getAbstractStr()+","
+					+ info.getContent() + ", def=" + info.getDefaultVal() + "]");
-					+"content "+info.getContent()+","
-					+"def "+info.getDefaultVal()+",");
 
-			if ((abstractStr==null || abstractStr.trim().length()==0) && (payload!= null && payload.trim().length()>0))
+			if ((abstractStr == null || abstractStr.trim().length() == 0)
+					&& (payload != null && payload.trim().length() > 0))
 				abstractStr = info.getName();
 			else if (abstractStr == null)
 				abstractStr = "";
 
-			//geospatialized
+			// geospatialized
-//			XMLString += "		<ogr:Result fid=\"F" + count+ "\">" + "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+ "			<d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA[" + (info.getAbstractStr() != null ? info.getAbstractStr() : "") + "]]></d4science:Description>\n" + "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</ogr:Result>\n";
+			// XMLString += " <ogr:Result fid=\"F" + count+ "\">" +
-			XMLString += "		<ogr:Result fid=\"F" + count+ "\">" + "			<d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA[" + abstractStr + "]]></d4science:Description>\n" + "			<d4science:MimeType>" + mimetype + "</d4science:MimeType>\n" + "		</ogr:Result>\n";
+			// "<ogr:geometryProperty><gml:Point><gml:coordinates>0,0</gml:coordinates></gml:Point></ogr:geometryProperty>"+
+			// " <d4science:Data><![CDATA[" + payload + "]]></d4science:Data>\n"
+			// + " <d4science:Description><![CDATA[" + (info.getAbstractStr() !=
+			// null ? info.getAbstractStr() : "") +
+			// "]]></d4science:Description>\n" + " <d4science:MimeType>" +
+			// mimetype + "</d4science:MimeType>\n" + " </ogr:Result>\n";
+			XMLString += "		<ogr:Result fid=\"F" + count + "\">" + "			<d4science:Data><![CDATA[" + payload
+					+ "]]></d4science:Data>\n" + "			<d4science:Description><![CDATA[" + abstractStr
+					+ "]]></d4science:Description>\n" + "			<d4science:MimeType>" + mimetype
+					+ "</d4science:MimeType>\n" + "		</ogr:Result>\n";
 			count++;
 		}
 		XMLString += "	</gml:featureMember>\n</ogr:FeatureCollection>";
 
-		
-		
 		LOGGER.debug("Non deterministic output: " + XMLString);
 
 		XmlObject xmlData = XmlObject.Factory.newInstance();
@@ -285,10 +337,10 @@ public class OutputsManager {
 		return xmlData;
 	}
 
-	public void shutdown(){
+	public void shutdown() {
-		try{
+		try {
-		storageclient.close();
+			storageclient.close();
-		}catch(Exception e){
+		} catch (Exception e) {
 
 		}
 	}

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/DataspaceManager.java

@@ -13,16 +13,15 @@ import java.util.List;
 import java.util.Map;
 import java.util.UUID;
 
-import org.gcube.common.homelibrary.home.Home;
+import org.gcube.common.authorization.library.provider.AuthorizationProvider;
-import org.gcube.common.homelibrary.home.HomeLibrary;
+import org.gcube.common.storagehub.client.dsl.FileContainer;
-import org.gcube.common.homelibrary.home.HomeManager;
+import org.gcube.common.storagehub.client.dsl.FolderContainer;
-import org.gcube.common.homelibrary.home.HomeManagerFactory;
+import org.gcube.common.storagehub.client.dsl.ItemContainer;
-import org.gcube.common.homelibrary.home.User;
+import org.gcube.common.storagehub.client.dsl.StorageHubClient;
-import org.gcube.common.homelibrary.home.workspace.Workspace;
+import org.gcube.common.storagehub.model.Metadata;
-import org.gcube.common.homelibrary.home.workspace.WorkspaceFolder;
+import org.gcube.common.storagehub.model.exceptions.ItemLockedException;
-import org.gcube.common.homelibrary.home.workspace.WorkspaceItem;
+import org.gcube.common.storagehub.model.items.GCubeItem;
-import org.gcube.common.homelibrary.home.workspace.folder.FolderItem;
+import org.gcube.common.storagehub.model.items.Item;
-import org.gcube.common.homelibrary.util.WorkspaceUtil;
 import org.gcube.contentmanagement.lexicalmatcher.utils.FileTools;
 import org.gcube.dataanalysis.ecoengine.configuration.AlgorithmConfiguration;
 import org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.AbstractEcologicalEngineMapper;
@@ -64,12 +63,20 @@ public class DataspaceManager implements Runnable {
 	public static String operator = "operator_name";
 	public static String payload = "payload";
 
-	public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, List<File> generatedFiles) {
+	private String statusComputationName;
+	private static final String STATUS_POSTFIX="-STATUS";
+
+	public DataspaceManager(AlgorithmConfiguration config, ComputationData computation, List<StoredData> inputData,
+			List<StoredData> outputData, List<File> generatedFiles) {
 		this.config = config;
 		this.computation = computation;
 		this.inputData = inputData;
 		this.outputData = outputData;
 		this.generatedFiles = generatedFiles;
+		this.statusComputationName =  this.computation.id+STATUS_POSTFIX;
+
+		LOGGER.debug("DataspaceManager [config=" + config + ", computation=" + computation + ", inputData=" + inputData
+				+ ", outputData=" + outputData + ", generatedFiles=" + generatedFiles + "]");
 	}
 
 	public void run() {
@@ -88,78 +95,101 @@ public class DataspaceManager implements Runnable {
 
