initial commit

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" 
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
+    <modelVersion>4.0.0</modelVersion>
+
+    <groupId>es.bsc.inb.elixir</groupId>
+    <artifactId>openebench-tools-model</artifactId>
+    <version>1.0.0</version>
+    <packaging>jar</packaging>
+
+    <developers>
+        <developer>
+          <id>redmitry</id>
+          <name>Dmitry Repchevsky</name>
+          <email>redmitry@list.ru</email>
+        </developer>
+    </developers>
+
+    <properties>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+    </properties>
+    
+    <dependencies>
+        
+        <dependency>
+            <groupId>javax.json.bind</groupId>
+            <artifactId>javax.json.bind-api</artifactId>
+            <version>1.0</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.glassfish</groupId>
+            <artifactId>javax.json</artifactId>
+            <version>1.1</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.10</version>
+            <scope>test</scope>
+            <type>jar</type>
+        </dependency>
+
+    </dependencies>
+
+</project>
+

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Community.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Community {
+    private List<URI> socialMedia;
+    
+    @JsonbProperty("social_media")
+    public List<URI> getSocialMedia() {
+        if (socialMedia == null) {
+            socialMedia = new ArrayList<>();
+        }
+        return socialMedia;
+    }
+    
+    @JsonbProperty("social_media")
+    public void setSocialMedia(List<URI> socialMedias) {
+        this.socialMedia = socialMedias;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Contact.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Contact {
+    
+    private URI url;
+    private String email;
+    private String name;
+    private String phone;
+    
+    @JsonbProperty("url")
+    public URI getUrl() {
+        return url;
+    }
+
+    @JsonbProperty("url")
+    public void setUrl(URI url) {
+        this.url = url;
+    }
+
+    @JsonbProperty("email")
+    public String getEmail() {
+        return email;
+    }
+    
+    @JsonbProperty("email")
+    public void setEmail(String email) {
+        this.email = email;
+    }
+
+    @JsonbProperty("name")
+    public String getName() {
+        return name;
+    }
+
+    @JsonbProperty("name")
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    @JsonbProperty("phone")
+    public String getPhone() {
+        return phone;
+    }
+    
+    @JsonbProperty("phone")
+    public void setPhone(String phone) {
+        this.phone = phone;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Container.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import javax.json.bind.annotation.JsonbCreator;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Container {
+    
+    @JsonbProperty("type")
+    public final String type;
+    private URI uri;
+    
+    @JsonbCreator
+    public Container(@JsonbProperty("type") String type) {
+        this.type = type;
+    }
+    
+    @JsonbProperty("uri")
+    public URI getURI() {
+        return uri;
+    }
+
+    @JsonbProperty("uri")
+    public void setURI(URI uri) {
+        this.uri = uri;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Credit.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Credit {
+
+    private String name;
+    private String email;
+    private String type;
+    private String role;
+    private String orcid;
+    private URI url;
+    private String comment;
+
+    @JsonbProperty("name")
+    public String getName() {
+        return name;
+    }
+    
+    @JsonbProperty("name")
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    @JsonbProperty("email")
+    public String getEmail() {
+        return email;
+    }
+    
+    @JsonbProperty("email")
+    public void setEmail(String email) {
+        this.email = email;
+    }
+
+    @JsonbProperty("type")
+    public String getType() {
+        return type;
+    }
+    
+    @JsonbProperty("type")
+    public void setType(String type) {
+        this.type = type;
+    }
+
+    @JsonbProperty("role")
+    public String getRole() {
+        return role;
+    }
+    
+    @JsonbProperty("role")
+    public void setRole(String role) {
+        this.role = role;
+    }
+    
+    @JsonbProperty("orcid")
+    public String getOrcid() {
+        return orcid;
+    }
+    
+    @JsonbProperty("orcid")
+    public void setOrcid(String orcid) {
+        this.orcid = orcid;
+    }
+    
+    @JsonbProperty("url")
+    public URI getUrl() {
+        return url;
+    }
+    
+    @JsonbProperty("url")
+    public void setUrl(URI url) {
+        this.url = url;
+    }
+    
+    @JsonbProperty("comment")
+    public String getComment() {
+        return comment;
+    }
+    
+    @JsonbProperty("comment")
+    public void setComment(String comment) {
+        this.comment = comment;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Datatype.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Datatype {
+
+    private URI datatype;
+    private List<URI> formats;
+    
+    @JsonbProperty("datatype")
+    public URI getDatatype() {
+        return datatype;
+    }
+    
+    public void setDatatype(URI datatype) {
+        this.datatype = datatype;
+    }
+    
+    @JsonbProperty("formats")
+    public List<URI> getFormats() {
+        if (formats == null) {
+            formats = new ArrayList<>();
+        }
+        return formats;
+    }
+    
