initial commit

.gitlab-ci.yml

+default:
+  tags:
+    - docker
+
+variables:
+  MAVEN_OPTS: "-Dhttps.protocols=TLSv1.2 -Dmaven.repo.local=$CI_PROJECT_DIR/.m2/repository -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=WARN -Dorg.slf4j.simpleLogger.showDateTime=true -Djava.awt.headless=true"
+  MAVEN_CLI_OPTS: "--batch-mode --errors --fail-at-end --show-version -DinstallAtEnd=true -DdeployAtEnd=true"
+
+# This template uses open-jdk 11 for verifying and deploying images
+image: maven:3.8.5-openjdk-11-slim
+
+# Cache downloaded dependencies and plugins between builds.
+# To keep cache across branches add 'key: "$CI_JOB_NAME"'
+cache:
+  paths:
+    - .m2/repository
+
+# For merge requests do not `deploy` but only run `verify`.
+# See https://maven.apache.org/guides/introduction/introduction-to-the-lifecycle.html
+.verify: &verify
+  stage: test
+  script:
+    - 'mvn $MAVEN_CLI_OPTS verify'
+  except:
+    variables:
+      - $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
+
+# Verify merge requests using JDK11
+verify:jdk11:
+  <<: *verify
+
+deploy:jdk11:
+  stage: deploy
+  script:
+    - if [ ! -f settings.xml ];
+        then echo "CI settings missing\! If deploying to GitLab Maven Repository, please see https://docs.gitlab.com/ee/user/packages/maven_repository/index.html#create-maven-packages-with-gitlab-cicd for instructions.";
+      fi
+    - 'mvn $MAVEN_CLI_OPTS deploy -s settings.xml'
+  only:
+    variables:
+      - $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH

beacon-nosql-model/pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+  Copyright (C) 2022 Spanish National Bioinformatics Institute (INB) and
+  Barcelona Supercomputing Center
+
+  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
+-->
+<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>
+
+    <parent>
+        <groupId>es.bsc.inb.ga4gh</groupId>
+        <artifactId>beacon-v2-bsc</artifactId>
+        <version>2.0.0-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>beacon-nosql-model</artifactId>
+    <packaging>jar</packaging>
+
+    <description>
+        Beacon NoSQL Data Model version 2.0.0
+    </description>
+
+    <organization>
+        <name>Barcelona Supercomputing Center</name>
+        <url>https://www.bsc.es/</url>
+    </organization>
+
+    <developers>
+        <developer>
+          <id>redmitry</id>
+          <name>Dmitry Repchevsky</name>
+          <email>redmitry@list.ru</email>
+        </developer>
+    </developers>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+    
+    <dependencies>
+        <dependency>
+            <groupId>es.bsc.inb.ga4gh</groupId>
+            <artifactId>beacon-data-model</artifactId>
+            <version>2.0.0-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.nosql.mapping</groupId>
+            <artifactId>mapping-core</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.nosql.communication</groupId>
+            <artifactId>communication-document</artifactId>
+            <version>1.0.0-SNAPSHOT</version>
+            <type>jar</type>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.json</groupId>
+            <artifactId>jakarta.json-api</artifactId>
+            <version>${jakarta.json.version}</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>jakarta.json.bind</groupId>
+            <artifactId>jakarta.json.bind-api</artifactId>
+            <version>${jakarta.json.bind.version}</version>
+            <scope>provided</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.13.2</version>
+            <scope>test</scope>
+        </dependency>
+
+    </dependencies>     
+
+    <repositories>
+        <repository>
+            <id>gitlab-bsc-maven</id>
+           <url>https://inb.bsc.es/maven</url>
+        </repository>
+        <repository>
+            <id>jakarta.sonatype.org-snapshot</id>
+            <url>https://jakarta.oss.sonatype.org/content/repositories/snapshots/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+        <repository>
+            <id>oss.sonatype.org-snapshot</id>
+            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+    </repositories>
+
+    <distributionManagement>
+        <repository>
+            <id>gitlab-bsc-maven</id>
+            <url>https://inb.bsc.es/maven</url>
+        </repository>
+        <snapshotRepository>
+            <id>gitlab-bsc-maven</id>
+            <url>https://inb.bsc.es/maven</url>
+        </snapshotRepository>
+    </distributionManagement>
+
+</project>