 	}
 
-	public void createFoldersNetwork(Workspace ws, WorkspaceFolder root) throws Exception {
+	public FolderContainer createFoldersNetwork() throws Exception {
 
 		LOGGER.debug("Dataspace->Creating folders for DataMiner");
 
-		// manage folders: create the folders network
+		StorageHubClient shc = new StorageHubClient();
-		if (!ws.exists(dataminerFolder, root.getId())) {
-			LOGGER.debug("Dataspace->Creating DataMiner main folder");
-			root.createFolder(dataminerFolder, "A folder collecting DataMiner experiments data and computation information");
-			((WorkspaceFolder) root.find(dataminerFolder)).setSystemFolder(true);
-		}
-		WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
 
-		if (!ws.exists(importedDataFolder, dataminerFolderWS.getId())) {
+		FolderContainer root = shc.getWSRoot();
+
+		List<ItemContainer<? extends Item>> dataminerItems = root.findByName(dataminerFolder).getContainers();
+
+		FolderContainer dataminerFolderContainer;
+
+		// manage folders: create the folders network
+		if (dataminerItems.isEmpty()) {
+			LOGGER.debug("Dataspace->Creating DataMiner main folder");
+			dataminerFolderContainer = root.newFolder(dataminerFolder,
+					"A folder collecting DataMiner experiments data and computation information");
+			// ((WorkspaceFolder)
+			// root.find(dataminerFolder)).setSystemFolder(true);
+		} else if (dataminerItems.size() > 1)
+			throw new Exception("found more than one dataminer folder (impossible!!!)");
+		else
+			dataminerFolderContainer = (FolderContainer) dataminerItems.get(0);
+
+		if (dataminerFolderContainer.findByName(importedDataFolder).getContainers().isEmpty()) {
 			LOGGER.debug("Dataspace->Creating DataMiner imported data folder");
-			dataminerFolderWS.createFolder(importedDataFolder, "A folder collecting DataMiner imported data");
+			dataminerFolderContainer.newFolder(importedDataFolder, "A folder collecting DataMiner imported data");
 		}
-		if (!ws.exists(computedDataFolder, dataminerFolderWS.getId())) {
+
+		if (dataminerFolderContainer.findByName(computedDataFolder).getContainers().isEmpty()) {
 			LOGGER.debug("Dataspace->Creating DataMiner computed data folder");
-			dataminerFolderWS.createFolder(computedDataFolder, "A folder collecting DataMiner computed data");
+			dataminerFolderContainer.newFolder(computedDataFolder, "A folder collecting DataMiner computed data");
 		}
-		if (!ws.exists(computationsFolder, dataminerFolderWS.getId())) {
+		if (dataminerFolderContainer.findByName(computationsFolder).getContainers().isEmpty()) {
 			LOGGER.debug("Dataspace->Creating DataMiner computations folder");
-			dataminerFolderWS.createFolder(computationsFolder, "A folder collecting DataMiner computations information");
+			dataminerFolderContainer.newFolder(computationsFolder,
+					"A folder collecting DataMiner computations information");
 		}
+
+		return dataminerFolderContainer;
 	}
-	public String uploadData(StoredData data, WorkspaceFolder wsFolder) throws Exception {
+
-		return uploadData(data, wsFolder, true);
+	public String uploadData(StoredData data, FolderContainer destinationFolder) throws Exception {
+		return uploadData(data, destinationFolder, true);
 	}
-	public String uploadData(StoredData data, WorkspaceFolder wsFolder, boolean changename) throws Exception {
+
+	public String uploadData(StoredData data, FolderContainer destinationFolder, boolean changename) throws Exception {
 		LOGGER.debug("Dataspace->Analysing " + data);
-		// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name, wsFolder);
+		// String filenameonwsString = WorkspaceUtil.getUniqueName(data.name,
-		String filenameonwsString = data.name ;
+		// wsFolder);
+		String filenameonwsString = data.name;
 		if (changename)
-			filenameonwsString = data.name + "_[" + data.computationId + "]"+getExtension(data.payload, data.type);// ("_"+UUID.randomUUID()).replace("-", "");
+			filenameonwsString = String.format("%s_(%s)%s", data.name, data.computationId,
+					getExtension(data.payload));
 
 		InputStream in = null;
 		String url = "";
 		try {
-			long size = 0;
+			//long size = 0;
-			if (data.type.equals("text/csv")||data.type.equals("application/d4science")||data.type.equals("image/png")) {
+			if (data.type.equals("text/csv") || data.type.equals("application/d4science")
+					|| data.type.equals("image/png")) {
 
 				if (new File(data.payload).exists() || !data.payload.startsWith("http")) {
-					LOGGER.debug("Dataspace->Uploading file " + data.payload);
+					LOGGER.debug("Dataspace->Uploading file {}", data.payload);
 					in = new FileInputStream(new File(data.payload));
-					size = new File(data.payload).length();
+					//size = new File(data.payload).length();
 				} else {
-					LOGGER.debug("Dataspace->Uploading via URL " + data.payload);
+					LOGGER.debug("Dataspace->Uploading via URL {}", data.payload);
 					int tries = 10;
-					for (int i=0;i<tries;i++){
+					for (int i = 0; i < tries; i++) {
 						try {
 							URL urlc = new URL(data.payload);
+							url = urlc.toString();
 							HttpURLConnection urlConnection = (HttpURLConnection) urlc.openConnection();
 							urlConnection.setConnectTimeout(10000);
 							urlConnection.setReadTimeout(10000);
 							in = new BufferedInputStream(urlConnection.getInputStream());
-						}catch(Exception ee){
+						} catch (Exception ee) {
-							LOGGER.warn("Dataspace->Retrying connection to {} number {} ",data.payload,(i+1),ee);
+							LOGGER.warn("Dataspace->Retrying connection to {} number {} ", data.payload, (i + 1), ee);
-							in =null;
+							in = null;
 						}
-						if (in!=null)
+						if (in != null)
 							break;
 						else
 							Thread.sleep(10000);
 					}
 