+    @JsonbProperty("formats")
+    public void setFormats(List<URI> formats) {
+        this.formats = formats;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Dependencies.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Dependencies {
+    private String buildSystem;
+    private List<URI> build;
+    private List<URI> runtime;
+    
+    @JsonbProperty("build_system")
+    public String getBuildSystem() {
+        return buildSystem;
+    }
+    
+    @JsonbProperty("build_system")
+    public void setBuildSystem(String buildSystem) {
+        this.buildSystem = buildSystem;
+    }
+    
+    @JsonbProperty("build")
+    public List<URI> getBuildDependencies() {
+        if (build == null) {
+            build = new ArrayList<>();
+        }
+        return build;
+    }
+    
+    @JsonbProperty("build")
+    public void setBuildDependencies(List<URI> build) {
+        this.build = build;
+    }
+    
+    @JsonbProperty("runtime")
+    public List<URI> getRuntimeDependencies() {
+        if (runtime == null) {
+            runtime = new ArrayList<>();
+        }
+        return runtime;
+    }
+    
+    @JsonbProperty("runtime")
+    public void setRuntimeDependencies(List<URI> runtime) {
+        this.runtime = runtime;
+    }
+
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Distributions.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Distributions {
+    
+    private List<URI> binaries;
+    private List<URI> binaryPackages;
+
+    private List<URI> sourcecode;
+    private List<URI> sourcePackages;
+
+    private List<URI> vre;
+    
+    private List<Container> containers;
+    private List<VMImage> vmImages;
+    
+    @JsonbProperty("binaries")
+    public List<URI> getBinaryDistributions() {
+        if (binaries == null) {
+            binaries = new ArrayList<>();
+        }
+        return binaries;
+    }
+
+    @JsonbProperty("binaries")
+    public void setBinaryDistributions(List<URI> binaries) {
+        this.binaries = binaries;
+    }
+    
+    @JsonbProperty("binary_packages")
+    public List<URI> getBinaryPackagesDistributions() {
+        if (binaryPackages == null) {
+            binaryPackages = new ArrayList<>();
+        }
+        return binaryPackages;
+    }
+
+    @JsonbProperty("binary_packages")
+    public void setBinaryPackagesDistributions(List<URI> binaryPackages) {
+        this.binaryPackages = binaryPackages;
+    }
+
+    @JsonbProperty("sourcecode")
+    public List<URI> getSourcecodeDistributions() {
+        if (sourcecode == null) {
+            sourcecode = new ArrayList<>();
+        }
+        return sourcecode;
+    }
+
+    @JsonbProperty("sourcecode")
+    public void setSourcecodeDistributions(List<URI> sourcecode) {
+        this.sourcecode = sourcecode;
+    }
+    
+    @JsonbProperty("vre")
+    public void setVirtualResearchEnvironment(List<URI> vre) {
+        this.vre = vre;
+    }
+    
+    @JsonbProperty("vre")
+    public List<URI> getVirtualResearchEnvironment() {
+        if (vre == null) {
+            vre = new ArrayList<>();
+        }
+        return vre;
+    }
+    
+    @JsonbProperty("source_packages")
+    public List<URI> getSourcePackagesDistributions() {
+        if (sourcePackages == null) {
+            sourcePackages = new ArrayList<>();
+        }
+        return sourcePackages;
+    }
+
+    @JsonbProperty("source_packages")
+    public void setSourcePackagesDistributions(List<URI> sourcePackages) {
+        this.sourcePackages = sourcePackages;
+    }
+    
+    @JsonbProperty("containers")
+    public List<Container> getContainers() {
+        if (containers == null) {
+            containers = new ArrayList<>();
+        }
+        return containers;
+    }
+
+    @JsonbProperty("containers")
+    public void setContainers(List<Container> containers) {
+        this.containers = containers;
+    }
+    
+    @JsonbProperty("vm_images")
+    public List<VMImage> getVirtualMachineImages() {
+        if (vmImages == null) {
+            vmImages = new ArrayList<>();
+        }
+        return vmImages;
+    }
+
+    @JsonbProperty("vm_images")
+    public void setVirtualMachineImages(List<VMImage> vmImages) {
+        this.vmImages = vmImages;
+    }
+}

src/main/java/es/bsc/inb/elixir/openebench/model/tools/Documentation.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2020 ELIXIR ES, Spanish National Bioinformatics Institute (INB)
+ * and Barcelona Supercomputing Center (BSC)
+ *
+ * Modifications to the initial code base are copyright of their respective
+ * authors, or their employers as appropriate.
+ * 
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+ * MA 02110-1301  USA
+ *****************************************************************************
+ */
+
+package es.bsc.inb.elixir.openebench.model.tools;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+import javax.json.bind.annotation.JsonbProperty;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+public class Documentation {
+    
+    private List<URI> docLinks;
+    private URI help;
+    private URI faq;
+    private URI general;
+    private URI build;
+    private URI manual;
+    private URI tutorial;
+    private URI api;
+    private URI termsOfUse;
+    private URI trainingMaterial;
+    private URI citationInstructions;
+    
+    @JsonbProperty("doc_links")
+    public List<URI> getDocumentationLinks() {
+        if (docLinks == null) {
+            docLinks = new ArrayList<>();
+        }
+        return docLinks;
+    }
+
+    @JsonbProperty("doc_links")