beacon-nosql-model/src/main/java/es/bsc/inb/ga4gh/beacon/nosql/AgeEntity.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.ga4gh.beacon.nosql;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.common.Age;
+import jakarta.nosql.mapping.Column;
+import jakarta.nosql.mapping.Entity;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+@Entity("Age")
+public class AgeEntity implements Age {
+    
+    @Column("iso8601duration")
+    private String iso8601duration;
+
+    @Override
+    public String getIso8601duration() {
+        return iso8601duration;
+    }
+
+    @Override
+    public void setIso8601duration(String iso8601duration) {
+        this.iso8601duration = iso8601duration;
+    }
+
+}

beacon-nosql-model/src/main/java/es/bsc/inb/ga4gh/beacon/nosql/AgeRangeEntity.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.ga4gh.beacon.nosql;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.common.AgeRange;
+import jakarta.nosql.mapping.Column;
+import jakarta.nosql.mapping.Entity;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+@Entity("AgeRange")
+public class AgeRangeEntity implements AgeRange<AgeEntity> {
+
+    @Column("start")
+    private AgeEntity start;
+    
+    @Column("end")
+    private AgeEntity end;
+
+    @Override
+    public AgeEntity getStart() {
+        return start;
+    }
+
+    @Override
+    public void setStart(AgeEntity start) {
+        this.start = start;
+    }
+
+    @Override
+    public AgeEntity getEnd() {
+        return end;
+    }
+
+    @Override
+    public void setEnd(AgeEntity end) {
+        this.end = end;
+    }
+}

beacon-nosql-model/src/main/java/es/bsc/inb/ga4gh/beacon/nosql/AnalysisEntity.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.ga4gh.beacon.nosql;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.analysis.Analysis;
+import jakarta.json.JsonObject;
+import jakarta.nosql.mapping.Column;
+import jakarta.nosql.mapping.Entity;
+import jakarta.nosql.mapping.Id;
+import java.time.LocalDate;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+@Entity("Analyses")
+public class AnalysisEntity implements Analysis {
+
+    @Id
+    private String _id;
+
+    @Column("id")
+    private String id;
+    
+    @Column("runId")
+    private String runId;
+    
+    @Column("biosampleId")
+    private String biosampleId;
+
+    @Column("individualId")
+    private String individualId;    
+
+    @Column("analysisDate")
+    private LocalDate analysisDate;
+    
+    @Column("pipelineName")
+    private String pipelineName;
+    
+    @Column("pipelineRef")
+    private String pipelineRef;
+    
+    @Column("aligner")
+    private String aligner;
+    
+    @Column("variantCaller")
+    private String variantCaller;
+    
+    @Column("info")
+    private JsonObject info;
+
+    @Override
+    public String getId() {
+        return id;
+    }
+
+    @Override
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    @Override
+    public String getRunId() {
+        return runId;
+    }
+
+    @Override
+    public void setRunId(String runId) {
+        this.runId = runId;
+    }
+    
+    @Override
+    public String getBiosampleId() {
+        return biosampleId;
+    }
+    
+    @Override
+    public void setBiosampleId(String biosampleId) {
+        this.biosampleId = biosampleId;
+    }
+    
+    @Override
+    public String getIndividualId() {
+        return individualId;
+    }
+
+    @Override
+    public void setIndividualId(String individualId) {
+        this.individualId = individualId;
+    }
+    
+    @Override
+    public LocalDate getAnalysisDate() {
+        return analysisDate;
+    }
+
+    @Override
+    public void setAnalysisDate(LocalDate analysisDate) {
+        this.analysisDate = analysisDate;
+    }
+
+    @Override
+    public String getPipelineName() {
+        return pipelineName;
+    }
+
+    @Override
+    public void setPipelineName(String pipelineName) {
+        this.pipelineName = pipelineName;
+    }
+
+    @Override
+    public String getPipelineRef() {
+        return pipelineRef;
+    }
+
+    @Override
+    public void setPipelineRef(String pipelineRef) {
+        this.pipelineRef = pipelineRef;
+    }
+
+    @Override
+    public String getAligner() {
+        return aligner;
+    }
+
+    @Override
+    public void setAligner(String aligner) {
+        this.aligner = aligner;
+    }
+
+    @Override
+    public String getVariantCaller() {
+        return variantCaller;
+    }
+
+    @Override
+    public void setVariantCaller(String variantCaller) {
+        this.variantCaller = variantCaller;
+    }
+
+    @Override
+    public JsonObject getInfo() {
+        return info;
+    }
+
+    @Override
+    public void setInfo(final JsonObject info) {
+        this.info = info;
+    }
+}