 				}
-				if (in==null)
+				if (in == null)
-					throw new Exception("Impossible to open stream from "+data.payload);
+					throw new Exception("Impossible to open stream from " + data.payload);
 
-				// LOGGER.debug("Dataspace->final file name on ws " + data.name+" description "+data.description);
+				// LOGGER.debug("Dataspace->final file name on ws " +
+				// data.name+" description "+data.description);
 				LOGGER.debug("Dataspace->WS OP saving the following file on the WS " + filenameonwsString);
-				LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
+				Map<String, Object> properties = new LinkedHashMap<String, Object>();
 
 				properties.put(computation_id, data.computationId);
 				properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
@@ -172,238 +202,230 @@ public class DataspaceManager implements Runnable {
 				properties.put(data_type, data.type);
 				properties.put(payload, url);
 
-				FolderItem fileItem = WorkspaceUtil.createExternalFile(wsFolder, filenameonwsString, data.description, in,properties,data.type,size);
+				FileContainer fileContainer = destinationFolder.uploadFile(in, filenameonwsString, data.description);
-				//fileItem.getProperties().addProperties(properties);
+				fileContainer.setMetadata(new Metadata(properties));
+
 				LOGGER.debug("Dataspace->WS OP file saved on the WS " + filenameonwsString);
 
-				url = fileItem.getPublicLink(false);
+				url = fileContainer.getPublicLink().toString();
 				LOGGER.debug("Dataspace->WS OP url produced for the file " + url);
 
 				data.payload = url;
 				try {
 					in.close();
 				} catch (Exception e) {
-					LOGGER.debug("Dataspace->Error creating file " + e.getMessage());
+					LOGGER.debug("Dataspace->Error creating file {}", e.getMessage());
-					//LOGGER.debug(e);
+					// LOGGER.debug(e);
 				}
-				LOGGER.debug("Dataspace->File created " + filenameonwsString);
+				LOGGER.debug("Dataspace->File created {}", filenameonwsString);
 			} else {
-				LOGGER.debug("Dataspace->String parameter " + data.payload);
+				LOGGER.debug("Dataspace->String parameter {}", data.payload);
 				url = data.payload;
 			}
 		} catch (Throwable e) {
-			LOGGER.error("Dataspace->Could not retrieve input payload {} ",data.payload,e);
+			LOGGER.error("Dataspace->Could not retrieve input payload {} ", data.payload, e);
-			//LOGGER.debug(e);
+			// LOGGER.debug(e);
 			url = "payload was not made available for this dataset";
 			data.payload = url;
 		}
 		return url;
 	}
 
-	public List<String> uploadInputData(List<StoredData> inputData, WorkspaceFolder dataminerFolder) throws Exception {
+	public List<String> uploadInputData(List<StoredData> inputData, FolderContainer dataminerFolder) throws Exception {
-		LOGGER.debug("Dataspace->uploading input data; Number of data: " + inputData.size());
+		LOGGER.debug("Dataspace->uploading input data; Number of data: {}", inputData.size());
-		WorkspaceItem folderItem = dataminerFolder.find(importedDataFolder);
+		FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(importedDataFolder)
+				.getContainers().get(0);
 		List<String> urls = new ArrayList<String>();
-		if (folderItem != null && folderItem.isFolder()) {
+		for (StoredData input : inputData) {
-			WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
+			List<ItemContainer<? extends Item>> items = null;
-			for (StoredData input : inputData) {
-				WorkspaceItem item = null;
 
-				if (input.type.equals("text/csv")||input.type.equals("application/d4science")||input.type.equals("image/png")) 
+			if (input.type.equals("text/csv") || input.type.equals("application/d4science")
-					item = destinationFolder.find(input.name);
+					|| input.type.equals("image/png"))
+				items = destinationFolder.findByName(input.name).getContainers();
 
-				if (item==null){
+			if (items == null || items.isEmpty()) {
-					String url = uploadData(input, destinationFolder,false);
+				String url = uploadData(input, destinationFolder, false);
-					LOGGER.debug("Dataspace->returning property "+url);
+				LOGGER.debug("Dataspace->returning property {}", url);
-					urls.add(url);
+				urls.add(url);
-				}
+			} else {
-				else{
+				FileContainer item = (FileContainer) items.get(0);
-					LOGGER.debug("Dataspace->Input item "+input.name+" is already available in the input folder");
+				LOGGER.debug("Dataspace->Input item {} is already available in the input folder", input.name);
-					String url = item.getPublicLink(false);
+				String url = item.getPublicLink().toString();
-					LOGGER.debug("Dataspace->returning WS url "+url);
+				LOGGER.debug("Dataspace->returning WS url {}", url);
-					urls.add(url);
+				urls.add(url);
-				}
 			}
-		} else
+		}
-			LOGGER.debug("Dataspace->folder is not valid");
 
 		LOGGER.debug("Dataspace->finished uploading input data");
 		return urls;
 	}
 
-	public List<String> uploadOutputData(List<StoredData> outputData, WorkspaceFolder dataminerFolder) throws Exception {
+	public List<String> uploadOutputData(List<StoredData> outputData, FolderContainer dataminerFolder)
+			throws Exception {
 		LOGGER.debug("Dataspace->uploading output data; Number of data: " + outputData.size());
-		WorkspaceItem folderItem = dataminerFolder.find(computedDataFolder);
+		FolderContainer destinationFolder = (FolderContainer) dataminerFolder.findByName(computedDataFolder)
+				.getContainers().get(0);
 		List<String> urls = new ArrayList<String>();
-		if (folderItem != null && folderItem.isFolder()) {
+		for (StoredData output : outputData) {
-			WorkspaceFolder destinationFolder = (WorkspaceFolder) folderItem;
+			String url = uploadData(output, destinationFolder);
-			for (StoredData output : outputData) {
+			urls.add(url);
-				String url = uploadData(output, destinationFolder);
+		}
-				urls.add(url);
-			}
-		} else
-			LOGGER.debug("Dataspace->folder is not valid");
 		LOGGER.debug("Dataspace->finished uploading output data");
 		return urls;
 	}
 