beacon-nosql-model/src/main/java/es/bsc/inb/ga4gh/beacon/nosql/BiosampleEntity.java

+/**
+ * *****************************************************************************
+ * Copyright (C) 2022 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.ga4gh.beacon.nosql;
+
+import es.bsc.inb.ga4gh.beacon.model.v200.biosample.Biosample;
+import jakarta.json.JsonObject;
+import jakarta.nosql.mapping.Column;
+import jakarta.nosql.mapping.Entity;
+import jakarta.nosql.mapping.Id;
+import java.time.LocalDate;
+import java.util.List;
+
+/**
+ * @author Dmitry Repchevsky
+ */
+
+@Entity("Biosamples")
+public class BiosampleEntity 
+        implements Biosample<OntologyTermEntity, ProcedureEntity, PhenotypicFeatureEntity, MeasurementEntity> {
+
+    @Id
+    private String _id;
+    
+    @Column("id")
+    private String id;
+    
+    @Column("individualId")
+    private String individualId;
+
+    @Column("notes")
+    private String notes;
+
+    @Column("biosampleStatus")
+    private OntologyTermEntity biosampleStatus;
+    
+    @Column("collectionDate")
+    private LocalDate collectionDate;
+    
+    @Column("collectionMoment")
+    private String collectionMoment;
+    
+    @Column("sampleOriginType")
+    private OntologyTermEntity sampleOriginType;
+    
+    @Column("sampleOriginDetail")
+    private OntologyTermEntity sampleOriginDetail;
+    
+    @Column("obtentionProcedure")
+    private ProcedureEntity obtentionProcedure;
+    
+    @Column("tumorProgression")
+    private OntologyTermEntity tumorProgression;
+
+    @Column("tumorGrade")
+    private OntologyTermEntity tumorGrade;
+    
+    @Column("pathologicalStage")
+    private OntologyTermEntity pathologicalStage;
+
+    @Column("pathologicalTnmFinding")
+    private OntologyTermEntity pathologicalTnmFinding;
+    
+    @Column("histologicalDiagnosis")
+    private OntologyTermEntity histologicalDiagnosis;
+    
+    @Column("diagnosticMarkers")
+    private OntologyTermEntity diagnosticMarkers;
+    
+    @Column("phenotypicFeatures")
+    private List<PhenotypicFeatureEntity> phenotypicFeatures;
+    
+    @Column("measurements")
+    private List<MeasurementEntity> measurements;
+    
+    @Column("sampleProcessing")
+    private OntologyTermEntity sampleProcessing;
+
+    @Column("sampleStorage")
+    private OntologyTermEntity sampleStorage;
+    
+    @Column("info")
+    private JsonObject info;
+
+    @Override
+    public String getId() {
+        return id;
+    }
+    
+    @Override
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    @Override
+    public String getIndividualId() {
+        return individualId;
+    }
+
+    @Override
+    public void setIndividualId(String individualId) {
+        this.individualId = individualId;
+    }
+    
+    @Override
+    public String getNotes() {