-	public void uploadComputationData(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData, WorkspaceFolder dataminerFolder, Workspace ws) throws Exception {
+	public void uploadComputationData(ComputationData computation, List<StoredData> inputData,
+			List<StoredData> outputData, FolderContainer dataminerFolder) throws Exception {
 		LOGGER.debug("Dataspace->uploading computation data");
-		WorkspaceItem folderItem = dataminerFolder.find(computationsFolder);
+		FolderContainer computationContainer = (FolderContainer) dataminerFolder.findByName(computationsFolder)
-		if (folderItem != null && folderItem.isFolder()) {
+				.getContainers().get(0);
-			// create a folder in here
+		// create a folder in here
-			LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
+		LOGGER.debug("Dataspace->Creating computation folder " + computation.id);
-			WorkspaceFolder cfolder = ((WorkspaceFolder) folderItem);
+		String cfoldername = computation.id;
-			String cfoldername = computation.id;
+		FolderContainer newcomputationFolder = null;
-			WorkspaceFolder newcomputationFolder = null;
+		try {
-			try{
+			newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
-				newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
+		} catch (java.lang.ClassCastException e) {
-			}catch(java.lang.ClassCastException e){
+			LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
-				LOGGER.debug("Dataspace->concurrency exception - deleting remaining item");
+			deleteRunningComputationData();
-				deleteRunningComputationData();
+			newcomputationFolder = computationContainer.newFolder(cfoldername, computation.operatorDescription);
-				newcomputationFolder = cfolder.createFolder(cfoldername, computation.operatorDescription);
-			}
-			//String itemType = "COMPUTATION";
-
-			// create IO folders
-			LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
-			newcomputationFolder.createFolder(importedDataFolder, importedDataFolder);
-			newcomputationFolder.createFolder(computedDataFolder, computedDataFolder);
-
-			// copy IO in those folders
-			LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
-			List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
-			LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
-			List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
-
-			LOGGER.debug("Dataspace->*****adding properties to the folder*****");
-
-			LOGGER.debug("Dataspace->creating Folder Properties");
-
-			// write a computation item for the computation
-			LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
-			properties.put(computation_id, computation.id);
-
-			properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
-			
-			properties.put(vre, computation.vre);
-
-			properties.put(operator_name, config.getAgent());
-
-			properties.put(operator_id, computation.operatorId);
-
-			properties.put(operator_description, computation.operatorDescription);
-
-			properties.put(start_date, computation.startDate);
-
-			properties.put(end_date, computation.endDate);
-
-			properties.put(status, getStatus(computation.status));
-
-			properties.put(execution_platform, computation.infrastructure);
-
-			int ninput = inputurls.size();
-			int noutput = outputurls.size();
-
-			LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
-			for (int i = 1; i <= ninput; i++) {
-				StoredData input = inputData.get(i - 1);
-				if (input.payload.contains("|")){
-					String payload = input .payload;
-					LOGGER.debug("Dataspace->Managing complex input "+input.name+" : "+payload);
-					//delete the names that are not useful
-
-					for (StoredData subinput:inputData){
-						if (input.description.equals(subinput.description)){
-							payload = payload.replace(subinput.name,subinput.payload);
-							subinput.name=null;
-						}
-					}
-
-					input.name = null;
-
-					//delete last pipe character
-					if (payload.endsWith("|"))
-						payload = payload.substring(0,payload.length()-1);
-					LOGGER.debug("Dataspace->Complex input after processing "+payload);
-					properties.put("input" + i + "_" + input.description, payload);
-					input.payload=payload;
-
-				}
-			}
-
-			for (int i = 1; i <= ninput; i++) {
-				StoredData input = inputData.get(i - 1);
-				if (input.name!=null){
-					properties.put("input" + i + "_" + input.name, inputurls.get(i - 1));
-
-				}
-			}
-
-			LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
-			for (int i = 1; i <= noutput; i++) {
-				properties.put("output" + i + "_" + outputData.get(i - 1).name, outputurls.get(i - 1));
-
-			}
-
-			LOGGER.debug("Dataspace->Properties of the folder: " + properties);
-
-			LOGGER.debug("Dataspace->Saving properties to ProvO XML file " + noutput + " outputs");
-
-			/*
-			 * XStream xstream = new XStream(); String xmlproperties = xstream.toXML(properties);
-			 */
-			try {
-				String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
-
-				File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
-				FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
-				InputStream sis = new FileInputStream(xmltosave);
-				WorkspaceUtil.createExternalFile(newcomputationFolder, computation.id + ".xml", computation.operatorDescription, sis,null,"text/xml",xmltosave.length());
-				sis.close();
-				xmltosave.delete();
-			} catch (Exception e) {
-				LOGGER.error("Dataspace->Failed creating ProvO XML file ",e);
-			}
-			//List<String> scopes = new ArrayList<String>();
-			//scopes.add(config.getGcubeScope());
-			//ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, newcomputationFolder.getId());
-			newcomputationFolder.getProperties().addProperties(properties);
 		}
+		// String itemType = "COMPUTATION";
+
+		// create IO folders
+		LOGGER.debug("Dataspace->creating IO folders under " + cfoldername);
+		newcomputationFolder.newFolder(importedDataFolder, importedDataFolder);
+		newcomputationFolder.newFolder(computedDataFolder, computedDataFolder);
+
+		// copy IO in those folders
+		LOGGER.debug("Dataspace->*****uploading inputs in IO folder*****");
+		List<String> inputurls = uploadInputData(inputData, newcomputationFolder);
+		LOGGER.debug("Dataspace->*****uploading outputs in IO folder*****");
+		List<String> outputurls = uploadOutputData(outputData, newcomputationFolder);
+
+		LOGGER.debug("Dataspace->*****adding properties to the folder*****");
+
+		LOGGER.debug("Dataspace->creating Folder Properties");
+
+		// write a computation item for the computation
+		Map<String, Object> properties = new LinkedHashMap<String, Object>();
+		properties.put(computation_id, computation.id);
+
+		properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
+
+		properties.put(vre, computation.vre);
+
+		properties.put(operator_name, config.getAgent());
+
+		properties.put(operator_id, computation.operatorId);
+
+		properties.put(operator_description, computation.operatorDescription);
+
+		properties.put(start_date, computation.startDate);
+
+		properties.put(end_date, computation.endDate);
+
+		properties.put(status, getStatus(computation.status));
+
+		properties.put(execution_platform, computation.infrastructure);
+
+		int ninput = inputurls.size();
+		int noutput = outputurls.size();
+
+		LOGGER.debug("Dataspace->Adding input properties for " + ninput + " inputs");
+		for (int i = 1; i <= ninput; i++) {
+			StoredData input = inputData.get(i - 1);
+			if (input.payload.contains("|")) {
+				String payload = input.payload;
+				LOGGER.debug("Dataspace->Managing complex input {} : {}", input.name, payload);
+				// delete the names that are not useful
+
+				for (StoredData subinput : inputData) {
+					if (input.description.equals(subinput.description)) {
+						payload = payload.replace(subinput.name, subinput.payload);
+						subinput.name = null;
+					}
+				}
+
+				input.name = null;
+
+				// delete last pipe character
+				if (payload.endsWith("|"))
+					payload = payload.substring(0, payload.length() - 1);
+				LOGGER.debug("Dataspace->Complex input after processing " + payload);
+				properties.put("input" + i + "_" + input.description, payload);
+				input.payload = payload;
+
+			}
+		}
+
+		for (int i = 1; i <= ninput; i++) {
+			StoredData input = inputData.get(i - 1);
+			if (input.name != null) {
+				properties.put(String.format("input%d_%s", i, input.name), inputurls.get(i - 1));
+
+			}
+		}
+
+		LOGGER.debug("Dataspace->Adding output properties for " + noutput + " outputs");
+		for (int i = 1; i <= noutput; i++) {
+			properties.put(String.format("output%d_%s", i, outputData.get(i - 1).name), outputurls.get(i - 1));
+
+		}
+
+		LOGGER.debug("Dataspace->Properties of the folder: {} ", properties);
+
+		LOGGER.debug("Dataspace->Saving properties to ProvO XML file {} outputs", noutput);
+
+		/*
+		 * XStream xstream = new XStream(); String xmlproperties =
+		 * xstream.toXML(properties);
+		 */
+		try {
+			String xmlproperties = ProvOGenerator.toProvO(computation, inputData, outputData);
+
+			File xmltosave = new File(config.getPersistencePath(), "prov_o_" + UUID.randomUUID());
+			FileTools.saveString(xmltosave.getAbsolutePath(), xmlproperties, true, "UTF-8");
+			try (InputStream sis = new FileInputStream(xmltosave)) {
+				newcomputationFolder.uploadFile(sis, computation.id + ".xml", computation.operatorDescription);
+			}
+			xmltosave.delete();
+		} catch (Exception e) {
+			LOGGER.error("Dataspace->Failed creating ProvO XML file ", e);
+		}
+		/*
+		 * List<String> scopes = new ArrayList<String>();
+		 * scopes.add(config.getGcubeScope());
+		 * ws.createGcubeItem(computation.id, computation.operatorDescription,
+		 * scopes, computation.user, itemType, properties,
+		 * newcomputationFolder.getId());
+		 */
+		newcomputationFolder.setMetadata(new Metadata(properties));
 
 		LOGGER.debug("Dataspace->finished uploading computation data");
 	}
 
-	public String buildCompositePayload(List<StoredData> inputData,String payload, String inputName){
+	public String buildCompositePayload(List<StoredData> inputData, String payload, String inputName) {
 
-		for (StoredData input:inputData){
+		for (StoredData input : inputData) {
-			if (inputName.equals(input.description)){
+			if (inputName.equals(input.description)) {
-				payload = payload.replace(input.name,input.payload);
+				payload = payload.replace(input.name, input.payload);
 			}
 		}
 		return payload;
 	}
 
-
+	public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData)
-	public void writeProvenance(ComputationData computation, List<StoredData> inputData, List<StoredData> outputData) throws Exception {
+			throws Exception {
 		LOGGER.debug("Dataspace->connecting to Workspace");
-		HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
-		HomeManager manager = factory.getHomeManager();
-		LOGGER.debug("Dataspace->getting user");
-		User user = manager.createUser(computation.user);
-		Home home = manager.getHome(user);
-		LOGGER.debug("Dataspace->getting root folder");
-		Workspace ws = home.getWorkspace();
-		WorkspaceFolder root = ws.getRoot();
 		LOGGER.debug("Dataspace->create folders network");
-		createFoldersNetwork(ws, root);
+		FolderContainer dataminerFolder = createFoldersNetwork();
-		WorkspaceFolder dataminerItem = (WorkspaceFolder) root.find(dataminerFolder);
 		LOGGER.debug("Dataspace->****uploading input files****");
-		uploadInputData(inputData, dataminerItem);
+		uploadInputData(inputData, dataminerFolder);
 		LOGGER.debug("Dataspace->****uploading output files****");
-		uploadOutputData(outputData, dataminerItem);
+		uploadOutputData(outputData, dataminerFolder);
 		LOGGER.debug("Dataspace->****uploading computation files****");
-		uploadComputationData(computation, inputData, outputData, dataminerItem, ws);
+		uploadComputationData(computation, inputData, outputData, dataminerFolder);
 		LOGGER.debug("Dataspace->provenance management finished");
 		LOGGER.debug("Dataspace->deleting generated files");
 		AbstractEcologicalEngineMapper.deleteGeneratedFiles(generatedFiles);
@@ -414,29 +436,20 @@ public class DataspaceManager implements Runnable {
 		try {
 			deleteRunningComputationData();
 		} catch (Exception e) {
-			LOGGER.debug("Dataspace->impossible to delete running computation : {} ",e.getMessage());
+			LOGGER.debug("Dataspace->impossible to delete running computation : {} ", e.getMessage());
 		}
-		// LOGGER.debug("Dataspace->updating computation status");
+
-		// LOGGER.debug("Dataspace->connecting to Workspace");
-		HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
-		HomeManager manager = factory.getHomeManager();
-		// LOGGER.debug("Dataspace->getting user");
-		User user = manager.createUser(computation.user);
-		Home home = manager.getHome(user);
-		// LOGGER.debug("Dataspace->getting root folder");
-		Workspace ws = home.getWorkspace();
-		WorkspaceFolder root = ws.getRoot();
 		// LOGGER.debug("Dataspace->create folders network");
-		createFoldersNetwork(ws, root);
+		FolderContainer folderContainer = createFoldersNetwork();
-		WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
+
-		WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
+		FolderContainer computationsContainer = (FolderContainer) folderContainer.findByName(computationsFolder)
-		// LOGGER.debug("Dataspace->Creating computation item " + computation.id+" with status"+computation.status);
+				.getContainers().get(0);
+		// LOGGER.debug("Dataspace->Creating computation item " +
+		// computation.id+" with status"+computation.status);
 		String itemType = "COMPUTATION";
 
-		
-		
 		// write a computation item for the computation
-		LinkedHashMap<String, String> properties = new LinkedHashMap<String, String>();
+		Map<String, Object> properties = new LinkedHashMap<String, Object>();
 		properties.put(computation_id, computation.id);
 		properties.put(hostname, WPSConfig.getInstance().getWPSConfig().getServer().getHostname());
 		properties.put(vre, computation.vre);
@@ -452,24 +465,34 @@ public class DataspaceManager implements Runnable {
 
 		List<String> scopes = new ArrayList<String>();
 		scopes.add(config.getGcubeScope());
-		ws.createGcubeItem(computation.id, computation.operatorDescription, scopes, computation.user, itemType, properties, computationsFolderItem.getId());
+		
+		//TODO: update gcubeItem not recreate it...
+		GCubeItem gcubeItem = new GCubeItem();
+		gcubeItem.setName(this.statusComputationName);
+		gcubeItem.setDescription(computation.operatorDescription);
+		gcubeItem.setScopes(scopes.toArray(new String[scopes.size()]));
+		gcubeItem.setItemType(itemType);
+		gcubeItem.setMetadata(new Metadata(properties));
+		gcubeItem.setCreator(AuthorizationProvider.instance.get().getClient().getId());
+
+		computationsContainer.newGcubeItem(gcubeItem);
 
 		LOGGER.debug("Dataspace->finished uploading computation data");
 	}
 
-	public String getStatus(String status){
+	public String getStatus(String status) {
 		double statusD = 0;
-		try{
+		try {
 			statusD = Double.parseDouble(status);
-		}catch(Exception e){
+		} catch (Exception e) {
 			return status;
 		}
 
-		if (statusD==100)
+		if (statusD == 100)
 			return "completed";
-		else if (statusD==-2)
+		else if (statusD == -2)
 			return "error";
-		else if (statusD==-1)
+		else if (statusD == -1)
 			return "cancelled";
 		else
 			return status;
@@ -479,66 +502,76 @@ public class DataspaceManager implements Runnable {
 
 		LOGGER.debug("Dataspace->deleting computation item");
 		LOGGER.debug("Dataspace->connecting to Workspace");
-		HomeManagerFactory factory = HomeLibrary.getHomeManagerFactory();
+		StorageHubClient shc = new StorageHubClient();
-		HomeManager manager = factory.getHomeManager();
+		FolderContainer dataminerContainer = (FolderContainer) shc.getWSRoot().findByName(dataminerFolder)
-		LOGGER.debug("Dataspace->getting user");
+				.getContainers().get(0);
-		User user = manager.createUser(computation.user);
+		FolderContainer computationContainer = (FolderContainer) dataminerContainer.findByName(computationsFolder)
-		Home home = manager.getHome(user);
+				.getContainers().get(0);
-		LOGGER.debug("Dataspace->getting root folder");
-		Workspace ws = home.getWorkspace();
-		WorkspaceFolder root = ws.getRoot();
-		WorkspaceFolder dataminerFolderWS = (WorkspaceFolder) root.find(dataminerFolder);
-		WorkspaceItem computationsFolderItem = dataminerFolderWS.find(computationsFolder);
 		LOGGER.debug("Dataspace->removing computation data");
-		WorkspaceFolder computationsFolderWs = ((WorkspaceFolder) computationsFolderItem);
-		WorkspaceItem wi = computationsFolderWs.find(computation.id);
-		if (wi!=null){
-			LOGGER.debug("Dataspace->Found "+computation.id+" under "+computationsFolderWs.getName()+" - removing");
-			wi.remove();
-		}
-		else
-			LOGGER.debug("Dataspace->Warning Could not find "+computation.id+" under "+computationsFolderWs.getName());
 
-		int maxtries = 3;
+		List<ItemContainer<? extends Item>> wi = computationContainer.findByName(this.statusComputationName).getContainers();
-		int i =1;
+		if (!wi.isEmpty()) {
-		while (ws.exists(computation.id,computationsFolderWs.getId()) && i<maxtries){
+			for (ItemContainer<? extends Item> container : wi) {
-			LOGGER.debug("Dataspace->computation data still exist... retrying "+i);
+				boolean retry = false;
-			Thread.sleep(1000);
+				do {
-			computationsFolderWs.find(computation.id).remove();
+					try {
-			i++;
+						container.forceDelete();
-		}
+						retry = false;
+					}catch (ItemLockedException e) {
+						LOGGER.warn("item locked, retrying");
+						Thread.sleep(1000);
+						retry = true;
+					}
+				}while (retry);
+			}
+		} else
+			LOGGER.debug("Dataspace->Warning Could not find {} under {}", this.statusComputationName,
+					computationContainer.get().getName());
 
-		LOGGER.debug("Dataspace->finished removing computation data - success "+!ws.exists(computation.id,computationsFolderWs.getId()));
+
+		/*
+		 * TODO: ASK GIANPAOLO int maxtries = 3; int i =1; while
+		 * (ws.exists(computation.id,computationsFolderWs.getId()) &&
+		 * i<maxtries){
+		 * LOGGER.debug("Dataspace->computation data still exist... retrying "+i
+		 * ); Thread.sleep(1000);
+		 * computationsFolderWs.find(computation.id).remove(); i++; }
+		 */
+
+		LOGGER.debug("Dataspace->finished removing computation data ");
 	}
 
-	public static String getExtension(String payload, String type){
+	// TODO
-		String extension = "";
+	public static String getExtension(String payload) {
-		if (type.toLowerCase().equals("text/plain")){}
+		LOGGER.debug("DataSpace->Get Extension from: " + payload);
-		else if (payload.toLowerCase().startsWith("http")){
+		String extension="";
+		if (payload.toLowerCase().startsWith("http")) {
 			try {
-				URL obj= new URL(payload);
+				URL obj = new URL(payload);
 				URLConnection conn = obj.openConnection();
 				// get all headers
 				Map<String, List<String>> map = conn.getHeaderFields();
 				for (Map.Entry<String, List<String>> entry : map.entrySet()) {
 					String value = entry.getValue().toString();
-					if (value.toLowerCase().contains("filename=")){
+					LOGGER.debug("Header value: " + value);
-						System.out.println("DataSpace->Searching in http header: found "+value);
+					if (value.toLowerCase().contains("filename")) {
-						extension = value.substring(value.lastIndexOf("."),value.lastIndexOf("\""));
+						LOGGER.debug("DataSpace->Searching in http header: found " + value);
+						extension = value.substring(value.lastIndexOf("."), value.lastIndexOf("\""));
+						break;
 					}
 				}
 				conn.getInputStream().close();
 			} catch (Exception e) {
-				System.out.println("DataSpace->Error in the payload http link "+e.getMessage());
+				LOGGER.warn("DataSpace->Error in the payload http link ", e);
 			}
-		}
+		} else {
-		else {
 			File paylFile = new File(payload);
-			if (paylFile.exists()){
+			if (paylFile.exists()) {
 				String paylname = paylFile.getName();
 				extension = paylname.substring(paylname.lastIndexOf("."));
 			}
 		}
+		LOGGER.debug("DataSpace->Extension retrieved: " + extension);
 		return extension;
 	}
 

src/main/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/mapping/dataspace/ProvOGenerator.java

@@ -2,7 +2,6 @@ package org.gcube.dataanalysis.wps.statisticalmanager.synchserver.mapping.datasp
 
 import java.io.StringReader;
 import java.io.StringWriter;
-import java.util.ArrayList;
 import java.util.List;
 
 import javax.xml.parsers.DocumentBuilder;

src/main/resources/templates/setup.cfg

@@ -1,3 +1,3 @@
-maxcomputations=4
+maxcomputations=1
 saveond4sstorage=true
 simulationMode=false

src/main/resources/templates/wpsCapabilitiesSkeleton.xml

@@ -5,7 +5,7 @@
 	xsi:schemaLocation="http://www.opengis.net/wps/1.0.0 http://schemas.opengis.net/wps/1.0.0/wpsGetCapabilities_response.xsd"
 	updateSequence="1">
 	<ows:ServiceIdentification>
-		<ows:Title>D4Science WPS Service for synchronous executions</ows:Title>
+		<ows:Title>D4Science DataMiner Service</ows:Title>
 		<ows:Abstract>Service based on the 52°North implementation of WPS 1.0.0</ows:Abstract>
 		<ows:Keywords>
 			<ows:Keyword>WPS</ows:Keyword>
@@ -19,8 +19,8 @@
 		<ows:AccessConstraints>NONE</ows:AccessConstraints>
 	</ows:ServiceIdentification>
 	<ows:ServiceProvider>
-		<ows:ProviderName>National Research Council of Italy</ows:ProviderName>
+		<ows:ProviderName>D4Science</ows:ProviderName>
-		<ows:ProviderSite xlink:href="www.d4science.org" />
+		<ows:ProviderSite xlink:href="https://www.d4science.org" />
 		<ows:ServiceContact>
 			<ows:IndividualName>Gianpaolo Coro</ows:IndividualName>
 			<ows:PositionName>Researcher</ows:PositionName>
@@ -34,7 +34,7 @@
 					<ows:AdministrativeArea>Istituto di Scienza e Tecnologie dell'Informazione A. Faedo</ows:AdministrativeArea>
 					<ows:PostalCode>56124</ows:PostalCode>
 					<ows:Country>Italy</ows:Country>
-					<ows:ElectronicMailAddress>gianpaolo.coro@isti.cnr.it</ows:ElectronicMailAddress>
+					<ows:ElectronicMailAddress>dataminer-managers@d4science.org</ows:ElectronicMailAddress>
 				</ows:Address>
 			</ows:ContactInfo>
 		</ows:ServiceContact>
@@ -43,31 +43,29 @@
 		<ows:Operation name="GetCapabilities">
 			<ows:DCP>
 				<ows:HTTP>
-					<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
-					<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
 				</ows:HTTP>
 			</ows:DCP>
 		</ows:Operation>
 		<ows:Operation name="DescribeProcess">
 			<ows:DCP>
 				<ows:HTTP>
-					<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
-					<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
 				</ows:HTTP>
 			</ows:DCP>
 		</ows:Operation>
 		<ows:Operation name="Execute">
 			<ows:DCP>
 				<ows:HTTP>
-					<ows:Get xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Get xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
-					<ows:Post xlink:href="http://#HOST#:#PORT#/wps/WebProcessingService?" />
+					<ows:Post xlink:href="#PROTOCOL#://#HOST#:#PORT#/wps/WebProcessingService?" />
 				</ows:HTTP>
 			</ows:DCP>
 		</ows:Operation>
 	</ows:OperationsMetadata>
-	<wps:ProcessOfferings>
+	<wps:ProcessOfferings>#PROCESSES#</wps:ProcessOfferings>
-	#PROCESSES#
-	</wps:ProcessOfferings>
 	<wps:Languages>
 		<wps:Default>
 			<ows:Language>en-GB</ows:Language>

src/test/java/org/gcube/dataanalysis/wps/statisticalmanager/synchserver/test/AlgorithmTest.java

@@ -17,21 +17,21 @@ import org.junit.Test;
 
 public class AlgorithmTest {
 
-	List<String> executeOnly = Arrays.asList();
+	List<String> executeOnly = Arrays.asList("#BIONYM", "#AQUAMAPS_SUITABLE", "#AQUAMAPS_SUITABLE 21 sp", "#BIONYM1024","#CMSY2");
 			
 	@Test
 	public void executeAlgorithmsFromFile() throws Exception{
 		
 		String env = "dev";
 		
-		Properties prop = new Properties();
+		/*Properties prop = new Properties();
 		prop.load(AlgorithmTest.class.getResourceAsStream("/test_params.properties"));
-			
+			*/
 		
 		String protocol = "http";
-		String hostname = prop.getProperty(env+".host");
+		String hostname = "dataminer-genericworkers.d4science.org";
-		String token = prop.getProperty(env+".token");
+		String token = "257800d8-24bf-4bae-83cd-ea99369e7dd6-843339462";
-		String layerID = prop.getProperty(env+".layer");
+		String layerID = "08ee0d70-4d8b-4f42-8b06-d709482bca95";
 						 
 		Iterator<String> uris =  getUrisIterator();
 		
@@ -43,7 +43,7 @@ public class AlgorithmTest {
 			if (nextLine.startsWith("#"))
 				algorithmName = nextLine;
 			else{
-				if (!(executeOnly.isEmpty() || executeOnly.contains(algorithmName))) continue;
+				if (executeOnly.contains(algorithmName)) continue;
 				String callUrl = nextLine.replace("{PROTOCOL}", protocol).replace("{HOST}", hostname).replace("{TOKEN}", token).replace("{LAYERID}", layerID);
 				try{
 					long start = System.currentTimeMillis();